Starting phenix.real_space_refine on Mon Aug 25 14:23:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bmw_16126/08_2025/8bmw_16126.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bmw_16126/08_2025/8bmw_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bmw_16126/08_2025/8bmw_16126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bmw_16126/08_2025/8bmw_16126.map" model { file = "/net/cci-nas-00/data/ceres_data/8bmw_16126/08_2025/8bmw_16126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bmw_16126/08_2025/8bmw_16126.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 6.34, per 1000 atoms: 0.22 Number of scatterers: 28658 At special positions: 0 Unit cell: (126.566, 119.244, 242.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 107 16.00 P 47 15.00 O 5580 8.00 N 4786 7.00 C 18138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS J 223 " - pdb=" SG CYS J 255 " distance=2.03 Simple disulfide: pdb=" SG CYS L 58 " - pdb=" SG CYS L 75 " distance=2.03 Simple disulfide: pdb=" SG CYS L 58 " - pdb=" SG CYS L 78 " distance=2.03 Simple disulfide: pdb=" SG CYS L 75 " - pdb=" SG CYS L 78 " distance=2.03 Simple disulfide: pdb=" SG CYS L 180 " - pdb=" SG CYS L 185 " distance=2.03 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 105 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 80 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 82 " - pdb=" SG CYS H 123 " distance=2.02 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 120 " distance=2.03 Simple disulfide: pdb=" SG CYS K 261 " - pdb=" SG CYS K 278 " distance=2.03 Simple disulfide: pdb=" SG CYS K 265 " - pdb=" SG CYS K 275 " distance=2.03 Simple disulfide: pdb=" SG CYS M 220 " - pdb=" SG CYS M 224 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds 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: 2.89 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: 5.41 Time building geometry restraints manager: 3.32 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: 17724 35.71 - 71.42: 263 71.42 - 107.14: 9 107.14 - 142.85: 0 142.85 - 178.56: 11 Dihedral angle restraints: 18007 sinusoidal: 7890 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 18004 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: 3.050 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.730 Find NCS groups from input model: 0.290 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 : 12.902 178.559 11466 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 aren 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 covalent geometry : bond 0.00317 (29237) covalent geometry : angle 0.53678 (39593) SS BOND : bond 0.00347 ( 15) SS BOND : angle 1.98010 ( 30) hydrogen bonds : bond 0.15673 ( 1274) hydrogen bonds : angle 6.62998 ( 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 : 1.212 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: 0.8841 (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: 0.8515 (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: 0.8761 (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: 0.9422 (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: 0.8845 (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: 0.9341 (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: 0.2076 time to fit residues: 275.9050 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 : 0.743 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN D 73 GLN E 39 ASN E 134 ASN J 148 GLN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN G 141 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 GLN M 46 GLN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.053457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.044785 restraints weight = 142895.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.046578 restraints weight = 74189.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.047827 restraints weight = 46569.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.048705 restraints weight = 32638.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.049294 restraints weight = 24653.285| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29252 Z= 0.154 Angle : 0.664 12.258 39623 Z= 0.345 Chirality : 0.044 0.213 4524 Planarity : 0.004 0.054 4852 Dihedral : 13.258 178.636 4577 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.26 % Favored : 94.62 % Rotamer: Outliers : 2.85 % Allowed : 17.83 % Favored : 79.32 % 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 aren not related in a simple way. whole: 0.31 (0.15), residues: 3441 helix: 2.02 (0.14), residues: 1466 sheet: 0.10 (0.25), residues: 431 loop : -1.65 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 786 TYR 0.022 0.002 TYR A 69 PHE 0.033 0.001 PHE K 245 TRP 0.009 0.001 TRP K 749 HIS 0.004 0.001 HIS M 113 Details of bonding type rmsd covalent geometry : bond 0.00336 (29237) covalent geometry : angle 0.66200 (39593) SS BOND : bond 0.00460 ( 15) SS BOND : angle 1.87194 ( 30) hydrogen bonds : bond 0.04118 ( 1274) hydrogen bonds : angle 5.29339 ( 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 735 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 647 time to evaluate : 1.203 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: A 22 ASP cc_start: 0.8632 (m-30) cc_final: 0.8156 (t0) REVERT: A 29 ILE cc_start: 0.9379 (tp) cc_final: 0.9038 (tt) REVERT: A 42 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7827 (mm-30) REVERT: A 56 PHE cc_start: 0.8940 (t80) cc_final: 0.8522 (t80) REVERT: A 60 ARG cc_start: 0.9270 (mmp80) cc_final: 0.8863 (mmm160) REVERT: A 79 ILE cc_start: 0.8916 (mm) cc_final: 0.8631 (mp) REVERT: A 110 TYR cc_start: 0.9087 (t80) cc_final: 0.8778 (t80) REVERT: A 111 ASP cc_start: 0.9002 (t0) cc_final: 0.8719 (t0) REVERT: A 131 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9014 (mt-10) REVERT: B 22 ASP cc_start: 0.8864 (m-30) cc_final: 0.8027 (m-30) REVERT: B 26 ARG cc_start: 0.9104 (ptp-110) cc_final: 0.8431 (ptp90) REVERT: B 42 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8042 (mm-30) REVERT: B 44 TYR cc_start: 0.9403 (t80) cc_final: 0.9040 (t80) REVERT: B 56 PHE cc_start: 0.9435 (t80) cc_final: 0.9104 (t80) REVERT: B 73 GLN cc_start: 0.9311 (tp40) cc_final: 0.9068 (tp40) REVERT: B 78 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8491 (mm-30) REVERT: B 90 SER cc_start: 0.9602 (m) cc_final: 0.9189 (p) REVERT: B 103 LEU cc_start: 0.9783 (mt) cc_final: 0.9447 (tp) REVERT: B 128 THR cc_start: 0.9361 (p) cc_final: 0.8468 (p) REVERT: B 129 PHE cc_start: 0.9269 (t80) cc_final: 0.9011 (t80) REVERT: B 131 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8727 (mt-10) REVERT: B 134 ASN cc_start: 0.9225 (m-40) cc_final: 0.8870 (m110) REVERT: C 22 ASP cc_start: 0.9108 (m-30) cc_final: 0.8691 (m-30) REVERT: C 45 VAL cc_start: 0.9319 (t) cc_final: 0.9011 (p) REVERT: C 71 MET cc_start: 0.9442 (mtm) cc_final: 0.9041 (mtm) REVERT: C 77 ASP cc_start: 0.9105 (t0) cc_final: 0.8893 (t0) REVERT: C 80 ASP cc_start: 0.8712 (t70) cc_final: 0.8459 (t70) REVERT: C 105 TYR cc_start: 0.9379 (m-80) cc_final: 0.9156 (m-80) REVERT: C 134 ASN cc_start: 0.9683 (m-40) cc_final: 0.9420 (m110) REVERT: D 26 ARG cc_start: 0.9575 (mtm-85) cc_final: 0.9202 (ptp90) REVERT: D 44 TYR cc_start: 0.9164 (t80) cc_final: 0.8764 (t80) REVERT: D 58 GLN cc_start: 0.9478 (mp10) cc_final: 0.9170 (mm-40) REVERT: D 82 GLU cc_start: 0.9586 (tt0) cc_final: 0.9351 (tm-30) REVERT: D 83 THR cc_start: 0.9545 (m) cc_final: 0.9289 (p) REVERT: D 90 SER cc_start: 0.9442 (m) cc_final: 0.9226 (p) REVERT: D 101 ASN cc_start: 0.9551 (m110) cc_final: 0.9337 (m110) REVERT: D 131 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8847 (mt-10) REVERT: E 48 SER cc_start: 0.9775 (m) cc_final: 0.9559 (p) REVERT: E 55 SER cc_start: 0.9792 (m) cc_final: 0.9533 (p) REVERT: E 71 MET cc_start: 0.9317 (mtp) cc_final: 0.9072 (ptp) REVERT: E 76 ARG cc_start: 0.9481 (mmm-85) cc_final: 0.8698 (mmm160) REVERT: E 78 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8054 (mp0) REVERT: E 82 GLU cc_start: 0.9384 (tm-30) cc_final: 0.9024 (tm-30) REVERT: E 101 ASN cc_start: 0.9484 (m110) cc_final: 0.8978 (m110) REVERT: E 105 TYR cc_start: 0.9340 (m-10) cc_final: 0.8727 (m-80) REVERT: E 114 THR cc_start: 0.9476 (m) cc_final: 0.9215 (p) REVERT: E 130 LYS cc_start: 0.9545 (ptmt) cc_final: 0.9225 (ttpp) REVERT: E 131 GLU cc_start: 0.9086 (tp30) cc_final: 0.8611 (tm-30) REVERT: E 134 ASN cc_start: 0.9455 (m110) cc_final: 0.8816 (m-40) REVERT: E 135 ILE cc_start: 0.9595 (mm) cc_final: 0.9232 (mm) REVERT: J 6 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8187 (tp) REVERT: J 44 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7710 (pp20) REVERT: J 46 MET cc_start: 0.8335 (mtp) cc_final: 0.7724 (mtp) REVERT: J 56 VAL cc_start: 0.9478 (OUTLIER) cc_final: 0.8540 (m) REVERT: J 81 LEU cc_start: 0.9374 (mt) cc_final: 0.9169 (mp) REVERT: J 146 PHE cc_start: 0.9190 (m-80) cc_final: 0.8879 (m-80) REVERT: J 148 GLN cc_start: 0.9382 (OUTLIER) cc_final: 0.9142 (mm-40) REVERT: J 159 MET cc_start: 0.8883 (tpp) cc_final: 0.8671 (tpp) REVERT: J 166 SER cc_start: 0.9025 (m) cc_final: 0.8589 (t) REVERT: J 172 MET cc_start: 0.8462 (tmm) cc_final: 0.8257 (tmm) REVERT: J 209 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8372 (mp0) REVERT: J 229 MET cc_start: 0.8615 (mtp) cc_final: 0.8279 (ttm) REVERT: L 40 LYS cc_start: 0.9340 (tttt) cc_final: 0.8999 (tttm) REVERT: L 62 GLU cc_start: 0.8900 (tp30) cc_final: 0.8139 (mp0) REVERT: L 113 LYS cc_start: 0.9409 (ttmm) cc_final: 0.9117 (tppt) REVERT: L 115 GLN cc_start: 0.8904 (mm110) cc_final: 0.8547 (mm-40) REVERT: L 118 LYS cc_start: 0.9409 (tppp) cc_final: 0.9171 (tppt) REVERT: L 178 GLU cc_start: 0.9109 (pt0) cc_final: 0.8858 (pm20) REVERT: N 39 VAL cc_start: 0.9404 (m) cc_final: 0.9001 (t) REVERT: N 49 MET cc_start: 0.9616 (tmm) cc_final: 0.9271 (tmm) REVERT: N 72 VAL cc_start: 0.8823 (t) cc_final: 0.8494 (p) REVERT: N 155 MET cc_start: 0.8831 (pmm) cc_final: 0.8602 (pmm) REVERT: N 161 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8803 (p) REVERT: N 196 GLU cc_start: 0.8369 (tp30) cc_final: 0.7662 (tp30) REVERT: N 229 GLU cc_start: 0.8248 (tp30) cc_final: 0.7874 (tp30) REVERT: N 249 ARG cc_start: 0.9317 (mtp-110) cc_final: 0.9095 (ptm-80) REVERT: G 40 ASP cc_start: 0.9137 (m-30) cc_final: 0.8879 (p0) REVERT: G 66 GLU cc_start: 0.9293 (mt-10) cc_final: 0.9054 (mt-10) REVERT: G 167 MET cc_start: 0.7821 (tpp) cc_final: 0.7525 (tpp) REVERT: G 168 MET cc_start: 0.8775 (ttp) cc_final: 0.8559 (ttm) REVERT: F 33 GLN cc_start: 0.9258 (mp10) cc_final: 0.8892 (mp10) REVERT: F 73 ASN cc_start: 0.9508 (t0) cc_final: 0.9232 (t0) REVERT: F 121 TYR cc_start: 0.8813 (m-80) cc_final: 0.8471 (m-80) REVERT: F 137 MET cc_start: 0.8280 (ptp) cc_final: 0.7964 (ptp) REVERT: F 169 MET cc_start: 0.8995 (mtp) cc_final: 0.8738 (mtp) REVERT: H 56 ILE cc_start: 0.9391 (pt) cc_final: 0.9055 (mm) REVERT: H 110 GLN cc_start: 0.9613 (tp40) cc_final: 0.9204 (mp10) REVERT: H 145 TYR cc_start: 0.8264 (p90) cc_final: 0.7785 (p90) REVERT: H 174 ASP cc_start: 0.8641 (t0) cc_final: 0.8184 (t70) REVERT: H 182 LYS cc_start: 0.9236 (ttmt) cc_final: 0.9009 (tttm) REVERT: H 193 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9106 (pt) REVERT: H 200 MET cc_start: 0.9243 (tpp) cc_final: 0.8753 (tmm) REVERT: H 255 ASP cc_start: 0.9117 (m-30) cc_final: 0.8662 (p0) REVERT: H 261 MET cc_start: 0.9602 (mmp) cc_final: 0.9282 (mmm) REVERT: H 265 MET cc_start: 0.9547 (mtp) cc_final: 0.9235 (mtt) REVERT: H 266 GLU cc_start: 0.9507 (mt-10) cc_final: 0.9228 (mt-10) REVERT: I 80 GLU cc_start: 0.8941 (tt0) cc_final: 0.8596 (pt0) REVERT: I 99 ASP cc_start: 0.9490 (m-30) cc_final: 0.9217 (p0) REVERT: I 110 GLN cc_start: 0.9629 (tp40) cc_final: 0.9337 (tp40) REVERT: I 118 TYR cc_start: 0.9055 (m-10) cc_final: 0.8732 (m-10) REVERT: I 129 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.9045 (mmm) REVERT: I 152 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7477 (mmm) REVERT: I 182 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.7918 (tptp) REVERT: I 261 MET cc_start: 0.9708 (mmm) cc_final: 0.9382 (mmm) REVERT: I 265 MET cc_start: 0.9626 (mtm) cc_final: 0.8986 (mtm) REVERT: K 56 ASP cc_start: 0.9096 (m-30) cc_final: 0.8788 (m-30) REVERT: K 60 MET cc_start: 0.9207 (tmm) cc_final: 0.8768 (tmm) REVERT: K 61 ILE cc_start: 0.9180 (mt) cc_final: 0.8744 (mt) REVERT: K 128 ARG cc_start: 0.9526 (ttm110) cc_final: 0.9207 (ptp-110) REVERT: K 160 LEU cc_start: 0.9456 (mm) cc_final: 0.9220 (mt) REVERT: K 202 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8211 (mt-10) REVERT: K 270 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8244 (t) REVERT: K 273 LYS cc_start: 0.9496 (tppt) cc_final: 0.8913 (mttm) REVERT: K 274 GLU cc_start: 0.8565 (mp0) cc_final: 0.8050 (mp0) REVERT: K 330 PHE cc_start: 0.9123 (m-80) cc_final: 0.8457 (m-80) REVERT: K 336 MET cc_start: 0.8875 (mmm) cc_final: 0.8417 (mmm) REVERT: K 369 ILE cc_start: 0.9357 (mt) cc_final: 0.8922 (mm) REVERT: K 406 SER cc_start: 0.9188 (m) cc_final: 0.8946 (p) REVERT: K 438 MET cc_start: 0.8724 (mmt) cc_final: 0.8388 (mmt) REVERT: K 474 ARG cc_start: 0.2905 (mtt180) cc_final: 0.2255 (mtt180) REVERT: K 481 LEU cc_start: 0.8596 (tp) cc_final: 0.8279 (tp) REVERT: K 520 ASP cc_start: 0.7998 (m-30) cc_final: 0.7695 (m-30) REVERT: K 527 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8766 (mmtt) REVERT: K 619 TYR cc_start: 0.8817 (p90) cc_final: 0.8565 (p90) REVERT: K 625 ILE cc_start: 0.9447 (mt) cc_final: 0.9124 (mm) REVERT: K 627 LEU cc_start: 0.9549 (mt) cc_final: 0.9342 (tp) REVERT: K 667 GLN cc_start: 0.9121 (pm20) cc_final: 0.8785 (pm20) REVERT: K 677 MET cc_start: 0.8912 (ttp) cc_final: 0.8529 (ttp) REVERT: M 5 LYS cc_start: 0.9589 (OUTLIER) cc_final: 0.9232 (tttp) REVERT: M 16 MET cc_start: 0.8663 (mmt) cc_final: 0.8250 (mmp) REVERT: M 40 LEU cc_start: 0.9513 (mm) cc_final: 0.9279 (mt) REVERT: M 82 ILE cc_start: 0.9323 (pt) cc_final: 0.8963 (tt) REVERT: M 144 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8347 (mm110) REVERT: M 231 LYS cc_start: 0.9248 (mmtt) cc_final: 0.9045 (mmtp) outliers start: 88 outliers final: 29 residues processed: 708 average time/residue: 0.1642 time to fit residues: 187.0786 Evaluate side-chains 579 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 540 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 148 GLN Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 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 129 MET Chi-restraints excluded: chain I residue 152 MET 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 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 661 LYS Chi-restraints excluded: chain K residue 824 SER Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 157 TYR Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 136 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 72 optimal weight: 0.5980 chunk 243 optimal weight: 9.9990 chunk 331 optimal weight: 0.9980 chunk 270 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 340 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN J 148 GLN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 HIS ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 734 ASN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.053374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.044943 restraints weight = 143056.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.046698 restraints weight = 74017.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.047903 restraints weight = 46283.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.048734 restraints weight = 32451.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.049339 restraints weight = 24623.638| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29252 Z= 0.170 Angle : 0.637 9.879 39623 Z= 0.332 Chirality : 0.043 0.368 4524 Planarity : 0.004 0.050 4852 Dihedral : 13.199 178.872 4571 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.90 % Rotamer: Outliers : 3.46 % Allowed : 18.35 % Favored : 78.19 % 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 aren not related in a simple way. whole: 0.17 (0.15), residues: 3441 helix: 1.88 (0.14), residues: 1464 sheet: -0.02 (0.24), residues: 452 loop : -1.70 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 47 TYR 0.019 0.002 TYR F 212 PHE 0.037 0.001 PHE E 56 TRP 0.008 0.001 TRP K 749 HIS 0.003 0.001 HIS L 70 Details of bonding type rmsd covalent geometry : bond 0.00371 (29237) covalent geometry : angle 0.63583 (39593) SS BOND : bond 0.00347 ( 15) SS BOND : angle 1.76671 ( 30) hydrogen bonds : bond 0.03856 ( 1274) hydrogen bonds : angle 5.12874 ( 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 679 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 572 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8701 (m-30) cc_final: 0.8219 (t0) REVERT: A 29 ILE cc_start: 0.9387 (tp) cc_final: 0.9152 (tp) REVERT: A 42 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7854 (mm-30) REVERT: A 56 PHE cc_start: 0.8972 (t80) cc_final: 0.8569 (t80) REVERT: A 60 ARG cc_start: 0.9268 (mmp80) cc_final: 0.8865 (mmm160) REVERT: A 79 ILE cc_start: 0.8958 (mm) cc_final: 0.8680 (mp) REVERT: A 110 TYR cc_start: 0.9063 (t80) cc_final: 0.8821 (t80) REVERT: A 111 ASP cc_start: 0.8977 (t0) cc_final: 0.8708 (t70) REVERT: A 131 GLU cc_start: 0.9428 (mt-10) cc_final: 0.8998 (mt-10) REVERT: B 22 ASP cc_start: 0.8900 (m-30) cc_final: 0.8148 (m-30) REVERT: B 26 ARG cc_start: 0.9093 (ptp-110) cc_final: 0.8381 (ptp90) REVERT: B 44 TYR cc_start: 0.9380 (t80) cc_final: 0.9046 (t80) REVERT: B 78 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8556 (mm-30) REVERT: B 90 SER cc_start: 0.9629 (m) cc_final: 0.9233 (p) REVERT: B 129 PHE cc_start: 0.9185 (t80) cc_final: 0.8961 (t80) REVERT: B 131 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8753 (mt-10) REVERT: B 134 ASN cc_start: 0.9197 (m-40) cc_final: 0.8830 (m110) REVERT: C 22 ASP cc_start: 0.9108 (m-30) cc_final: 0.8776 (m-30) REVERT: C 44 TYR cc_start: 0.9104 (t80) cc_final: 0.8805 (t80) REVERT: C 45 VAL cc_start: 0.9411 (t) cc_final: 0.9109 (p) REVERT: C 71 MET cc_start: 0.9410 (mtm) cc_final: 0.9076 (mtm) REVERT: C 77 ASP cc_start: 0.9122 (t0) cc_final: 0.8814 (t0) REVERT: C 134 ASN cc_start: 0.9694 (m-40) cc_final: 0.9404 (m110) REVERT: D 26 ARG cc_start: 0.9569 (mtm-85) cc_final: 0.9267 (ptp90) REVERT: D 44 TYR cc_start: 0.9218 (t80) cc_final: 0.8775 (t80) REVERT: D 58 GLN cc_start: 0.9476 (mp10) cc_final: 0.9162 (mm-40) REVERT: D 90 SER cc_start: 0.9454 (m) cc_final: 0.9245 (p) REVERT: D 134 ASN cc_start: 0.9102 (m-40) cc_final: 0.8628 (m110) REVERT: E 42 GLU cc_start: 0.8554 (pt0) cc_final: 0.8272 (pm20) REVERT: E 48 SER cc_start: 0.9756 (m) cc_final: 0.9512 (p) REVERT: E 55 SER cc_start: 0.9771 (m) cc_final: 0.9513 (p) REVERT: E 56 PHE cc_start: 0.9463 (t80) cc_final: 0.9222 (t80) REVERT: E 82 GLU cc_start: 0.9346 (tm-30) cc_final: 0.9002 (tm-30) REVERT: E 94 ARG cc_start: 0.8661 (mmm-85) cc_final: 0.8456 (mtt90) REVERT: E 101 ASN cc_start: 0.9485 (m110) cc_final: 0.9061 (m110) REVERT: E 105 TYR cc_start: 0.9279 (m-10) cc_final: 0.8719 (m-80) REVERT: E 114 THR cc_start: 0.9468 (m) cc_final: 0.9209 (p) REVERT: E 130 LYS cc_start: 0.9528 (ptmt) cc_final: 0.9173 (ttpp) REVERT: E 131 GLU cc_start: 0.9022 (tp30) cc_final: 0.8654 (tm-30) REVERT: E 134 ASN cc_start: 0.9419 (m110) cc_final: 0.8779 (m-40) REVERT: E 135 ILE cc_start: 0.9576 (mm) cc_final: 0.9222 (mm) REVERT: J 46 MET cc_start: 0.8262 (mtp) cc_final: 0.7879 (mtt) REVERT: J 82 MET cc_start: 0.8774 (mmt) cc_final: 0.8540 (mmt) REVERT: J 146 PHE cc_start: 0.9205 (m-80) cc_final: 0.8917 (m-80) REVERT: J 148 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.9007 (mm110) REVERT: J 166 SER cc_start: 0.9049 (m) cc_final: 0.8575 (t) REVERT: J 209 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8411 (mp0) REVERT: J 229 MET cc_start: 0.8518 (mtp) cc_final: 0.8206 (ttm) REVERT: L 40 LYS cc_start: 0.9362 (tttt) cc_final: 0.9093 (tttp) REVERT: L 113 LYS cc_start: 0.9428 (ttmm) cc_final: 0.9146 (tppt) REVERT: L 115 GLN cc_start: 0.9004 (mm110) cc_final: 0.8592 (mm110) REVERT: L 118 LYS cc_start: 0.9516 (tppp) cc_final: 0.9197 (tppt) REVERT: L 127 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9005 (mp) REVERT: N 49 MET cc_start: 0.9612 (tmm) cc_final: 0.9277 (tmm) REVERT: N 137 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.7378 (p90) REVERT: N 161 THR cc_start: 0.9083 (p) cc_final: 0.8870 (p) REVERT: N 196 GLU cc_start: 0.8323 (tp30) cc_final: 0.7638 (tp30) REVERT: N 229 GLU cc_start: 0.8226 (tp30) cc_final: 0.7760 (tp30) REVERT: N 249 ARG cc_start: 0.9240 (mtp-110) cc_final: 0.9020 (ptm-80) REVERT: G 66 GLU cc_start: 0.9310 (mt-10) cc_final: 0.9005 (mt-10) REVERT: G 137 MET cc_start: 0.8970 (mpp) cc_final: 0.8663 (mpp) REVERT: G 156 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: F 33 GLN cc_start: 0.9294 (mp10) cc_final: 0.8950 (mp10) REVERT: F 73 ASN cc_start: 0.9498 (t0) cc_final: 0.9234 (t0) REVERT: F 121 TYR cc_start: 0.8791 (m-80) cc_final: 0.8374 (m-80) REVERT: F 137 MET cc_start: 0.8350 (ptp) cc_final: 0.8020 (ptp) REVERT: F 207 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7294 (mtp85) REVERT: H 19 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8140 (tm-30) REVERT: H 56 ILE cc_start: 0.9429 (pt) cc_final: 0.9068 (mm) REVERT: H 145 TYR cc_start: 0.8327 (p90) cc_final: 0.7886 (p90) REVERT: H 174 ASP cc_start: 0.8620 (t0) cc_final: 0.8168 (t70) REVERT: H 200 MET cc_start: 0.9285 (tpp) cc_final: 0.8980 (tpp) REVERT: H 255 ASP cc_start: 0.9076 (m-30) cc_final: 0.8574 (p0) REVERT: H 265 MET cc_start: 0.9501 (mtp) cc_final: 0.9167 (mtt) REVERT: I 17 MET cc_start: 0.8546 (tpp) cc_final: 0.8304 (tpp) REVERT: I 99 ASP cc_start: 0.9490 (m-30) cc_final: 0.9197 (p0) REVERT: I 110 GLN cc_start: 0.9622 (tp40) cc_final: 0.9339 (tp40) REVERT: I 118 TYR cc_start: 0.9037 (m-10) cc_final: 0.8655 (m-10) REVERT: I 129 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9092 (mmm) REVERT: I 152 MET cc_start: 0.7733 (mmm) cc_final: 0.7477 (mmm) REVERT: I 182 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.7974 (tptp) REVERT: K 56 ASP cc_start: 0.9123 (m-30) cc_final: 0.8821 (m-30) REVERT: K 60 MET cc_start: 0.9232 (tmm) cc_final: 0.8802 (tmm) REVERT: K 61 ILE cc_start: 0.9185 (mt) cc_final: 0.8757 (mt) REVERT: K 81 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8544 (mt-10) REVERT: K 128 ARG cc_start: 0.9522 (ttm110) cc_final: 0.9103 (ptp-110) REVERT: K 160 LEU cc_start: 0.9420 (mm) cc_final: 0.9204 (mt) REVERT: K 201 ASP cc_start: 0.9190 (t0) cc_final: 0.8776 (t0) REVERT: K 202 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8209 (mt-10) REVERT: K 205 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8186 (mm-30) REVERT: K 220 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9098 (pp) REVERT: K 273 LYS cc_start: 0.9430 (tppt) cc_final: 0.8885 (mttm) REVERT: K 274 GLU cc_start: 0.8769 (mp0) cc_final: 0.8124 (mp0) REVERT: K 330 PHE cc_start: 0.9129 (m-80) cc_final: 0.8480 (m-80) REVERT: K 336 MET cc_start: 0.8842 (mmm) cc_final: 0.8401 (mmm) REVERT: K 369 ILE cc_start: 0.9389 (mt) cc_final: 0.8967 (mm) REVERT: K 406 SER cc_start: 0.9179 (m) cc_final: 0.8935 (p) REVERT: K 435 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8368 (t80) REVERT: K 438 MET cc_start: 0.8785 (mmt) cc_final: 0.8389 (mmt) REVERT: K 474 ARG cc_start: 0.2980 (mtt180) cc_final: 0.2335 (mtt180) REVERT: K 481 LEU cc_start: 0.8599 (tp) cc_final: 0.8287 (tp) REVERT: K 520 ASP cc_start: 0.8162 (m-30) cc_final: 0.7764 (m-30) REVERT: K 527 LYS cc_start: 0.8969 (mmmt) cc_final: 0.8730 (mmtt) REVERT: K 538 ILE cc_start: 0.9291 (tp) cc_final: 0.9066 (tp) REVERT: K 588 MET cc_start: 0.9146 (mtm) cc_final: 0.8662 (mtp) REVERT: K 619 TYR cc_start: 0.8851 (p90) cc_final: 0.8585 (p90) REVERT: K 625 ILE cc_start: 0.9423 (mt) cc_final: 0.9105 (mm) REVERT: K 627 LEU cc_start: 0.9490 (mt) cc_final: 0.9215 (tp) REVERT: K 637 PHE cc_start: 0.9533 (t80) cc_final: 0.9277 (t80) REVERT: K 667 GLN cc_start: 0.9117 (pm20) cc_final: 0.8868 (pm20) REVERT: K 677 MET cc_start: 0.8922 (ttp) cc_final: 0.8511 (ttp) REVERT: K 727 ASP cc_start: 0.9468 (m-30) cc_final: 0.8808 (t0) REVERT: K 745 MET cc_start: 0.8992 (mpp) cc_final: 0.8731 (mpp) REVERT: M 16 MET cc_start: 0.8691 (mmt) cc_final: 0.8325 (mmp) REVERT: M 69 TYR cc_start: 0.8123 (t80) cc_final: 0.7887 (t80) REVERT: M 144 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8379 (mm110) REVERT: M 167 LYS cc_start: 0.9389 (mmmt) cc_final: 0.9181 (mmtp) REVERT: M 169 PHE cc_start: 0.9041 (m-10) cc_final: 0.8719 (m-80) outliers start: 107 outliers final: 48 residues processed: 646 average time/residue: 0.1609 time to fit residues: 168.4730 Evaluate side-chains 566 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 509 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 126 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 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 148 GLN 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 127 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain G residue 156 ASP 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 I residue 129 MET Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 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 435 TYR 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 628 LEU Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain K residue 824 SER Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 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: 4.9990 chunk 209 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 311 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 328 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN E 51 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN G 141 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 ASN K 734 ASN ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.054654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.046122 restraints weight = 142835.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.047901 restraints weight = 73237.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.049112 restraints weight = 45793.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.049972 restraints weight = 32063.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.050561 restraints weight = 24206.354| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29252 Z= 0.179 Angle : 0.647 14.043 39623 Z= 0.334 Chirality : 0.044 0.291 4524 Planarity : 0.004 0.056 4852 Dihedral : 13.203 178.767 4571 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.96 % Rotamer: Outliers : 3.59 % Allowed : 19.71 % Favored : 76.70 % 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 aren not related in a simple way. whole: 0.11 (0.15), residues: 3441 helix: 1.78 (0.14), residues: 1468 sheet: -0.16 (0.23), residues: 457 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 0.002 TYR N 222 PHE 0.032 0.001 PHE F 166 TRP 0.009 0.001 TRP K 749 HIS 0.004 0.001 HIS M 146 Details of bonding type rmsd covalent geometry : bond 0.00391 (29237) covalent geometry : angle 0.64334 (39593) SS BOND : bond 0.00365 ( 15) SS BOND : angle 2.61112 ( 30) hydrogen bonds : bond 0.03716 ( 1274) hydrogen bonds : angle 5.10366 ( 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 638 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 527 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8718 (m-30) cc_final: 0.8237 (t0) REVERT: A 29 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9106 (tp) REVERT: A 42 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7818 (mm-30) REVERT: A 56 PHE cc_start: 0.9005 (t80) cc_final: 0.8602 (t80) REVERT: A 60 ARG cc_start: 0.9283 (mmp80) cc_final: 0.8885 (mmm160) REVERT: A 79 ILE cc_start: 0.8970 (mm) cc_final: 0.8681 (mp) REVERT: A 110 TYR cc_start: 0.9068 (t80) cc_final: 0.8815 (t80) REVERT: A 111 ASP cc_start: 0.8976 (t0) cc_final: 0.8704 (t70) REVERT: A 131 GLU cc_start: 0.9438 (mt-10) cc_final: 0.8913 (mt-10) REVERT: B 22 ASP cc_start: 0.8896 (m-30) cc_final: 0.8135 (m-30) REVERT: B 26 ARG cc_start: 0.9087 (ptp-110) cc_final: 0.8392 (ptp90) REVERT: B 73 GLN cc_start: 0.9282 (tp40) cc_final: 0.9010 (tp-100) REVERT: B 78 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8277 (tp30) REVERT: B 90 SER cc_start: 0.9635 (m) cc_final: 0.9241 (p) REVERT: B 129 PHE cc_start: 0.9216 (t80) cc_final: 0.8896 (t80) REVERT: B 134 ASN cc_start: 0.9227 (m-40) cc_final: 0.8876 (m110) REVERT: C 22 ASP cc_start: 0.9081 (m-30) cc_final: 0.8702 (m-30) REVERT: C 44 TYR cc_start: 0.9184 (t80) cc_final: 0.8778 (t80) REVERT: C 45 VAL cc_start: 0.9525 (t) cc_final: 0.9255 (p) REVERT: C 71 MET cc_start: 0.9399 (mtm) cc_final: 0.9080 (mtm) REVERT: C 77 ASP cc_start: 0.9125 (t0) cc_final: 0.8803 (t0) REVERT: C 103 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9373 (tp) REVERT: C 105 TYR cc_start: 0.9353 (m-80) cc_final: 0.9085 (m-80) REVERT: C 134 ASN cc_start: 0.9705 (m-40) cc_final: 0.9401 (m110) REVERT: D 26 ARG cc_start: 0.9563 (mtm-85) cc_final: 0.9230 (ptp90) REVERT: D 44 TYR cc_start: 0.9261 (t80) cc_final: 0.8843 (t80) REVERT: D 58 GLN cc_start: 0.9485 (mp10) cc_final: 0.9172 (mm-40) REVERT: D 66 LEU cc_start: 0.9686 (tt) cc_final: 0.9346 (mm) REVERT: D 82 GLU cc_start: 0.9504 (tt0) cc_final: 0.9128 (tm-30) REVERT: D 90 SER cc_start: 0.9450 (m) cc_final: 0.9238 (p) REVERT: D 134 ASN cc_start: 0.9172 (m-40) cc_final: 0.8677 (m110) REVERT: E 48 SER cc_start: 0.9762 (m) cc_final: 0.9547 (p) REVERT: E 55 SER cc_start: 0.9755 (m) cc_final: 0.9490 (p) REVERT: E 56 PHE cc_start: 0.9507 (t80) cc_final: 0.9263 (t80) REVERT: E 71 MET cc_start: 0.9375 (mtp) cc_final: 0.9161 (ptp) REVERT: E 82 GLU cc_start: 0.9361 (tm-30) cc_final: 0.9007 (tm-30) REVERT: E 94 ARG cc_start: 0.8726 (mmm-85) cc_final: 0.8486 (mtt90) REVERT: E 101 ASN cc_start: 0.9507 (m110) cc_final: 0.9082 (m110) REVERT: E 105 TYR cc_start: 0.9300 (m-10) cc_final: 0.8712 (m-80) REVERT: E 114 THR cc_start: 0.9483 (m) cc_final: 0.9222 (p) REVERT: E 131 GLU cc_start: 0.9022 (tp30) cc_final: 0.8642 (tm-30) REVERT: E 135 ILE cc_start: 0.9593 (mm) cc_final: 0.9251 (mm) REVERT: J 57 GLU cc_start: 0.8216 (mp0) cc_final: 0.7940 (tm-30) REVERT: J 146 PHE cc_start: 0.9202 (m-80) cc_final: 0.8879 (m-80) REVERT: J 166 SER cc_start: 0.9023 (m) cc_final: 0.8605 (t) REVERT: J 209 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8419 (mp0) REVERT: J 229 MET cc_start: 0.8578 (mtp) cc_final: 0.8242 (mtp) REVERT: L 40 LYS cc_start: 0.9386 (tttt) cc_final: 0.9089 (tttp) REVERT: L 113 LYS cc_start: 0.9445 (ttmm) cc_final: 0.9168 (tppt) REVERT: L 115 GLN cc_start: 0.9027 (mm110) cc_final: 0.8592 (mm110) REVERT: L 118 LYS cc_start: 0.9554 (tppp) cc_final: 0.9224 (tppt) REVERT: L 127 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9060 (mp) REVERT: N 40 MET cc_start: 0.8701 (tmm) cc_final: 0.8464 (tmm) REVERT: N 49 MET cc_start: 0.9616 (tmm) cc_final: 0.9279 (tmm) REVERT: N 137 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7411 (p90) REVERT: N 155 MET cc_start: 0.8934 (pmm) cc_final: 0.8694 (pmm) REVERT: N 161 THR cc_start: 0.9081 (p) cc_final: 0.8868 (p) REVERT: G 66 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8993 (mt-10) REVERT: F 33 GLN cc_start: 0.9303 (mp10) cc_final: 0.8963 (mp10) REVERT: F 73 ASN cc_start: 0.9524 (t0) cc_final: 0.9263 (t0) REVERT: F 121 TYR cc_start: 0.8754 (m-80) cc_final: 0.8313 (m-80) REVERT: F 137 MET cc_start: 0.8384 (ptp) cc_final: 0.8034 (ptp) REVERT: F 167 MET cc_start: 0.8944 (tpp) cc_final: 0.8640 (tpp) REVERT: F 207 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7315 (mtp85) REVERT: H 5 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8701 (m) REVERT: H 19 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8166 (tm-30) REVERT: H 56 ILE cc_start: 0.9411 (pt) cc_final: 0.9066 (mm) REVERT: H 145 TYR cc_start: 0.8384 (p90) cc_final: 0.7986 (p90) REVERT: H 174 ASP cc_start: 0.8668 (t0) cc_final: 0.8226 (t70) REVERT: H 200 MET cc_start: 0.9323 (tpp) cc_final: 0.8951 (mmm) REVERT: H 255 ASP cc_start: 0.9090 (m-30) cc_final: 0.8583 (p0) REVERT: H 265 MET cc_start: 0.9492 (mtp) cc_final: 0.9146 (mtt) REVERT: I 99 ASP cc_start: 0.9497 (m-30) cc_final: 0.9199 (p0) REVERT: I 110 GLN cc_start: 0.9610 (tp40) cc_final: 0.9337 (tp40) REVERT: I 129 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.9125 (mmm) REVERT: I 182 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8027 (tptp) REVERT: K 56 ASP cc_start: 0.9110 (m-30) cc_final: 0.8797 (m-30) REVERT: K 60 MET cc_start: 0.9207 (tmm) cc_final: 0.8800 (tmm) REVERT: K 61 ILE cc_start: 0.9190 (mt) cc_final: 0.8760 (mt) REVERT: K 81 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8581 (mt-10) REVERT: K 160 LEU cc_start: 0.9374 (mm) cc_final: 0.9171 (mt) REVERT: K 201 ASP cc_start: 0.9201 (t0) cc_final: 0.8737 (t0) REVERT: K 202 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8239 (mt-10) REVERT: K 205 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8175 (mm-30) REVERT: K 220 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9124 (pp) REVERT: K 273 LYS cc_start: 0.9434 (tppt) cc_final: 0.8896 (mttm) REVERT: K 330 PHE cc_start: 0.9130 (m-80) cc_final: 0.8413 (m-80) REVERT: K 336 MET cc_start: 0.8851 (mmm) cc_final: 0.8398 (mmm) REVERT: K 369 ILE cc_start: 0.9420 (mt) cc_final: 0.8993 (mm) REVERT: K 406 SER cc_start: 0.9204 (m) cc_final: 0.8947 (p) REVERT: K 435 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.8368 (t80) REVERT: K 438 MET cc_start: 0.8824 (mmt) cc_final: 0.8402 (mmt) REVERT: K 454 VAL cc_start: 0.7480 (OUTLIER) cc_final: 0.6744 (m) REVERT: K 474 ARG cc_start: 0.2924 (mtt180) cc_final: 0.2274 (mtt180) REVERT: K 481 LEU cc_start: 0.8608 (tp) cc_final: 0.8288 (tp) REVERT: K 520 ASP cc_start: 0.8192 (m-30) cc_final: 0.7841 (m-30) REVERT: K 527 LYS cc_start: 0.8977 (mmmt) cc_final: 0.8763 (mmtt) REVERT: K 538 ILE cc_start: 0.9334 (tp) cc_final: 0.9078 (tp) REVERT: K 587 LYS cc_start: 0.9191 (mmtm) cc_final: 0.8669 (tppt) REVERT: K 588 MET cc_start: 0.9241 (mtm) cc_final: 0.8746 (mtp) REVERT: K 619 TYR cc_start: 0.8919 (p90) cc_final: 0.8650 (p90) REVERT: K 625 ILE cc_start: 0.9398 (mt) cc_final: 0.9103 (mm) REVERT: K 667 GLN cc_start: 0.9149 (pm20) cc_final: 0.8892 (pm20) REVERT: K 677 MET cc_start: 0.8942 (ttp) cc_final: 0.8694 (ttp) REVERT: K 727 ASP cc_start: 0.9499 (m-30) cc_final: 0.8816 (t0) REVERT: K 730 GLU cc_start: 0.9034 (tt0) cc_final: 0.8722 (tp30) REVERT: K 745 MET cc_start: 0.8954 (mpp) cc_final: 0.8630 (mtm) REVERT: M 5 LYS cc_start: 0.9572 (OUTLIER) cc_final: 0.9308 (tttp) REVERT: M 16 MET cc_start: 0.8741 (mmt) cc_final: 0.8338 (mmp) REVERT: M 167 LYS cc_start: 0.9400 (mmmt) cc_final: 0.9176 (mmtp) REVERT: M 169 PHE cc_start: 0.9013 (m-10) cc_final: 0.8737 (m-80) outliers start: 111 outliers final: 62 residues processed: 605 average time/residue: 0.1556 time to fit residues: 152.8137 Evaluate side-chains 576 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 502 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 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 L residue 127 ILE Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 193 ILE 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 174 LEU 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 435 TYR Chi-restraints excluded: chain K residue 454 VAL Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 628 LEU Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain M residue 5 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 291 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 186 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 319 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 ASN N 59 ASN N 193 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 269 ASN K 80 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.049047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.040831 restraints weight = 149261.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.042491 restraints weight = 76747.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.043634 restraints weight = 48086.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.044450 restraints weight = 33833.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.044990 restraints weight = 25713.540| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 29252 Z= 0.356 Angle : 0.776 12.816 39623 Z= 0.406 Chirality : 0.046 0.273 4524 Planarity : 0.005 0.063 4852 Dihedral : 13.436 179.517 4571 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.00 % Favored : 92.85 % Rotamer: Outliers : 4.72 % Allowed : 19.13 % Favored : 76.15 % 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 aren not related in a simple way. whole: -0.34 (0.14), residues: 3441 helix: 1.29 (0.14), residues: 1472 sheet: -0.40 (0.23), residues: 468 loop : -1.76 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 72 TYR 0.025 0.002 TYR I 145 PHE 0.038 0.002 PHE K 245 TRP 0.022 0.002 TRP G 182 HIS 0.007 0.002 HIS M 146 Details of bonding type rmsd covalent geometry : bond 0.00739 (29237) covalent geometry : angle 0.77408 (39593) SS BOND : bond 0.00533 ( 15) SS BOND : angle 2.23344 ( 30) hydrogen bonds : bond 0.04270 ( 1274) hydrogen bonds : angle 5.47423 ( 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 628 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 482 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8726 (m-30) cc_final: 0.8244 (t0) REVERT: A 42 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7944 (mm-30) REVERT: A 56 PHE cc_start: 0.9003 (t80) cc_final: 0.8587 (t80) REVERT: A 60 ARG cc_start: 0.9288 (mmp80) cc_final: 0.8889 (mmm-85) REVERT: A 79 ILE cc_start: 0.9073 (mm) cc_final: 0.8801 (mp) REVERT: A 111 ASP cc_start: 0.9016 (t0) cc_final: 0.8675 (t0) REVERT: A 131 GLU cc_start: 0.9468 (mt-10) cc_final: 0.8990 (mt-10) REVERT: B 22 ASP cc_start: 0.8868 (m-30) cc_final: 0.8140 (m-30) REVERT: B 26 ARG cc_start: 0.9120 (ptp-110) cc_final: 0.8375 (ptp90) REVERT: B 73 GLN cc_start: 0.9366 (tp40) cc_final: 0.9155 (tp-100) REVERT: B 78 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8354 (tp30) REVERT: B 90 SER cc_start: 0.9630 (m) cc_final: 0.9242 (p) REVERT: B 129 PHE cc_start: 0.9298 (t80) cc_final: 0.9024 (t80) REVERT: B 131 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8770 (mt-10) REVERT: B 134 ASN cc_start: 0.9242 (m-40) cc_final: 0.8943 (m110) REVERT: C 22 ASP cc_start: 0.9102 (m-30) cc_final: 0.8700 (m-30) REVERT: C 44 TYR cc_start: 0.9340 (t80) cc_final: 0.9083 (t80) REVERT: C 71 MET cc_start: 0.9457 (mtm) cc_final: 0.9087 (mtm) REVERT: C 77 ASP cc_start: 0.9253 (t0) cc_final: 0.9003 (t0) REVERT: C 103 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9421 (tp) REVERT: C 134 ASN cc_start: 0.9744 (m-40) cc_final: 0.9430 (m110) REVERT: D 26 ARG cc_start: 0.9617 (mtm-85) cc_final: 0.9293 (ptp90) REVERT: D 32 ILE cc_start: 0.9115 (tp) cc_final: 0.8905 (tp) REVERT: D 44 TYR cc_start: 0.9262 (t80) cc_final: 0.8725 (t80) REVERT: D 58 GLN cc_start: 0.9506 (mp10) cc_final: 0.9275 (mm-40) REVERT: D 90 SER cc_start: 0.9498 (m) cc_final: 0.9260 (p) REVERT: D 95 GLU cc_start: 0.8594 (tp30) cc_final: 0.8206 (tm-30) REVERT: D 134 ASN cc_start: 0.9248 (m-40) cc_final: 0.8731 (m110) REVERT: E 78 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8090 (mt-10) REVERT: E 82 GLU cc_start: 0.9354 (tm-30) cc_final: 0.9029 (tm-30) REVERT: E 101 ASN cc_start: 0.9570 (m110) cc_final: 0.9103 (m110) REVERT: E 105 TYR cc_start: 0.9356 (m-10) cc_final: 0.8839 (m-80) REVERT: E 131 GLU cc_start: 0.9081 (tp30) cc_final: 0.8707 (tm-30) REVERT: E 135 ILE cc_start: 0.9610 (mm) cc_final: 0.9289 (mm) REVERT: J 146 PHE cc_start: 0.9208 (m-80) cc_final: 0.8865 (m-80) REVERT: J 166 SER cc_start: 0.9091 (m) cc_final: 0.8638 (t) REVERT: J 209 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8537 (mp0) REVERT: J 229 MET cc_start: 0.8701 (mtp) cc_final: 0.8259 (mtp) REVERT: L 115 GLN cc_start: 0.9205 (mm110) cc_final: 0.8877 (mm110) REVERT: L 118 LYS cc_start: 0.9646 (tppp) cc_final: 0.9287 (tppt) REVERT: L 127 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9091 (mp) REVERT: N 49 MET cc_start: 0.9601 (tmm) cc_final: 0.9313 (tmm) REVERT: N 137 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7552 (p90) REVERT: N 155 MET cc_start: 0.8750 (pmm) cc_final: 0.8525 (pmm) REVERT: N 249 ARG cc_start: 0.9161 (ptm-80) cc_final: 0.8774 (ptm-80) REVERT: G 66 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8990 (mt-10) REVERT: F 33 GLN cc_start: 0.9340 (mp10) cc_final: 0.8955 (mp10) REVERT: F 73 ASN cc_start: 0.9577 (t0) cc_final: 0.9343 (t0) REVERT: F 134 GLN cc_start: 0.9190 (tt0) cc_final: 0.8980 (tt0) REVERT: F 137 MET cc_start: 0.8750 (ptp) cc_final: 0.8360 (mpp) REVERT: H 145 TYR cc_start: 0.8731 (p90) cc_final: 0.8248 (p90) REVERT: H 174 ASP cc_start: 0.8821 (t0) cc_final: 0.8383 (t70) REVERT: H 255 ASP cc_start: 0.9193 (m-30) cc_final: 0.8735 (p0) REVERT: I 110 GLN cc_start: 0.9658 (tp40) cc_final: 0.9261 (tp-100) REVERT: I 118 TYR cc_start: 0.9279 (m-10) cc_final: 0.8916 (m-10) REVERT: I 200 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9094 (ttp) REVERT: I 265 MET cc_start: 0.9657 (mtm) cc_final: 0.9317 (mtm) REVERT: K 56 ASP cc_start: 0.9226 (m-30) cc_final: 0.8897 (m-30) REVERT: K 60 MET cc_start: 0.9283 (tmm) cc_final: 0.8889 (tmm) REVERT: K 61 ILE cc_start: 0.9205 (mt) cc_final: 0.8764 (mt) REVERT: K 81 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8550 (mt-10) REVERT: K 148 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8743 (t) REVERT: K 160 LEU cc_start: 0.9421 (mm) cc_final: 0.9220 (mt) REVERT: K 202 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8294 (mt-10) REVERT: K 205 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8426 (mm-30) REVERT: K 336 MET cc_start: 0.8895 (mmm) cc_final: 0.8642 (mmm) REVERT: K 369 ILE cc_start: 0.9515 (mt) cc_final: 0.9103 (mm) REVERT: K 406 SER cc_start: 0.9292 (m) cc_final: 0.9046 (p) REVERT: K 438 MET cc_start: 0.8877 (mmt) cc_final: 0.8577 (mmt) REVERT: K 474 ARG cc_start: 0.2963 (mtt180) cc_final: 0.2375 (mtt180) REVERT: K 481 LEU cc_start: 0.8640 (tp) cc_final: 0.8280 (tp) REVERT: K 502 LYS cc_start: 0.9434 (mtpt) cc_final: 0.9124 (mtmm) REVERT: K 520 ASP cc_start: 0.8249 (m-30) cc_final: 0.7967 (m-30) REVERT: K 538 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9192 (tp) REVERT: K 587 LYS cc_start: 0.9255 (mmtm) cc_final: 0.8847 (tppt) REVERT: K 588 MET cc_start: 0.9357 (mtm) cc_final: 0.8872 (mtp) REVERT: K 625 ILE cc_start: 0.9373 (mt) cc_final: 0.9022 (mm) REVERT: K 677 MET cc_start: 0.9001 (ttp) cc_final: 0.8747 (ttp) REVERT: K 727 ASP cc_start: 0.9489 (m-30) cc_final: 0.8871 (t0) REVERT: K 730 GLU cc_start: 0.9040 (tt0) cc_final: 0.8788 (tp30) REVERT: K 745 MET cc_start: 0.8971 (mpp) cc_final: 0.8684 (mpp) REVERT: M 5 LYS cc_start: 0.9574 (OUTLIER) cc_final: 0.9243 (tttp) REVERT: M 16 MET cc_start: 0.8677 (mmt) cc_final: 0.8345 (mmp) REVERT: M 62 ILE cc_start: 0.9649 (OUTLIER) cc_final: 0.9366 (mm) REVERT: M 144 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8401 (mm110) REVERT: M 169 PHE cc_start: 0.9062 (m-10) cc_final: 0.8837 (m-80) REVERT: M 170 ASP cc_start: 0.9069 (t0) cc_final: 0.8777 (t0) REVERT: M 290 MET cc_start: 0.8949 (pmm) cc_final: 0.8746 (pmm) outliers start: 146 outliers final: 96 residues processed: 584 average time/residue: 0.1634 time to fit residues: 154.9098 Evaluate side-chains 554 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 450 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 121 ASN 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 120 THR Chi-restraints excluded: chain J residue 177 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 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 126 GLN Chi-restraints excluded: chain L residue 127 ILE Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 169 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 187 VAL Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain G residue 35 PHE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain F residue 157 TYR 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 123 CYS Chi-restraints excluded: chain H residue 135 VAL 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 56 ILE Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 182 LYS Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 200 MET Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain K residue 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 220 LEU Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 538 ILE Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 ILE Chi-restraints excluded: chain M residue 103 GLU Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 132 ASN 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 291 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 222 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 282 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 223 optimal weight: 0.5980 chunk 156 optimal weight: 5.9990 chunk 317 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.051069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.042828 restraints weight = 145190.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.044536 restraints weight = 73798.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.045699 restraints weight = 45954.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.046520 restraints weight = 32196.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.047094 restraints weight = 24351.429| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3674 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= 0.185 Angle : 0.678 14.104 39623 Z= 0.351 Chirality : 0.044 0.277 4524 Planarity : 0.004 0.060 4852 Dihedral : 13.412 179.243 4571 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.13 % Favored : 93.75 % Rotamer: Outliers : 3.82 % Allowed : 21.00 % Favored : 75.18 % 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 aren not related in a simple way. whole: -0.13 (0.14), residues: 3441 helix: 1.51 (0.14), residues: 1472 sheet: -0.33 (0.23), residues: 463 loop : -1.69 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 114 TYR 0.047 0.002 TYR K 62 PHE 0.030 0.001 PHE E 56 TRP 0.056 0.002 TRP G 182 HIS 0.006 0.001 HIS N 173 Details of bonding type rmsd covalent geometry : bond 0.00402 (29237) covalent geometry : angle 0.67621 (39593) SS BOND : bond 0.00927 ( 15) SS BOND : angle 2.04527 ( 30) hydrogen bonds : bond 0.03909 ( 1274) hydrogen bonds : angle 5.17706 ( 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 617 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 499 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8683 (m-30) cc_final: 0.8197 (t0) REVERT: A 42 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7987 (mm-30) REVERT: A 56 PHE cc_start: 0.8924 (t80) cc_final: 0.8523 (t80) REVERT: A 60 ARG cc_start: 0.9294 (mmp80) cc_final: 0.8910 (mmm-85) REVERT: A 69 TYR cc_start: 0.9300 (t80) cc_final: 0.9012 (t80) REVERT: A 79 ILE cc_start: 0.9048 (mm) cc_final: 0.8766 (mp) REVERT: A 110 TYR cc_start: 0.9001 (t80) cc_final: 0.8768 (t80) REVERT: A 111 ASP cc_start: 0.8967 (t0) cc_final: 0.8673 (t70) REVERT: A 131 GLU cc_start: 0.9469 (mt-10) cc_final: 0.8978 (mt-10) REVERT: B 22 ASP cc_start: 0.8881 (m-30) cc_final: 0.8210 (m-30) REVERT: B 26 ARG cc_start: 0.9137 (ptp-110) cc_final: 0.8468 (ptp90) REVERT: B 73 GLN cc_start: 0.9331 (tp40) cc_final: 0.9043 (tp-100) REVERT: B 78 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8183 (tp30) REVERT: B 90 SER cc_start: 0.9637 (m) cc_final: 0.9232 (p) REVERT: B 129 PHE cc_start: 0.9199 (t80) cc_final: 0.8929 (t80) REVERT: B 131 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8772 (mt-10) REVERT: B 134 ASN cc_start: 0.9207 (m-40) cc_final: 0.8882 (m110) REVERT: C 22 ASP cc_start: 0.9061 (m-30) cc_final: 0.8642 (m-30) REVERT: C 44 TYR cc_start: 0.9264 (t80) cc_final: 0.8754 (t80) REVERT: C 71 MET cc_start: 0.9391 (mtm) cc_final: 0.9087 (mtm) REVERT: C 77 ASP cc_start: 0.9288 (t0) cc_final: 0.9048 (t0) REVERT: C 105 TYR cc_start: 0.9348 (m-80) cc_final: 0.9086 (m-80) REVERT: C 134 ASN cc_start: 0.9729 (m-40) cc_final: 0.9407 (m110) REVERT: D 22 ASP cc_start: 0.8949 (m-30) cc_final: 0.8706 (t0) REVERT: D 29 ILE cc_start: 0.8898 (mm) cc_final: 0.8603 (tp) REVERT: D 32 ILE cc_start: 0.9193 (tp) cc_final: 0.8965 (tp) REVERT: D 44 TYR cc_start: 0.9173 (t80) cc_final: 0.8666 (t80) REVERT: D 58 GLN cc_start: 0.9483 (mp10) cc_final: 0.9231 (mm-40) REVERT: D 90 SER cc_start: 0.9497 (m) cc_final: 0.9271 (p) REVERT: D 95 GLU cc_start: 0.8691 (tp30) cc_final: 0.8472 (tp30) REVERT: D 101 ASN cc_start: 0.9576 (m110) cc_final: 0.9334 (m-40) REVERT: D 134 ASN cc_start: 0.9252 (m-40) cc_final: 0.8767 (m110) REVERT: E 55 SER cc_start: 0.9795 (m) cc_final: 0.9540 (p) REVERT: E 78 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8175 (mt-10) REVERT: E 82 GLU cc_start: 0.9315 (tm-30) cc_final: 0.8935 (tm-30) REVERT: E 101 ASN cc_start: 0.9538 (m110) cc_final: 0.9046 (m110) REVERT: E 105 TYR cc_start: 0.9304 (m-10) cc_final: 0.8759 (m-80) REVERT: E 114 THR cc_start: 0.9516 (m) cc_final: 0.9257 (p) REVERT: E 131 GLU cc_start: 0.8997 (tp30) cc_final: 0.8618 (tm-30) REVERT: E 135 ILE cc_start: 0.9574 (mm) cc_final: 0.9255 (mm) REVERT: J 57 GLU cc_start: 0.8390 (mp0) cc_final: 0.7993 (tm-30) REVERT: J 99 MET cc_start: 0.9459 (ttp) cc_final: 0.9211 (ppp) REVERT: J 146 PHE cc_start: 0.9188 (m-80) cc_final: 0.8864 (m-80) REVERT: J 166 SER cc_start: 0.9061 (m) cc_final: 0.8605 (t) REVERT: J 229 MET cc_start: 0.8625 (mtp) cc_final: 0.8239 (mtp) REVERT: L 43 MET cc_start: 0.8887 (ttp) cc_final: 0.8616 (tpp) REVERT: L 115 GLN cc_start: 0.9137 (mm110) cc_final: 0.8819 (mm110) REVERT: L 118 LYS cc_start: 0.9644 (tppp) cc_final: 0.9216 (tppp) REVERT: L 127 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9055 (mp) REVERT: N 49 MET cc_start: 0.9589 (tmm) cc_final: 0.9304 (tmm) REVERT: N 137 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7278 (p90) REVERT: N 249 ARG cc_start: 0.9191 (ptm-80) cc_final: 0.8825 (ptm-80) REVERT: G 66 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8902 (mt-10) REVERT: F 33 GLN cc_start: 0.9367 (mp10) cc_final: 0.8950 (mp10) REVERT: F 73 ASN cc_start: 0.9535 (t0) cc_final: 0.9277 (t0) REVERT: F 134 GLN cc_start: 0.9189 (tt0) cc_final: 0.8947 (tt0) REVERT: F 137 MET cc_start: 0.8633 (ptp) cc_final: 0.8320 (mpp) REVERT: F 207 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6861 (mtp85) REVERT: H 5 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8563 (t) REVERT: H 19 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8092 (tm-30) REVERT: H 145 TYR cc_start: 0.8711 (p90) cc_final: 0.8202 (p90) REVERT: H 174 ASP cc_start: 0.8771 (t0) cc_final: 0.8344 (t70) REVERT: H 255 ASP cc_start: 0.9164 (m-30) cc_final: 0.8685 (p0) REVERT: H 265 MET cc_start: 0.9500 (mtp) cc_final: 0.9196 (mtt) REVERT: I 98 ARG cc_start: 0.9010 (tpp80) cc_final: 0.8803 (tpp80) REVERT: I 110 GLN cc_start: 0.9627 (tp40) cc_final: 0.9318 (tp40) REVERT: I 118 TYR cc_start: 0.9174 (m-10) cc_final: 0.8255 (m-10) REVERT: I 200 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.8350 (tmm) REVERT: I 265 MET cc_start: 0.9639 (mtm) cc_final: 0.9127 (mtm) REVERT: I 275 TYR cc_start: 0.8994 (p90) cc_final: 0.8294 (p90) REVERT: I 277 LYS cc_start: 0.9368 (ttpt) cc_final: 0.9048 (pttt) REVERT: K 56 ASP cc_start: 0.9139 (m-30) cc_final: 0.8798 (m-30) REVERT: K 60 MET cc_start: 0.9235 (tmm) cc_final: 0.8820 (tmm) REVERT: K 61 ILE cc_start: 0.9152 (mt) cc_final: 0.8730 (mt) REVERT: K 148 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8715 (t) REVERT: K 160 LEU cc_start: 0.9380 (mm) cc_final: 0.9162 (mt) REVERT: K 202 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8245 (mt-10) REVERT: K 205 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8405 (mm-30) REVERT: K 220 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9215 (pp) REVERT: K 273 LYS cc_start: 0.9450 (tppt) cc_final: 0.8893 (mttm) REVERT: K 336 MET cc_start: 0.8911 (mmm) cc_final: 0.8558 (mmm) REVERT: K 369 ILE cc_start: 0.9344 (mt) cc_final: 0.8930 (mt) REVERT: K 406 SER cc_start: 0.9261 (m) cc_final: 0.9023 (p) REVERT: K 435 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.8339 (t80) REVERT: K 438 MET cc_start: 0.8950 (mmt) cc_final: 0.8491 (mmt) REVERT: K 474 ARG cc_start: 0.3012 (mtt180) cc_final: 0.2343 (mtt180) REVERT: K 481 LEU cc_start: 0.8663 (tp) cc_final: 0.8313 (tp) REVERT: K 502 LYS cc_start: 0.9382 (mtpt) cc_final: 0.9065 (mtmm) REVERT: K 520 ASP cc_start: 0.8218 (m-30) cc_final: 0.7933 (m-30) REVERT: K 538 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9091 (tp) REVERT: K 587 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8816 (tppt) REVERT: K 588 MET cc_start: 0.9369 (mtm) cc_final: 0.8775 (mtp) REVERT: K 619 TYR cc_start: 0.8988 (p90) cc_final: 0.8558 (p90) REVERT: K 625 ILE cc_start: 0.9384 (mt) cc_final: 0.9090 (mm) REVERT: K 677 MET cc_start: 0.8953 (ttp) cc_final: 0.8660 (ttp) REVERT: K 727 ASP cc_start: 0.9457 (m-30) cc_final: 0.8827 (t0) REVERT: K 730 GLU cc_start: 0.9023 (tt0) cc_final: 0.8714 (tp30) REVERT: K 745 MET cc_start: 0.9007 (mpp) cc_final: 0.8611 (mtm) REVERT: M 5 LYS cc_start: 0.9562 (OUTLIER) cc_final: 0.9226 (tttp) REVERT: M 16 MET cc_start: 0.8728 (mmt) cc_final: 0.8368 (mmp) REVERT: M 62 ILE cc_start: 0.9632 (OUTLIER) cc_final: 0.9364 (mm) REVERT: M 144 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8320 (mm110) REVERT: M 170 ASP cc_start: 0.9016 (t0) cc_final: 0.8712 (t0) REVERT: M 290 MET cc_start: 0.8872 (pmm) cc_final: 0.8602 (pmm) outliers start: 118 outliers final: 83 residues processed: 578 average time/residue: 0.1623 time to fit residues: 151.7132 Evaluate side-chains 572 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 477 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 88 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 49 THR 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 82 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 212 MET 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 L residue 127 ILE Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 103 ASN Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 157 TYR 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 I residue 88 ASP Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 183 MET Chi-restraints excluded: chain I residue 200 MET Chi-restraints excluded: chain I residue 209 GLN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 111 GLU 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 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 435 TYR 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 661 LYS Chi-restraints excluded: chain K residue 666 VAL Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 302 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 313 optimal weight: 8.9990 chunk 159 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 299 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.050199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.041956 restraints weight = 145815.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.043658 restraints weight = 74272.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.044848 restraints weight = 46198.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.045665 restraints weight = 32238.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.046222 restraints weight = 24419.685| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 29252 Z= 0.222 Angle : 0.708 13.723 39623 Z= 0.363 Chirality : 0.045 0.310 4524 Planarity : 0.004 0.061 4852 Dihedral : 13.462 179.598 4571 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.66 % Favored : 93.23 % Rotamer: Outliers : 4.53 % Allowed : 21.00 % Favored : 74.47 % 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 aren not related in a simple way. whole: -0.17 (0.14), residues: 3441 helix: 1.46 (0.14), residues: 1471 sheet: -0.31 (0.23), residues: 473 loop : -1.70 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 293 TYR 0.040 0.002 TYR K 62 PHE 0.041 0.002 PHE E 56 TRP 0.037 0.002 TRP G 182 HIS 0.005 0.001 HIS M 146 Details of bonding type rmsd covalent geometry : bond 0.00475 (29237) covalent geometry : angle 0.70653 (39593) SS BOND : bond 0.00468 ( 15) SS BOND : angle 2.00090 ( 30) hydrogen bonds : bond 0.03925 ( 1274) hydrogen bonds : angle 5.19342 ( 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 623 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 483 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8696 (m-30) cc_final: 0.8222 (t0) REVERT: A 42 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7940 (mm-30) REVERT: A 56 PHE cc_start: 0.8943 (t80) cc_final: 0.8552 (t80) REVERT: A 60 ARG cc_start: 0.9289 (mmp80) cc_final: 0.8888 (mmm160) REVERT: A 69 TYR cc_start: 0.9257 (t80) cc_final: 0.9037 (t80) REVERT: A 79 ILE cc_start: 0.9045 (mm) cc_final: 0.8762 (mp) REVERT: A 110 TYR cc_start: 0.9051 (t80) cc_final: 0.8813 (t80) REVERT: A 111 ASP cc_start: 0.8969 (t0) cc_final: 0.8608 (t0) REVERT: A 131 GLU cc_start: 0.9492 (mt-10) cc_final: 0.8835 (mt-10) REVERT: B 22 ASP cc_start: 0.8870 (m-30) cc_final: 0.8209 (m-30) REVERT: B 26 ARG cc_start: 0.9113 (ptp-110) cc_final: 0.8423 (ptp90) REVERT: B 73 GLN cc_start: 0.9334 (tp40) cc_final: 0.8993 (tp-100) REVERT: B 78 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8345 (tp30) REVERT: B 90 SER cc_start: 0.9642 (m) cc_final: 0.9251 (p) REVERT: B 129 PHE cc_start: 0.9185 (t80) cc_final: 0.8934 (t80) REVERT: B 131 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8790 (mt-10) REVERT: B 134 ASN cc_start: 0.9183 (m-40) cc_final: 0.8813 (m110) REVERT: C 22 ASP cc_start: 0.9095 (m-30) cc_final: 0.8683 (m-30) REVERT: C 44 TYR cc_start: 0.9248 (t80) cc_final: 0.8696 (t80) REVERT: C 71 MET cc_start: 0.9388 (mtm) cc_final: 0.9079 (mtm) REVERT: C 77 ASP cc_start: 0.9274 (t0) cc_final: 0.9035 (t0) REVERT: C 103 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9377 (tp) REVERT: C 105 TYR cc_start: 0.9372 (m-80) cc_final: 0.9131 (m-80) REVERT: C 134 ASN cc_start: 0.9734 (m-40) cc_final: 0.9412 (m110) REVERT: D 26 ARG cc_start: 0.9538 (mtm-85) cc_final: 0.9202 (ptp-110) REVERT: D 32 ILE cc_start: 0.9186 (tp) cc_final: 0.8937 (tp) REVERT: D 35 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.9106 (ttpt) REVERT: D 44 TYR cc_start: 0.9102 (t80) cc_final: 0.8653 (t80) REVERT: D 58 GLN cc_start: 0.9489 (mp10) cc_final: 0.9282 (mm-40) REVERT: D 90 SER cc_start: 0.9510 (m) cc_final: 0.9283 (p) REVERT: D 95 GLU cc_start: 0.8662 (tp30) cc_final: 0.8379 (tp30) REVERT: D 101 ASN cc_start: 0.9576 (m110) cc_final: 0.9329 (m-40) REVERT: D 134 ASN cc_start: 0.9278 (m-40) cc_final: 0.8797 (m110) REVERT: E 44 TYR cc_start: 0.8908 (t80) cc_final: 0.8630 (t80) REVERT: E 48 SER cc_start: 0.9759 (m) cc_final: 0.9544 (p) REVERT: E 55 SER cc_start: 0.9792 (m) cc_final: 0.9543 (p) REVERT: E 78 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8182 (mt-10) REVERT: E 82 GLU cc_start: 0.9335 (tm-30) cc_final: 0.9018 (tm-30) REVERT: E 101 ASN cc_start: 0.9546 (m110) cc_final: 0.9082 (m110) REVERT: E 105 TYR cc_start: 0.9323 (m-10) cc_final: 0.8815 (m-80) REVERT: E 114 THR cc_start: 0.9515 (m) cc_final: 0.9259 (p) REVERT: E 131 GLU cc_start: 0.9008 (tp30) cc_final: 0.8645 (tm-30) REVERT: E 135 ILE cc_start: 0.9580 (mm) cc_final: 0.9263 (mm) REVERT: J 44 GLU cc_start: 0.8835 (pp20) cc_final: 0.7345 (pp20) REVERT: J 46 MET cc_start: 0.8485 (mtt) cc_final: 0.7951 (mmm) REVERT: J 99 MET cc_start: 0.9497 (ttp) cc_final: 0.9228 (ppp) REVERT: J 146 PHE cc_start: 0.9220 (m-80) cc_final: 0.8893 (m-80) REVERT: J 166 SER cc_start: 0.9033 (m) cc_final: 0.8605 (t) REVERT: J 209 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8472 (mp0) REVERT: J 229 MET cc_start: 0.8602 (mtp) cc_final: 0.8207 (mtp) REVERT: L 98 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7669 (p) REVERT: L 113 LYS cc_start: 0.9369 (tppp) cc_final: 0.9148 (tppt) REVERT: L 115 GLN cc_start: 0.9199 (mm110) cc_final: 0.8972 (tp40) REVERT: L 118 LYS cc_start: 0.9642 (tppp) cc_final: 0.9218 (tppp) REVERT: N 49 MET cc_start: 0.9597 (tmm) cc_final: 0.9280 (tmm) REVERT: N 137 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7242 (p90) REVERT: N 249 ARG cc_start: 0.9223 (ptm-80) cc_final: 0.8873 (ptm-80) REVERT: G 7 ASP cc_start: 0.9299 (OUTLIER) cc_final: 0.9068 (p0) REVERT: G 66 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8921 (mt-10) REVERT: F 33 GLN cc_start: 0.9381 (mp10) cc_final: 0.8936 (mp10) REVERT: F 73 ASN cc_start: 0.9549 (t0) cc_final: 0.9300 (t0) REVERT: F 134 GLN cc_start: 0.9265 (tt0) cc_final: 0.9026 (tt0) REVERT: F 137 MET cc_start: 0.8652 (ptp) cc_final: 0.8309 (mpp) REVERT: F 207 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6840 (mtp85) REVERT: H 5 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8575 (t) REVERT: H 19 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8079 (tm-30) REVERT: H 145 TYR cc_start: 0.8742 (p90) cc_final: 0.8224 (p90) REVERT: H 174 ASP cc_start: 0.8832 (t0) cc_final: 0.8377 (t70) REVERT: H 200 MET cc_start: 0.9379 (tpp) cc_final: 0.9143 (tpp) REVERT: H 255 ASP cc_start: 0.9157 (m-30) cc_final: 0.8682 (p0) REVERT: I 110 GLN cc_start: 0.9630 (tp40) cc_final: 0.9331 (tp40) REVERT: I 118 TYR cc_start: 0.9161 (m-10) cc_final: 0.8758 (m-10) REVERT: I 129 MET cc_start: 0.9155 (mmm) cc_final: 0.8790 (mmp) REVERT: I 200 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.9022 (ttp) REVERT: I 202 ASN cc_start: 0.9276 (OUTLIER) cc_final: 0.8838 (t0) REVERT: I 265 MET cc_start: 0.9652 (mtm) cc_final: 0.9085 (mtm) REVERT: K 56 ASP cc_start: 0.9140 (m-30) cc_final: 0.8792 (m-30) REVERT: K 60 MET cc_start: 0.9206 (tmm) cc_final: 0.8760 (tmm) REVERT: K 61 ILE cc_start: 0.9132 (mt) cc_final: 0.8549 (mt) REVERT: K 148 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8903 (t) REVERT: K 160 LEU cc_start: 0.9393 (mm) cc_final: 0.9177 (mt) REVERT: K 202 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8311 (mt-10) REVERT: K 205 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8430 (mm-30) REVERT: K 220 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9215 (pp) REVERT: K 273 LYS cc_start: 0.9436 (tppt) cc_final: 0.8886 (mttm) REVERT: K 336 MET cc_start: 0.8896 (mmm) cc_final: 0.8560 (mmm) REVERT: K 369 ILE cc_start: 0.9367 (mt) cc_final: 0.8960 (mt) REVERT: K 406 SER cc_start: 0.9287 (m) cc_final: 0.9049 (p) REVERT: K 438 MET cc_start: 0.8937 (mmt) cc_final: 0.8488 (mmt) REVERT: K 474 ARG cc_start: 0.3096 (mtt180) cc_final: 0.2608 (mtt180) REVERT: K 481 LEU cc_start: 0.8639 (tp) cc_final: 0.8295 (tp) REVERT: K 502 LYS cc_start: 0.9408 (mtpt) cc_final: 0.9098 (mtmm) REVERT: K 520 ASP cc_start: 0.8247 (m-30) cc_final: 0.7960 (m-30) REVERT: K 538 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9117 (tp) REVERT: K 587 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8836 (tppt) REVERT: K 588 MET cc_start: 0.9391 (mtm) cc_final: 0.8808 (mtp) REVERT: K 619 TYR cc_start: 0.8996 (p90) cc_final: 0.8557 (p90) REVERT: K 625 ILE cc_start: 0.9383 (mt) cc_final: 0.9073 (mm) REVERT: K 677 MET cc_start: 0.8984 (ttp) cc_final: 0.8662 (ttp) REVERT: K 727 ASP cc_start: 0.9453 (m-30) cc_final: 0.8860 (t0) REVERT: K 730 GLU cc_start: 0.9030 (tt0) cc_final: 0.8726 (tp30) REVERT: K 745 MET cc_start: 0.8976 (mpp) cc_final: 0.8605 (mpp) REVERT: M 5 LYS cc_start: 0.9560 (OUTLIER) cc_final: 0.9230 (ptmm) REVERT: M 16 MET cc_start: 0.8728 (mmt) cc_final: 0.8379 (mmp) REVERT: M 62 ILE cc_start: 0.9632 (OUTLIER) cc_final: 0.9366 (mm) REVERT: M 144 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8350 (mm110) REVERT: M 170 ASP cc_start: 0.9029 (t0) cc_final: 0.8717 (t0) REVERT: M 290 MET cc_start: 0.8928 (pmm) cc_final: 0.8691 (pmm) outliers start: 140 outliers final: 97 residues processed: 584 average time/residue: 0.1650 time to fit residues: 156.0900 Evaluate side-chains 571 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 459 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 88 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 126 VAL 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 82 MET Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 212 MET Chi-restraints excluded: chain J residue 239 LYS 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 157 TYR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 157 TYR Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain I residue 88 ASP 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 200 MET Chi-restraints excluded: chain I residue 202 ASN 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 111 GLU 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 304 SER Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 538 ILE Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 587 LYS Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 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 5 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 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 211 LEU Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 232 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 63 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 273 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 314 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 73 GLN ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 ASN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.050690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.042333 restraints weight = 146334.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.044053 restraints weight = 75562.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.045248 restraints weight = 47334.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.046080 restraints weight = 33208.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.046664 restraints weight = 25198.825| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29252 Z= 0.182 Angle : 0.694 12.465 39623 Z= 0.355 Chirality : 0.045 0.294 4524 Planarity : 0.004 0.059 4852 Dihedral : 13.460 178.621 4571 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.36 % Favored : 93.52 % Rotamer: Outliers : 4.05 % Allowed : 21.94 % Favored : 74.01 % 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 aren not related in a simple way. whole: -0.13 (0.14), residues: 3441 helix: 1.47 (0.14), residues: 1473 sheet: -0.28 (0.23), residues: 470 loop : -1.66 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 244 TYR 0.026 0.002 TYR K 62 PHE 0.033 0.001 PHE E 56 TRP 0.028 0.001 TRP G 182 HIS 0.007 0.001 HIS K 153 Details of bonding type rmsd covalent geometry : bond 0.00397 (29237) covalent geometry : angle 0.69263 (39593) SS BOND : bond 0.00343 ( 15) SS BOND : angle 1.93248 ( 30) hydrogen bonds : bond 0.03806 ( 1274) hydrogen bonds : angle 5.13537 ( 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 613 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 488 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASP cc_start: 0.8661 (m-30) cc_final: 0.8192 (t0) REVERT: A 42 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8038 (mm-30) REVERT: A 56 PHE cc_start: 0.8918 (t80) cc_final: 0.8534 (t80) REVERT: A 60 ARG cc_start: 0.9294 (mmp80) cc_final: 0.8909 (mmm-85) REVERT: A 79 ILE cc_start: 0.9026 (mm) cc_final: 0.8736 (mp) REVERT: A 110 TYR cc_start: 0.9047 (t80) cc_final: 0.8794 (t80) REVERT: A 111 ASP cc_start: 0.8969 (t0) cc_final: 0.8608 (t0) REVERT: A 131 GLU cc_start: 0.9397 (mt-10) cc_final: 0.8952 (mt-10) REVERT: B 22 ASP cc_start: 0.8876 (m-30) cc_final: 0.8234 (m-30) REVERT: B 26 ARG cc_start: 0.9128 (ptp-110) cc_final: 0.8474 (ptp90) REVERT: B 73 GLN cc_start: 0.9266 (tp40) cc_final: 0.8900 (tp-100) REVERT: B 78 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8345 (tp30) REVERT: B 90 SER cc_start: 0.9634 (m) cc_final: 0.9247 (p) REVERT: B 129 PHE cc_start: 0.9166 (t80) cc_final: 0.8919 (t80) REVERT: B 131 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8794 (mt-10) REVERT: B 134 ASN cc_start: 0.9185 (m-40) cc_final: 0.8814 (m110) REVERT: C 22 ASP cc_start: 0.9117 (m-30) cc_final: 0.8716 (m-30) REVERT: C 44 TYR cc_start: 0.9232 (t80) cc_final: 0.8607 (t80) REVERT: C 71 MET cc_start: 0.9393 (mtm) cc_final: 0.9089 (mtm) REVERT: C 77 ASP cc_start: 0.9271 (t0) cc_final: 0.9056 (t0) REVERT: C 103 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9380 (tp) REVERT: C 105 TYR cc_start: 0.9370 (m-80) cc_final: 0.9117 (m-80) REVERT: C 134 ASN cc_start: 0.9735 (m-40) cc_final: 0.9411 (m110) REVERT: D 29 ILE cc_start: 0.8984 (mm) cc_final: 0.8718 (tp) REVERT: D 32 ILE cc_start: 0.9197 (tp) cc_final: 0.8968 (tp) REVERT: D 44 TYR cc_start: 0.9084 (t80) cc_final: 0.8674 (t80) REVERT: D 58 GLN cc_start: 0.9485 (mp10) cc_final: 0.9207 (mm-40) REVERT: D 90 SER cc_start: 0.9493 (m) cc_final: 0.9289 (p) REVERT: D 101 ASN cc_start: 0.9562 (m110) cc_final: 0.9182 (m-40) REVERT: D 134 ASN cc_start: 0.9259 (m-40) cc_final: 0.8762 (m110) REVERT: E 44 TYR cc_start: 0.8968 (t80) cc_final: 0.8663 (t80) REVERT: E 48 SER cc_start: 0.9756 (m) cc_final: 0.9542 (p) REVERT: E 55 SER cc_start: 0.9799 (m) cc_final: 0.9537 (p) REVERT: E 78 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8196 (mt-10) REVERT: E 82 GLU cc_start: 0.9338 (tm-30) cc_final: 0.9035 (tm-30) REVERT: E 101 ASN cc_start: 0.9543 (m110) cc_final: 0.9071 (m110) REVERT: E 105 TYR cc_start: 0.9323 (m-10) cc_final: 0.8801 (m-80) REVERT: E 114 THR cc_start: 0.9497 (m) cc_final: 0.9241 (p) REVERT: E 131 GLU cc_start: 0.9010 (tp30) cc_final: 0.8658 (tm-30) REVERT: E 135 ILE cc_start: 0.9576 (mm) cc_final: 0.9304 (mm) REVERT: J 44 GLU cc_start: 0.8742 (pp20) cc_final: 0.7288 (pp20) REVERT: J 46 MET cc_start: 0.8426 (mtt) cc_final: 0.7952 (mmm) REVERT: J 57 GLU cc_start: 0.8402 (mp0) cc_final: 0.7944 (tm-30) REVERT: J 81 LEU cc_start: 0.9373 (mt) cc_final: 0.9147 (mp) REVERT: J 99 MET cc_start: 0.9494 (ttp) cc_final: 0.9229 (ppp) REVERT: J 146 PHE cc_start: 0.9214 (m-80) cc_final: 0.8885 (m-80) REVERT: J 172 MET cc_start: 0.8341 (tpp) cc_final: 0.8122 (tpp) REVERT: J 209 GLU cc_start: 0.9358 (mm-30) cc_final: 0.8543 (mp0) REVERT: J 229 MET cc_start: 0.8642 (mtp) cc_final: 0.8237 (mtp) REVERT: L 113 LYS cc_start: 0.9374 (tppp) cc_final: 0.9134 (tppt) REVERT: L 115 GLN cc_start: 0.9199 (mm110) cc_final: 0.8956 (tp40) REVERT: L 118 LYS cc_start: 0.9635 (tppp) cc_final: 0.9213 (tppp) REVERT: N 49 MET cc_start: 0.9582 (tmm) cc_final: 0.9282 (tmm) REVERT: N 137 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.7290 (p90) REVERT: N 155 MET cc_start: 0.8958 (pmm) cc_final: 0.8742 (pmm) REVERT: N 249 ARG cc_start: 0.9246 (ptm-80) cc_final: 0.8904 (ptm-80) REVERT: G 66 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8939 (mt-10) REVERT: F 33 GLN cc_start: 0.9390 (mp10) cc_final: 0.8939 (mp10) REVERT: F 73 ASN cc_start: 0.9555 (t0) cc_final: 0.9308 (t0) REVERT: F 82 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8538 (tp) REVERT: F 134 GLN cc_start: 0.9284 (tt0) cc_final: 0.9011 (tt0) REVERT: F 137 MET cc_start: 0.8604 (ptp) cc_final: 0.8277 (mpp) REVERT: F 207 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6897 (mtp85) REVERT: H 5 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8669 (m) REVERT: H 19 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8078 (tm-30) REVERT: H 129 MET cc_start: 0.9280 (tpt) cc_final: 0.9023 (tpp) REVERT: H 145 TYR cc_start: 0.8743 (p90) cc_final: 0.8184 (p90) REVERT: H 174 ASP cc_start: 0.8834 (t0) cc_final: 0.8375 (t70) REVERT: H 200 MET cc_start: 0.9376 (tpp) cc_final: 0.9140 (tpp) REVERT: I 110 GLN cc_start: 0.9609 (tp40) cc_final: 0.9309 (tp40) REVERT: I 118 TYR cc_start: 0.9171 (m-10) cc_final: 0.8751 (m-10) REVERT: I 200 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8262 (tmm) REVERT: I 202 ASN cc_start: 0.9256 (OUTLIER) cc_final: 0.8827 (t0) REVERT: I 265 MET cc_start: 0.9657 (mtm) cc_final: 0.9032 (mtm) REVERT: I 275 TYR cc_start: 0.9032 (p90) cc_final: 0.8346 (p90) REVERT: K 56 ASP cc_start: 0.9121 (m-30) cc_final: 0.8775 (m-30) REVERT: K 60 MET cc_start: 0.9153 (tmm) cc_final: 0.8711 (tmm) REVERT: K 61 ILE cc_start: 0.9030 (mt) cc_final: 0.8620 (mt) REVERT: K 148 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8915 (t) REVERT: K 202 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8330 (mt-10) REVERT: K 205 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8451 (mm-30) REVERT: K 220 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9167 (pp) REVERT: K 273 LYS cc_start: 0.9437 (tppt) cc_final: 0.8919 (mttm) REVERT: K 336 MET cc_start: 0.8904 (mmm) cc_final: 0.8547 (mmm) REVERT: K 369 ILE cc_start: 0.9280 (mt) cc_final: 0.8858 (mt) REVERT: K 385 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8744 (tp) REVERT: K 406 SER cc_start: 0.9286 (m) cc_final: 0.9053 (p) REVERT: K 438 MET cc_start: 0.8952 (mmt) cc_final: 0.8483 (mmt) REVERT: K 474 ARG cc_start: 0.3042 (mtt180) cc_final: 0.2542 (mtt180) REVERT: K 481 LEU cc_start: 0.8635 (tp) cc_final: 0.8317 (tp) REVERT: K 502 LYS cc_start: 0.9386 (mtpt) cc_final: 0.9068 (mtmm) REVERT: K 520 ASP cc_start: 0.8230 (m-30) cc_final: 0.7942 (m-30) REVERT: K 538 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9106 (tp) REVERT: K 587 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8843 (tppt) REVERT: K 588 MET cc_start: 0.9405 (mtm) cc_final: 0.8815 (mtp) REVERT: K 619 TYR cc_start: 0.8953 (p90) cc_final: 0.8537 (p90) REVERT: K 625 ILE cc_start: 0.9381 (mt) cc_final: 0.9036 (mm) REVERT: K 626 MET cc_start: 0.9512 (tpp) cc_final: 0.9016 (tpp) REVERT: K 677 MET cc_start: 0.8972 (ttp) cc_final: 0.8648 (ttp) REVERT: K 727 ASP cc_start: 0.9457 (m-30) cc_final: 0.8857 (t0) REVERT: K 730 GLU cc_start: 0.9041 (tt0) cc_final: 0.8712 (tp30) REVERT: K 745 MET cc_start: 0.9036 (mpp) cc_final: 0.8636 (mtm) REVERT: M 5 LYS cc_start: 0.9552 (OUTLIER) cc_final: 0.9253 (ptmm) REVERT: M 16 MET cc_start: 0.8722 (mmt) cc_final: 0.8375 (mmp) REVERT: M 62 ILE cc_start: 0.9653 (OUTLIER) cc_final: 0.9405 (mm) REVERT: M 144 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8337 (mm110) REVERT: M 170 ASP cc_start: 0.9020 (t0) cc_final: 0.8713 (t0) REVERT: M 290 MET cc_start: 0.8913 (pmm) cc_final: 0.8667 (pmm) outliers start: 125 outliers final: 93 residues processed: 578 average time/residue: 0.1660 time to fit residues: 155.6267 Evaluate side-chains 580 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 473 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 88 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 49 THR 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 82 MET Chi-restraints excluded: chain J residue 90 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 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 61 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 76 THR Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain N residue 103 ASN Chi-restraints excluded: chain N residue 137 TYR Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 190 ILE Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 157 TYR 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 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 H residue 241 ILE Chi-restraints excluded: chain I residue 88 ASP 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 200 MET Chi-restraints excluded: chain I residue 202 ASN 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 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 310 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 538 ILE Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 587 LYS Chi-restraints excluded: chain K residue 602 ASP Chi-restraints excluded: chain K residue 628 LEU Chi-restraints excluded: chain K residue 646 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 5 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 211 LEU Chi-restraints excluded: chain M residue 218 LEU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 240 ILE 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: 5.9990 chunk 175 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 319 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 298 optimal weight: 0.0000 chunk 8 optimal weight: 2.9990 chunk 118 optimal weight: 0.0770 chunk 143 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 overall best weight: 1.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 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** 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 = 0.051895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.043692 restraints weight = 143405.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.045418 restraints weight = 72477.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046592 restraints weight = 44984.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.047403 restraints weight = 31335.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.047998 restraints weight = 23723.237| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29252 Z= 0.149 Angle : 0.701 15.909 39623 Z= 0.354 Chirality : 0.045 0.306 4524 Planarity : 0.004 0.059 4852 Dihedral : 13.433 178.342 4571 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.10 % Favored : 93.78 % Rotamer: Outliers : 3.69 % Allowed : 22.82 % Favored : 73.50 % 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 aren not related in a simple way. whole: -0.07 (0.15), residues: 3441 helix: 1.49 (0.14), residues: 1473 sheet: -0.19 (0.23), residues: 472 loop : -1.62 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 244 TYR 0.024 0.001 TYR B 105 PHE 0.033 0.001 PHE K 245 TRP 0.026 0.001 TRP G 182 HIS 0.005 0.001 HIS K 153 Details of bonding type rmsd covalent geometry : bond 0.00334 (29237) covalent geometry : angle 0.69895 (39593) SS BOND : bond 0.00518 ( 15) SS BOND : angle 1.84796 ( 30) hydrogen bonds : bond 0.03703 ( 1274) hydrogen bonds : angle 5.04422 ( 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 624 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 510 time to evaluate : 0.907 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: 0.8669 (m-30) cc_final: 0.8203 (t0) REVERT: A 42 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8062 (mm-30) REVERT: A 56 PHE cc_start: 0.8955 (t80) cc_final: 0.8540 (t80) REVERT: A 58 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8988 (mm-40) REVERT: A 60 ARG cc_start: 0.9272 (mmp80) cc_final: 0.8914 (mmm-85) REVERT: A 71 MET cc_start: 0.9031 (mmm) cc_final: 0.8776 (mmt) REVERT: A 79 ILE cc_start: 0.9027 (mm) cc_final: 0.8723 (mp) REVERT: A 110 TYR cc_start: 0.9030 (t80) cc_final: 0.8782 (t80) REVERT: A 111 ASP cc_start: 0.8948 (t0) cc_final: 0.8591 (t0) REVERT: A 131 GLU cc_start: 0.9432 (mt-10) cc_final: 0.8994 (mt-10) REVERT: B 22 ASP cc_start: 0.8902 (m-30) cc_final: 0.8289 (m-30) REVERT: B 26 ARG cc_start: 0.9135 (ptp-110) cc_final: 0.8503 (ptp90) REVERT: B 73 GLN cc_start: 0.9172 (tp40) cc_final: 0.8910 (tp-100) REVERT: B 78 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8546 (tp30) REVERT: B 90 SER cc_start: 0.9621 (m) cc_final: 0.9233 (p) REVERT: B 103 LEU cc_start: 0.9762 (mm) cc_final: 0.9512 (tp) REVERT: B 129 PHE cc_start: 0.9130 (t80) cc_final: 0.8879 (t80) REVERT: B 131 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8798 (mt-10) REVERT: B 134 ASN cc_start: 0.9173 (m-40) cc_final: 0.8766 (m110) REVERT: C 22 ASP cc_start: 0.9134 (m-30) cc_final: 0.8744 (m-30) REVERT: C 44 TYR cc_start: 0.9177 (t80) cc_final: 0.8507 (t80) REVERT: C 71 MET cc_start: 0.9357 (mtm) cc_final: 0.9051 (mtm) REVERT: C 77 ASP cc_start: 0.9252 (t0) cc_final: 0.9025 (t0) REVERT: C 103 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9370 (tp) REVERT: C 105 TYR cc_start: 0.9348 (m-80) cc_final: 0.9077 (m-80) REVERT: C 134 ASN cc_start: 0.9730 (m-40) cc_final: 0.9417 (m110) REVERT: D 22 ASP cc_start: 0.8782 (m-30) cc_final: 0.8417 (t0) REVERT: D 29 ILE cc_start: 0.9050 (mm) cc_final: 0.8758 (tp) REVERT: D 32 ILE cc_start: 0.9187 (tp) cc_final: 0.8966 (tp) REVERT: D 44 TYR cc_start: 0.9112 (t80) cc_final: 0.8697 (t80) REVERT: D 58 GLN cc_start: 0.9466 (mp10) cc_final: 0.9262 (mm-40) REVERT: D 66 LEU cc_start: 0.9691 (tt) cc_final: 0.9330 (mm) REVERT: D 73 GLN cc_start: 0.9600 (mm110) cc_final: 0.9390 (mm-40) REVERT: D 95 GLU cc_start: 0.8662 (tp30) cc_final: 0.8111 (tm-30) REVERT: D 101 ASN cc_start: 0.9466 (m110) cc_final: 0.9168 (m-40) REVERT: D 134 ASN cc_start: 0.9249 (m-40) cc_final: 0.8727 (m110) REVERT: E 44 TYR cc_start: 0.8911 (t80) cc_final: 0.8593 (t80) REVERT: E 46 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8460 (t70) REVERT: E 48 SER cc_start: 0.9752 (m) cc_final: 0.9546 (p) REVERT: E 55 SER cc_start: 0.9786 (m) cc_final: 0.9511 (p) REVERT: E 78 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8215 (mt-10) REVERT: E 82 GLU cc_start: 0.9321 (tm-30) cc_final: 0.9016 (tm-30) REVERT: E 101 ASN cc_start: 0.9528 (m110) cc_final: 0.9043 (m110) REVERT: E 105 TYR cc_start: 0.9293 (m-10) cc_final: 0.8784 (m-80) REVERT: E 114 THR cc_start: 0.9452 (m) cc_final: 0.9200 (p) REVERT: E 131 GLU cc_start: 0.8982 (tp30) cc_final: 0.8603 (tm-30) REVERT: E 135 ILE cc_start: 0.9571 (mm) cc_final: 0.9303 (mm) REVERT: J 44 GLU cc_start: 0.8734 (pp20) cc_final: 0.7323 (pp20) REVERT: J 46 MET cc_start: 0.8353 (mtt) cc_final: 0.7916 (mmm) REVERT: J 81 LEU cc_start: 0.9345 (mt) cc_final: 0.9128 (mp) REVERT: J 99 MET cc_start: 0.9472 (ttp) cc_final: 0.9241 (ppp) REVERT: J 146 PHE cc_start: 0.9213 (m-80) cc_final: 0.8893 (m-80) REVERT: J 172 MET cc_start: 0.8380 (tpp) cc_final: 0.8136 (tpp) REVERT: J 209 GLU cc_start: 0.9363 (mm-30) cc_final: 0.8532 (mp0) REVERT: J 229 MET cc_start: 0.8646 (mtp) cc_final: 0.8156 (mtp) REVERT: L 62 GLU cc_start: 0.8700 (tp30) cc_final: 0.8386 (mp0) REVERT: L 98 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7642 (p) REVERT: L 104 TYR cc_start: 0.8625 (p90) cc_final: 0.8286 (p90) REVERT: L 113 LYS cc_start: 0.9378 (tppp) cc_final: 0.9144 (tppt) REVERT: L 115 GLN cc_start: 0.9173 (mm110) cc_final: 0.8936 (tp40) REVERT: L 168 MET cc_start: 0.8842 (pmm) cc_final: 0.8632 (pmm) REVERT: L 187 GLU cc_start: 0.9150 (pm20) cc_final: 0.8943 (pm20) REVERT: L 188 GLU cc_start: 0.8677 (pt0) cc_final: 0.8317 (pm20) REVERT: N 49 MET cc_start: 0.9578 (tmm) cc_final: 0.9271 (tmm) REVERT: N 137 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7265 (p90) REVERT: N 155 MET cc_start: 0.8991 (pmm) cc_final: 0.8764 (pmm) REVERT: N 249 ARG cc_start: 0.9234 (ptm-80) cc_final: 0.8918 (ptm-80) REVERT: G 66 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8929 (mt-10) REVERT: G 167 MET cc_start: 0.8647 (tpt) cc_final: 0.8409 (tpp) REVERT: G 188 GLU cc_start: 0.9370 (mm-30) cc_final: 0.8897 (mp0) REVERT: F 33 GLN cc_start: 0.9370 (mp10) cc_final: 0.8925 (mp10) REVERT: F 73 ASN cc_start: 0.9529 (t0) cc_final: 0.9281 (t0) REVERT: F 82 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8560 (tp) REVERT: F 134 GLN cc_start: 0.9305 (tt0) cc_final: 0.9004 (tt0) REVERT: F 137 MET cc_start: 0.8525 (ptp) cc_final: 0.8231 (mpp) REVERT: F 207 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.6799 (mtp85) REVERT: F 225 TYR cc_start: 0.8877 (m-10) cc_final: 0.8416 (m-10) REVERT: H 5 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8641 (m) REVERT: H 19 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8067 (tm-30) REVERT: H 129 MET cc_start: 0.9257 (tpt) cc_final: 0.9017 (tpp) REVERT: H 145 TYR cc_start: 0.8743 (p90) cc_final: 0.7989 (p90) REVERT: H 174 ASP cc_start: 0.8796 (t0) cc_final: 0.8327 (t70) REVERT: H 200 MET cc_start: 0.9371 (tpp) cc_final: 0.9124 (tpp) REVERT: I 110 GLN cc_start: 0.9599 (tp40) cc_final: 0.9284 (tp40) REVERT: I 118 TYR cc_start: 0.9128 (m-10) cc_final: 0.8681 (m-10) REVERT: I 200 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8392 (tmm) REVERT: I 202 ASN cc_start: 0.9229 (OUTLIER) cc_final: 0.8809 (t0) REVERT: I 265 MET cc_start: 0.9642 (mtm) cc_final: 0.8994 (mtm) REVERT: I 275 TYR cc_start: 0.8992 (p90) cc_final: 0.8328 (p90) REVERT: K 56 ASP cc_start: 0.9098 (m-30) cc_final: 0.8739 (m-30) REVERT: K 60 MET cc_start: 0.9071 (tmm) cc_final: 0.8670 (tmm) REVERT: K 61 ILE cc_start: 0.8949 (mt) cc_final: 0.8430 (mt) REVERT: K 153 HIS cc_start: 0.8905 (OUTLIER) cc_final: 0.8689 (t70) REVERT: K 202 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8332 (mt-10) REVERT: K 205 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8371 (mm-30) REVERT: K 220 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9156 (pp) REVERT: K 273 LYS cc_start: 0.9418 (tppt) cc_final: 0.8927 (mttm) REVERT: K 336 MET cc_start: 0.8919 (mmm) cc_final: 0.8590 (mmm) REVERT: K 369 ILE cc_start: 0.9303 (mt) cc_final: 0.8889 (mt) REVERT: K 385 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8775 (tp) REVERT: K 406 SER cc_start: 0.9282 (m) cc_final: 0.9056 (p) REVERT: K 438 MET cc_start: 0.8954 (mmt) cc_final: 0.8472 (mmt) REVERT: K 474 ARG cc_start: 0.3084 (mtt180) cc_final: 0.2576 (mtt180) REVERT: K 481 LEU cc_start: 0.8606 (tp) cc_final: 0.8279 (tp) REVERT: K 502 LYS cc_start: 0.9371 (mtpt) cc_final: 0.9049 (mtmm) REVERT: K 520 ASP cc_start: 0.8252 (m-30) cc_final: 0.7985 (m-30) REVERT: K 538 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9083 (tp) REVERT: K 587 LYS cc_start: 0.9273 (mmtm) cc_final: 0.8829 (tppt) REVERT: K 588 MET cc_start: 0.9411 (mtm) cc_final: 0.8829 (mtp) REVERT: K 619 TYR cc_start: 0.8894 (p90) cc_final: 0.8548 (p90) REVERT: K 625 ILE cc_start: 0.9401 (mt) cc_final: 0.9082 (mm) REVERT: K 626 MET cc_start: 0.9469 (tpp) cc_final: 0.8936 (tpp) REVERT: K 677 MET cc_start: 0.8955 (ttp) cc_final: 0.8607 (ttp) REVERT: K 727 ASP cc_start: 0.9463 (m-30) cc_final: 0.8847 (t0) REVERT: K 730 GLU cc_start: 0.9044 (tt0) cc_final: 0.8706 (tp30) REVERT: K 745 MET cc_start: 0.9081 (mpp) cc_final: 0.8651 (mtm) REVERT: M 5 LYS cc_start: 0.9549 (OUTLIER) cc_final: 0.9247 (ptmm) REVERT: M 16 MET cc_start: 0.8752 (mmt) cc_final: 0.8349 (mmp) REVERT: M 62 ILE cc_start: 0.9653 (OUTLIER) cc_final: 0.9409 (mm) REVERT: M 170 ASP cc_start: 0.8965 (t0) cc_final: 0.8637 (t0) outliers start: 114 outliers final: 86 residues processed: 593 average time/residue: 0.1674 time to fit residues: 161.4773 Evaluate side-chains 591 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 490 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 49 THR 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 126 VAL 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 120 THR Chi-restraints excluded: chain J residue 208 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 61 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 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 32 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 157 TYR 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 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 210 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain I residue 88 ASP 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 200 MET Chi-restraints excluded: chain I residue 202 ASN 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 153 HIS Chi-restraints excluded: chain K residue 173 TYR 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 244 ARG Chi-restraints excluded: chain K residue 304 SER Chi-restraints excluded: chain K residue 310 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 538 ILE Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 628 LEU Chi-restraints excluded: chain K residue 646 LEU Chi-restraints excluded: chain K residue 661 LYS Chi-restraints excluded: chain K residue 666 VAL Chi-restraints excluded: chain M residue 5 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 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 232 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 259 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 281 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 340 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.049976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.041791 restraints weight = 146003.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.043493 restraints weight = 74065.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.044680 restraints weight = 46134.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.045498 restraints weight = 32166.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.046086 restraints weight = 24278.253| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29252 Z= 0.228 Angle : 0.733 14.933 39623 Z= 0.375 Chirality : 0.045 0.319 4524 Planarity : 0.004 0.059 4852 Dihedral : 13.515 179.354 4571 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.57 % Favored : 93.29 % Rotamer: Outliers : 3.46 % Allowed : 23.56 % 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 aren not related in a simple way. whole: -0.20 (0.14), residues: 3441 helix: 1.36 (0.14), residues: 1473 sheet: -0.25 (0.23), residues: 473 loop : -1.66 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 98 TYR 0.029 0.002 TYR I 145 PHE 0.032 0.002 PHE E 56 TRP 0.021 0.002 TRP G 182 HIS 0.005 0.001 HIS G 230 Details of bonding type rmsd covalent geometry : bond 0.00490 (29237) covalent geometry : angle 0.73158 (39593) SS BOND : bond 0.00410 ( 15) SS BOND : angle 1.94972 ( 30) hydrogen bonds : bond 0.03832 ( 1274) hydrogen bonds : angle 5.17958 ( 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 595 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 488 time to evaluate : 1.004 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: 0.8657 (m-30) cc_final: 0.8172 (t0) REVERT: A 42 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 56 PHE cc_start: 0.8998 (t80) cc_final: 0.8571 (t80) REVERT: A 60 ARG cc_start: 0.9285 (mmp80) cc_final: 0.8955 (mmm-85) REVERT: A 71 MET cc_start: 0.9067 (mmm) cc_final: 0.8829 (mmt) REVERT: A 79 ILE cc_start: 0.9046 (mm) cc_final: 0.8743 (mp) REVERT: A 110 TYR cc_start: 0.9056 (t80) cc_final: 0.8819 (t80) REVERT: A 111 ASP cc_start: 0.8965 (t0) cc_final: 0.8584 (t0) REVERT: A 131 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9012 (mt-10) REVERT: B 22 ASP cc_start: 0.8853 (m-30) cc_final: 0.8166 (m-30) REVERT: B 26 ARG cc_start: 0.9123 (ptp-110) cc_final: 0.8428 (ptp90) REVERT: B 73 GLN cc_start: 0.9154 (tp40) cc_final: 0.8891 (tp-100) REVERT: B 78 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8283 (tp30) REVERT: B 90 SER cc_start: 0.9641 (m) cc_final: 0.9258 (p) REVERT: B 129 PHE cc_start: 0.9110 (t80) cc_final: 0.8872 (t80) REVERT: B 131 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8653 (mt-10) REVERT: B 134 ASN cc_start: 0.9155 (m-40) cc_final: 0.8778 (m110) REVERT: C 22 ASP cc_start: 0.9170 (m-30) cc_final: 0.8770 (m-30) REVERT: C 44 TYR cc_start: 0.9202 (t80) cc_final: 0.8575 (t80) REVERT: C 45 VAL cc_start: 0.9601 (OUTLIER) cc_final: 0.9285 (p) REVERT: C 71 MET cc_start: 0.9382 (mtm) cc_final: 0.9099 (mtm) REVERT: C 77 ASP cc_start: 0.9277 (t0) cc_final: 0.9060 (t0) REVERT: C 103 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9401 (tp) REVERT: C 105 TYR cc_start: 0.9347 (m-80) cc_final: 0.9073 (m-80) REVERT: C 134 ASN cc_start: 0.9743 (m-40) cc_final: 0.9419 (m110) REVERT: D 29 ILE cc_start: 0.9115 (mm) cc_final: 0.8823 (tp) REVERT: D 32 ILE cc_start: 0.9181 (tp) cc_final: 0.8959 (tp) REVERT: D 44 TYR cc_start: 0.9151 (t80) cc_final: 0.8793 (t80) REVERT: D 58 GLN cc_start: 0.9484 (mp10) cc_final: 0.9221 (mm-40) REVERT: D 95 GLU cc_start: 0.8660 (tp30) cc_final: 0.7994 (tm-30) REVERT: D 98 ASP cc_start: 0.9528 (m-30) cc_final: 0.8830 (m-30) REVERT: D 101 ASN cc_start: 0.9378 (m110) cc_final: 0.9025 (m-40) REVERT: E 44 TYR cc_start: 0.8953 (t80) cc_final: 0.8623 (t80) REVERT: E 48 SER cc_start: 0.9754 (m) cc_final: 0.9520 (p) REVERT: E 55 SER cc_start: 0.9798 (m) cc_final: 0.9528 (p) REVERT: E 82 GLU cc_start: 0.9318 (tm-30) cc_final: 0.9031 (tm-30) REVERT: E 101 ASN cc_start: 0.9537 (m110) cc_final: 0.9062 (m110) REVERT: E 105 TYR cc_start: 0.9321 (m-10) cc_final: 0.8810 (m-80) REVERT: E 114 THR cc_start: 0.9479 (m) cc_final: 0.9229 (p) REVERT: E 131 GLU cc_start: 0.9009 (tp30) cc_final: 0.8664 (tm-30) REVERT: E 135 ILE cc_start: 0.9576 (mm) cc_final: 0.9259 (mm) REVERT: J 44 GLU cc_start: 0.8769 (pp20) cc_final: 0.7352 (pp20) REVERT: J 46 MET cc_start: 0.8448 (mtt) cc_final: 0.7947 (mmm) REVERT: J 81 LEU cc_start: 0.9360 (mt) cc_final: 0.9120 (mp) REVERT: J 99 MET cc_start: 0.9483 (ttp) cc_final: 0.9228 (ppp) REVERT: J 146 PHE cc_start: 0.9177 (m-80) cc_final: 0.8880 (m-80) REVERT: J 166 SER cc_start: 0.8973 (m) cc_final: 0.8560 (t) REVERT: J 209 GLU cc_start: 0.9378 (mm-30) cc_final: 0.8581 (mp0) REVERT: J 229 MET cc_start: 0.8592 (mtp) cc_final: 0.8152 (mtp) REVERT: L 32 LEU cc_start: 0.8799 (tp) cc_final: 0.8532 (tp) REVERT: L 98 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7707 (p) REVERT: L 115 GLN cc_start: 0.9242 (mm110) cc_final: 0.8978 (tp40) REVERT: L 118 LYS cc_start: 0.9608 (ttmm) cc_final: 0.9196 (ttmm) REVERT: L 168 MET cc_start: 0.8872 (pmm) cc_final: 0.8621 (pmm) REVERT: L 187 GLU cc_start: 0.9166 (pm20) cc_final: 0.8950 (pm20) REVERT: L 188 GLU cc_start: 0.8680 (pt0) cc_final: 0.8276 (pm20) REVERT: N 49 MET cc_start: 0.9583 (tmm) cc_final: 0.9269 (tmm) REVERT: N 137 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7289 (p90) REVERT: N 155 MET cc_start: 0.8991 (pmm) cc_final: 0.8761 (pmm) REVERT: N 249 ARG cc_start: 0.9268 (ptm-80) cc_final: 0.8961 (ptm-80) REVERT: G 167 MET cc_start: 0.8639 (tpt) cc_final: 0.8401 (tpp) REVERT: F 33 GLN cc_start: 0.9383 (mp10) cc_final: 0.8934 (mp10) REVERT: F 73 ASN cc_start: 0.9568 (t0) cc_final: 0.9324 (t0) REVERT: F 134 GLN cc_start: 0.9326 (tt0) cc_final: 0.9084 (tt0) REVERT: F 137 MET cc_start: 0.8631 (ptp) cc_final: 0.8295 (mpp) REVERT: F 207 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6948 (mtp85) REVERT: H 5 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8731 (m) REVERT: H 19 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8078 (tm-30) REVERT: H 145 TYR cc_start: 0.8768 (p90) cc_final: 0.8196 (p90) REVERT: H 174 ASP cc_start: 0.8809 (t0) cc_final: 0.8353 (t70) REVERT: H 200 MET cc_start: 0.9369 (tpp) cc_final: 0.9105 (tpp) REVERT: I 110 GLN cc_start: 0.9608 (tp40) cc_final: 0.9307 (tp40) REVERT: I 118 TYR cc_start: 0.9164 (m-10) cc_final: 0.8669 (m-10) REVERT: I 152 MET cc_start: 0.8569 (mmm) cc_final: 0.8338 (tpp) REVERT: I 200 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8283 (tmm) REVERT: I 202 ASN cc_start: 0.9262 (OUTLIER) cc_final: 0.8798 (t0) REVERT: I 265 MET cc_start: 0.9654 (mtm) cc_final: 0.8997 (mtm) REVERT: I 275 TYR cc_start: 0.9073 (p90) cc_final: 0.8368 (p90) REVERT: K 56 ASP cc_start: 0.9098 (m-30) cc_final: 0.8743 (m-30) REVERT: K 60 MET cc_start: 0.9104 (tmm) cc_final: 0.8673 (tmm) REVERT: K 61 ILE cc_start: 0.9010 (mt) cc_final: 0.8526 (mt) REVERT: K 81 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8529 (mt-10) REVERT: K 148 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8924 (t) REVERT: K 202 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8382 (mt-10) REVERT: K 205 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8454 (mm-30) REVERT: K 220 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9158 (pp) REVERT: K 273 LYS cc_start: 0.9423 (tppt) cc_final: 0.8916 (mttm) REVERT: K 336 MET cc_start: 0.8894 (mmm) cc_final: 0.8572 (mmm) REVERT: K 369 ILE cc_start: 0.9365 (mt) cc_final: 0.8941 (mt) REVERT: K 406 SER cc_start: 0.9328 (m) cc_final: 0.9102 (p) REVERT: K 438 MET cc_start: 0.8946 (mmt) cc_final: 0.8564 (mmt) REVERT: K 474 ARG cc_start: 0.3373 (mtt180) cc_final: 0.2851 (mtt180) REVERT: K 481 LEU cc_start: 0.8621 (tp) cc_final: 0.8259 (tp) REVERT: K 502 LYS cc_start: 0.9410 (mtpt) cc_final: 0.9097 (mtmm) REVERT: K 520 ASP cc_start: 0.8257 (m-30) cc_final: 0.7964 (m-30) REVERT: K 538 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9070 (tp) REVERT: K 587 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8838 (tppt) REVERT: K 588 MET cc_start: 0.9409 (mtm) cc_final: 0.8831 (mtp) REVERT: K 619 TYR cc_start: 0.8939 (p90) cc_final: 0.8585 (p90) REVERT: K 625 ILE cc_start: 0.9395 (mt) cc_final: 0.9079 (mm) REVERT: K 626 MET cc_start: 0.9496 (tpp) cc_final: 0.8946 (tpp) REVERT: K 677 MET cc_start: 0.9009 (ttp) cc_final: 0.8679 (ttp) REVERT: K 727 ASP cc_start: 0.9439 (m-30) cc_final: 0.8899 (t0) REVERT: K 730 GLU cc_start: 0.9041 (tt0) cc_final: 0.8729 (tp30) REVERT: K 745 MET cc_start: 0.9000 (mpp) cc_final: 0.8536 (mtm) REVERT: M 5 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9234 (ptmm) REVERT: M 16 MET cc_start: 0.8747 (mmt) cc_final: 0.8374 (mmp) REVERT: M 62 ILE cc_start: 0.9661 (OUTLIER) cc_final: 0.9420 (mm) REVERT: M 144 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8319 (mm110) REVERT: M 170 ASP cc_start: 0.9008 (t0) cc_final: 0.8699 (t0) outliers start: 107 outliers final: 89 residues processed: 567 average time/residue: 0.1641 time to fit residues: 151.4895 Evaluate side-chains 579 residues out of total 3097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 476 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain B residue 21 LEU 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 45 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 126 VAL 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 126 VAL 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 90 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 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 61 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 40 MET 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 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 90 CYS Chi-restraints excluded: chain H residue 123 CYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 88 ASP 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 200 MET Chi-restraints excluded: chain I residue 202 ASN 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 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 310 ASN Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 378 TYR Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 460 HIS Chi-restraints excluded: chain K residue 532 THR Chi-restraints excluded: chain K residue 538 ILE Chi-restraints excluded: chain K residue 576 ASP Chi-restraints excluded: chain K residue 587 LYS Chi-restraints excluded: chain K residue 624 ASP Chi-restraints excluded: chain K residue 628 LEU Chi-restraints excluded: chain K residue 646 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 5 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 211 LEU Chi-restraints excluded: chain M residue 220 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 240 optimal weight: 0.9990 chunk 308 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 339 optimal weight: 4.9990 chunk 336 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 210 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN L 174 ASN ** L 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** K 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.051382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.042987 restraints weight = 144948.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.044712 restraints weight = 74934.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.045920 restraints weight = 46992.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.046755 restraints weight = 32980.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.047352 restraints weight = 25086.083| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29252 Z= 0.152 Angle : 0.725 16.244 39623 Z= 0.365 Chirality : 0.045 0.339 4524 Planarity : 0.004 0.059 4852 Dihedral : 13.463 177.823 4571 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.34 % Favored : 93.52 % Rotamer: Outliers : 3.24 % Allowed : 23.98 % Favored : 72.78 % 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 aren not related in a simple way. whole: -0.12 (0.14), residues: 3441 helix: 1.40 (0.14), residues: 1473 sheet: -0.15 (0.24), residues: 463 loop : -1.60 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 98 TYR 0.028 0.002 TYR K 62 PHE 0.028 0.001 PHE E 129 TRP 0.022 0.001 TRP G 182 HIS 0.006 0.001 HIS K 224 Details of bonding type rmsd covalent geometry : bond 0.00341 (29237) covalent geometry : angle 0.72337 (39593) SS BOND : bond 0.00320 ( 15) SS BOND : angle 1.80018 ( 30) hydrogen bonds : bond 0.03703 ( 1274) hydrogen bonds : angle 5.04785 ( 3747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5087.76 seconds wall clock time: 89 minutes 15.02 seconds (5355.02 seconds total)