Starting phenix.real_space_refine on Fri Dec 27 23:27:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dfs_27412/12_2024/8dfs_27412.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfs_27412/12_2024/8dfs_27412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dfs_27412/12_2024/8dfs_27412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfs_27412/12_2024/8dfs_27412.map" model { file = "/net/cci-nas-00/data/ceres_data/8dfs_27412/12_2024/8dfs_27412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfs_27412/12_2024/8dfs_27412.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.043 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 S 139 5.16 5 C 15689 2.51 5 N 4508 2.21 5 O 4856 1.98 5 H 24538 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 49778 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3537 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "B" Number of atoms: 4193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 4193 Classifications: {'peptide': 270} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 2 Chain: "C" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "D" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "E" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "F" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "G" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "H" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4462 Classifications: {'peptide': 286} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "I" Number of atoms: 8728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 8728 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 31, 'TRANS': 523} Chain breaks: 5 Chain: "J" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1863 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "K" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1863 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain breaks: 1 Chain: "L" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1548 Classifications: {'RNA': 48} Modifications used: {'3*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 17, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 27} Chain: "M" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1274 Classifications: {'peptide': 87} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'TRANS': 86} Time building chain proxies: 18.74, per 1000 atoms: 0.38 Number of scatterers: 49778 At special positions: 0 Unit cell: (126.9, 119.38, 226.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 139 16.00 P 48 15.00 O 4856 8.00 N 4508 7.00 C 15689 6.00 H 24538 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.23 Conformation dependent library (CDL) restraints added in 3.4 seconds 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5774 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 37 sheets defined 38.5% alpha, 24.5% beta 0 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 19.96 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.746A pdb=" N LYS A 28 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 removed outlier: 3.602A pdb=" N ILE A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.717A pdb=" N MET A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'B' and resid 43 through 60 removed outlier: 3.749A pdb=" N LEU B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 113 through 119 Processing helix chain 'B' and resid 193 through 199 removed outlier: 3.597A pdb=" N LYS B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 221 removed outlier: 4.007A pdb=" N HIS B 220 " --> pdb=" O MET B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 254 removed outlier: 3.798A pdb=" N LEU B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'C' and resid 43 through 60 removed outlier: 3.543A pdb=" N LEU C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 Processing helix chain 'C' and resid 98 through 113 Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.585A pdb=" N LYS C 199 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'D' and resid 43 through 60 removed outlier: 3.599A pdb=" N LEU D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 86 removed outlier: 3.529A pdb=" N THR D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 113 removed outlier: 3.684A pdb=" N THR D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'E' and resid 43 through 60 removed outlier: 3.524A pdb=" N LEU E 47 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 87 Processing helix chain 'E' and resid 98 through 113 removed outlier: 3.749A pdb=" N MET E 109 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 120 Processing helix chain 'E' and resid 193 through 201 Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 217 through 221 removed outlier: 4.317A pdb=" N HIS E 220 " --> pdb=" O MET E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 253 Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'F' and resid 43 through 60 removed outlier: 3.573A pdb=" N LEU F 47 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 98 through 113 removed outlier: 3.683A pdb=" N ASN F 112 " --> pdb=" O TRP F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 120 Processing helix chain 'F' and resid 193 through 201 removed outlier: 3.503A pdb=" N LYS F 199 " --> pdb=" O PRO F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 Processing helix chain 'F' and resid 247 through 254 removed outlier: 3.567A pdb=" N LEU F 254 " --> pdb=" O LYS F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'G' and resid 24 through 28 removed outlier: 3.661A pdb=" N GLY G 28 " --> pdb=" O PRO G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 60 removed outlier: 3.593A pdb=" N LEU G 47 " --> pdb=" O THR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 86 Processing helix chain 'G' and resid 98 through 113 Processing helix chain 'G' and resid 113 through 120 Processing helix chain 'G' and resid 193 through 201 removed outlier: 3.545A pdb=" N LYS G 199 " --> pdb=" O PRO G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 216 Processing helix chain 'G' and resid 217 through 221 removed outlier: 4.032A pdb=" N HIS G 220 " --> pdb=" O MET G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 253 Processing helix chain 'G' and resid 269 through 271 No H-bonds generated for 'chain 'G' and resid 269 through 271' Processing helix chain 'H' and resid 24 through 28 removed outlier: 4.040A pdb=" N GLY H 28 " --> pdb=" O PRO H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 59 removed outlier: 3.568A pdb=" N LEU H 47 " --> pdb=" O THR H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 98 through 113 Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'H' and resid 193 through 201 removed outlier: 3.534A pdb=" N LYS H 199 " --> pdb=" O PRO H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 Processing helix chain 'H' and resid 247 through 254 Processing helix chain 'H' and resid 269 through 271 No H-bonds generated for 'chain 'H' and resid 269 through 271' Processing helix chain 'I' and resid 4 through 15 removed outlier: 3.737A pdb=" N ALA I 15 " --> pdb=" O GLN I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 20 removed outlier: 4.071A pdb=" N GLY I 20 " --> pdb=" O PRO I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 110 removed outlier: 3.686A pdb=" N LYS I 110 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 130 Processing helix chain 'I' and resid 140 through 144 removed outlier: 3.625A pdb=" N VAL I 143 " --> pdb=" O SER I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 161 Processing helix chain 'I' and resid 162 through 176 Processing helix chain 'I' and resid 222 through 226 Processing helix chain 'I' and resid 231 through 236 Processing helix chain 'I' and resid 239 through 255 Processing helix chain 'I' and resid 278 through 287 removed outlier: 3.788A pdb=" N ILE I 282 " --> pdb=" O PRO I 278 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA I 284 " --> pdb=" O GLU I 280 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLY I 285 " --> pdb=" O ASP I 281 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE I 287 " --> pdb=" O PHE I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 336 Processing helix chain 'I' and resid 338 through 343 removed outlier: 4.150A pdb=" N ILE I 342 " --> pdb=" O ARG I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 389 Processing helix chain 'I' and resid 402 through 409 Processing helix chain 'I' and resid 420 through 426 Processing helix chain 'I' and resid 429 through 434 Processing helix chain 'I' and resid 440 through 452 Processing helix chain 'I' and resid 455 through 459 Processing helix chain 'I' and resid 468 through 483 Processing helix chain 'I' and resid 497 through 517 Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.088A pdb=" N ARG I 527 " --> pdb=" O THR I 523 " (cutoff:3.500A) Processing helix chain 'I' and resid 528 through 535 Processing helix chain 'I' and resid 535 through 557 removed outlier: 3.776A pdb=" N VAL I 539 " --> pdb=" O ASN I 535 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N HIS I 541 " --> pdb=" O GLY I 537 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N MET I 542 " --> pdb=" O GLN I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 565 through 576 Processing helix chain 'I' and resid 586 through 603 Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 35 through 40 Processing helix chain 'J' and resid 40 through 47 Processing helix chain 'J' and resid 47 through 68 removed outlier: 3.697A pdb=" N VAL J 51 " --> pdb=" O ASN J 47 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS J 53 " --> pdb=" O GLY J 49 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N MET J 54 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 73 No H-bonds generated for 'chain 'J' and resid 73 through 73' Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.804A pdb=" N ASN J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 117 Processing helix chain 'K' and resid 9 through 29 Processing helix chain 'K' and resid 35 through 47 removed outlier: 5.801A pdb=" N ALA K 42 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N SER K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 69 removed outlier: 3.606A pdb=" N VAL K 51 " --> pdb=" O ASN K 47 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N HIS K 53 " --> pdb=" O GLY K 49 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N MET K 54 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP K 69 " --> pdb=" O LYS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 73 No H-bonds generated for 'chain 'K' and resid 73 through 73' Processing helix chain 'K' and resid 77 through 90 removed outlier: 3.667A pdb=" N ASN K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 118 Processing helix chain 'M' and resid 2 through 7 Processing helix chain 'M' and resid 10 through 20 removed outlier: 3.608A pdb=" N GLU M 14 " --> pdb=" O VAL M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 68 removed outlier: 3.506A pdb=" N ILE M 61 " --> pdb=" O ASP M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 76 Processing helix chain 'M' and resid 76 through 85 removed outlier: 3.718A pdb=" N GLU M 85 " --> pdb=" O GLU M 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 78 removed outlier: 6.226A pdb=" N ARG A 116 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR A 19 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 78 removed outlier: 7.618A pdb=" N ASP A 119 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL A 64 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL A 121 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE A 62 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU A 123 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 100 removed outlier: 5.251A pdb=" N PHE A 99 " --> pdb=" O GLN B 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 196 removed outlier: 5.733A pdb=" N ALA A 208 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR A 190 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE A 206 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU A 192 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU A 204 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASP A 194 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR A 202 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 42 removed outlier: 5.296A pdb=" N GLY B 40 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU B 185 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR B 183 " --> pdb=" O PRO B 146 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 174 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 136 through 138 removed outlier: 6.651A pdb=" N GLU B 9 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL B 236 " --> pdb=" O GLU B 9 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B 11 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU B 234 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 13 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 228 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU B 234 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 255 through 259 Processing sheet with id=AA8, first strand: chain 'C' and resid 41 through 42 removed outlier: 4.918A pdb=" N HIS C 189 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA C 141 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N VAL C 187 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLU C 17 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TYR C 183 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 19 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 41 through 42 removed outlier: 4.918A pdb=" N HIS C 189 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA C 141 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N VAL C 187 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP C 15 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N SER C 231 " --> pdb=" O ASP C 15 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLU C 17 " --> pdb=" O MET C 229 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N MET C 229 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 236 " --> pdb=" O LYS C 287 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 121 through 122 Processing sheet with id=AB2, first strand: chain 'C' and resid 255 through 259 Processing sheet with id=AB3, first strand: chain 'D' and resid 41 through 42 removed outlier: 3.606A pdb=" N ILE D 154 " --> pdb=" O GLY D 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 136 through 138 removed outlier: 6.732A pdb=" N TYR D 183 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLU D 17 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU D 185 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP D 15 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL D 187 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU D 13 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N HIS D 189 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL D 11 " --> pdb=" O HIS D 189 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE D 191 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU D 9 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP D 15 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N SER D 231 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLU D 17 " --> pdb=" O MET D 229 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N MET D 229 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AB6, first strand: chain 'D' and resid 255 through 258 Processing sheet with id=AB7, first strand: chain 'E' and resid 41 through 42 Processing sheet with id=AB8, first strand: chain 'E' and resid 136 through 138 removed outlier: 6.871A pdb=" N ASP E 15 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N SER E 231 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLU E 17 " --> pdb=" O MET E 229 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N MET E 229 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU E 234 " --> pdb=" O MET E 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 121 through 122 Processing sheet with id=AC1, first strand: chain 'E' and resid 255 through 259 Processing sheet with id=AC2, first strand: chain 'F' and resid 41 through 42 Processing sheet with id=AC3, first strand: chain 'F' and resid 136 through 138 removed outlier: 6.729A pdb=" N ASP F 15 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N SER F 231 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLU F 17 " --> pdb=" O MET F 229 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N MET F 229 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU F 234 " --> pdb=" O MET F 289 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 121 through 123 removed outlier: 3.589A pdb=" N GLY F 130 " --> pdb=" O MET F 123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 255 through 259 Processing sheet with id=AC6, first strand: chain 'G' and resid 41 through 42 removed outlier: 6.855A pdb=" N GLU G 17 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR G 183 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY G 19 " --> pdb=" O VAL G 181 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 136 through 138 removed outlier: 6.469A pdb=" N ASP G 15 " --> pdb=" O SER G 231 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N SER G 231 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLU G 17 " --> pdb=" O MET G 229 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N MET G 229 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 121 through 124 removed outlier: 6.630A pdb=" N ALA G 121 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLN G 131 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N MET G 123 " --> pdb=" O CYS G 129 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 158 through 159 removed outlier: 3.560A pdb=" N VAL G 159 " --> pdb=" O ALA H 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 255 through 259 Processing sheet with id=AD2, first strand: chain 'H' and resid 39 through 42 removed outlier: 5.156A pdb=" N GLY H 40 " --> pdb=" O SER H 143 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU H 185 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N TYR H 183 " --> pdb=" O PRO H 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 136 through 138 removed outlier: 6.427A pdb=" N TYR H 183 " --> pdb=" O GLU H 17 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU H 17 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU H 185 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASP H 15 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL H 187 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU H 13 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N HIS H 189 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL H 11 " --> pdb=" O HIS H 189 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE H 191 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU H 9 " --> pdb=" O PHE H 191 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP H 15 " --> pdb=" O SER H 231 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N SER H 231 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLU H 17 " --> pdb=" O MET H 229 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N MET H 229 " --> pdb=" O GLU H 17 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU H 234 " --> pdb=" O MET H 289 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 255 through 259 Processing sheet with id=AD5, first strand: chain 'I' and resid 26 through 31 Processing sheet with id=AD6, first strand: chain 'I' and resid 43 through 47 Processing sheet with id=AD7, first strand: chain 'I' and resid 51 through 52 Processing sheet with id=AD8, first strand: chain 'I' and resid 201 through 202 Processing sheet with id=AD9, first strand: chain 'I' and resid 261 through 264 removed outlier: 6.751A pdb=" N VAL I 354 " --> pdb=" O TRP I 369 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP I 369 " --> pdb=" O VAL I 354 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY I 356 " --> pdb=" O ARG I 367 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 21 through 27 removed outlier: 4.526A pdb=" N ALA M 22 " --> pdb=" O THR M 36 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR M 36 " --> pdb=" O ALA M 22 " (cutoff:3.500A) 1084 hydrogen bonds defined for protein. 3069 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 17.48 Time building geometry restraints manager: 12.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.27: 28709 1.27 - 1.70: 21435 1.70 - 2.13: 242 2.13 - 2.56: 0 2.56 - 2.99: 1 Bond restraints: 50387 Sorted by residual: bond pdb=" C LYS J 73 " pdb=" N ALA J 76 " ideal model delta sigma weight residual 1.332 2.993 -1.660 1.40e-02 5.10e+03 1.41e+04 bond pdb=" N ARG I 176 " pdb=" H ARG I 176 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" N ILE M 2 " pdb=" H ILE M 2 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.71e+01 bond pdb=" N ARG I 429 " pdb=" H ARG I 429 " ideal model delta sigma weight residual 0.860 1.034 -0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" N LEU I 427 " pdb=" H LEU I 427 " ideal model delta sigma weight residual 0.860 1.034 -0.174 2.00e-02 2.50e+03 7.58e+01 ... (remaining 50382 not shown) Histogram of bond angle deviations from ideal: 0.00 - 20.06: 91014 20.06 - 40.12: 2 40.12 - 60.19: 0 60.19 - 80.25: 0 80.25 - 100.31: 2 Bond angle restraints: 91018 Sorted by residual: angle pdb=" O LYS J 73 " pdb=" C LYS J 73 " pdb=" N ALA J 76 " ideal model delta sigma weight residual 122.03 37.24 84.79 1.08e+00 8.57e-01 6.16e+03 angle pdb=" C CYS I 181 " pdb=" N GLY I 182 " pdb=" H GLY I 182 " ideal model delta sigma weight residual 124.05 23.73 100.31 3.00e+00 1.11e-01 1.12e+03 angle pdb=" CA LYS J 73 " pdb=" C LYS J 73 " pdb=" N ALA J 76 " ideal model delta sigma weight residual 117.02 88.95 28.07 1.17e+00 7.31e-01 5.76e+02 angle pdb=" C LYS J 73 " pdb=" N ALA J 76 " pdb=" H ALA J 76 " ideal model delta sigma weight residual 124.38 93.56 30.82 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C2' U L 19 " pdb=" C1' U L 19 " pdb=" N1 U L 19 " ideal model delta sigma weight residual 112.00 124.03 -12.03 1.50e+00 4.44e-01 6.44e+01 ... (remaining 91013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 22720 35.99 - 71.98: 963 71.98 - 107.96: 60 107.96 - 143.95: 6 143.95 - 179.94: 24 Dihedral angle restraints: 23773 sinusoidal: 13443 harmonic: 10330 Sorted by residual: dihedral pdb=" C4' C L 18 " pdb=" C3' C L 18 " pdb=" C2' C L 18 " pdb=" C1' C L 18 " ideal model delta sinusoidal sigma weight residual -35.00 37.51 -72.51 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C5' G L 31 " pdb=" C4' G L 31 " pdb=" C3' G L 31 " pdb=" O3' G L 31 " ideal model delta sinusoidal sigma weight residual 147.00 74.75 72.25 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C5' C L 43 " pdb=" C4' C L 43 " pdb=" C3' C L 43 " pdb=" O3' C L 43 " ideal model delta sinusoidal sigma weight residual 147.00 75.47 71.53 1 8.00e+00 1.56e-02 1.02e+02 ... (remaining 23770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3441 0.078 - 0.156: 383 0.156 - 0.234: 40 0.234 - 0.312: 29 0.312 - 0.390: 14 Chirality restraints: 3907 Sorted by residual: chirality pdb=" P U L 32 " pdb=" OP1 U L 32 " pdb=" OP2 U L 32 " pdb=" O5' U L 32 " both_signs ideal model delta sigma weight residual True 2.41 -2.80 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" P G L 22 " pdb=" OP1 G L 22 " pdb=" OP2 G L 22 " pdb=" O5' G L 22 " both_signs ideal model delta sigma weight residual True 2.41 -2.79 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" P G L 31 " pdb=" OP1 G L 31 " pdb=" OP2 G L 31 " pdb=" O5' G L 31 " both_signs ideal model delta sigma weight residual True 2.41 -2.78 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 3904 not shown) Planarity restraints: 7380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 73 " 0.037 2.00e-02 2.50e+03 1.48e-01 2.18e+02 pdb=" N ALA J 76 " -0.250 2.00e-02 2.50e+03 pdb=" CA ALA J 76 " 0.096 2.00e-02 2.50e+03 pdb=" H ALA J 76 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS I 181 " -0.140 2.00e-02 2.50e+03 1.39e-01 1.93e+02 pdb=" N GLY I 182 " -0.077 2.00e-02 2.50e+03 pdb=" CA GLY I 182 " -0.011 2.00e-02 2.50e+03 pdb=" H GLY I 182 " 0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS J 73 " -0.064 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C LYS J 73 " 0.156 2.00e-02 2.50e+03 pdb=" O LYS J 73 " -0.138 2.00e-02 2.50e+03 pdb=" N ALA J 76 " 0.045 2.00e-02 2.50e+03 ... (remaining 7377 not shown) Histogram of nonbonded interaction distances: 0.97 - 1.70: 79 1.70 - 2.42: 24631 2.42 - 3.15: 153438 3.15 - 3.87: 203633 3.87 - 4.60: 329861 Warning: very small nonbonded interaction distances. Nonbonded interactions: 711642 Sorted by model distance: nonbonded pdb=" O CYS I 181 " pdb="HG12 ILE I 194 " model vdw 0.973 2.620 nonbonded pdb=" CB CYS I 181 " pdb=" HA PRO I 193 " model vdw 1.366 2.920 nonbonded pdb="HH12 ARG C 259 " pdb=" O GLY C 265 " model vdw 1.533 2.450 nonbonded pdb=" HE ARG G 7 " pdb=" OE2 GLU G 9 " model vdw 1.537 2.450 nonbonded pdb=" O ASP K 69 " pdb="HH12 ARG K 72 " model vdw 1.543 2.450 ... (remaining 711637 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 'B' selection = (chain 'C' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'D' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'E' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'F' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'G' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'H' and (resid 1 through 84 or resid 101 through 290)) } ncs_group { reference = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 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: 0.650 Extract box with map and model: 1.590 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 99.490 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:9.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 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 : 0.011 1.660 25849 Z= 0.458 Angle : 0.902 84.792 35177 Z= 0.586 Chirality : 0.057 0.390 3907 Planarity : 0.004 0.111 4447 Dihedral : 18.698 179.938 10036 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.23 % Allowed : 12.32 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.16), residues: 3028 helix: 1.79 (0.17), residues: 1014 sheet: 0.54 (0.21), residues: 602 loop : -0.37 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 211 HIS 0.003 0.001 HIS J 78 PHE 0.019 0.001 PHE K 117 TYR 0.012 0.001 TYR C 68 ARG 0.009 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 411 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 405 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.7882 (ptpp) cc_final: 0.7639 (ptmm) REVERT: B 1 MET cc_start: 0.0474 (mmt) cc_final: -0.0276 (mmm) REVERT: B 17 GLU cc_start: 0.8049 (tt0) cc_final: 0.7714 (tt0) REVERT: B 103 LYS cc_start: 0.5131 (pttm) cc_final: 0.4670 (mmtt) REVERT: B 177 ARG cc_start: 0.7647 (ptp-110) cc_final: 0.7352 (ptp-110) REVERT: B 240 GLN cc_start: 0.7998 (tp-100) cc_final: 0.7700 (tt0) REVERT: B 256 LYS cc_start: 0.8215 (mttp) cc_final: 0.7713 (mttm) REVERT: C 97 LYS cc_start: 0.8567 (tppt) cc_final: 0.8212 (tppt) REVERT: C 100 GLU cc_start: 0.6739 (mp0) cc_final: 0.6498 (tp30) REVERT: C 279 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7188 (mt0) REVERT: C 282 GLU cc_start: 0.7646 (pm20) cc_final: 0.7186 (tp30) REVERT: C 289 MET cc_start: 0.4413 (mpp) cc_final: 0.3746 (pp-130) REVERT: D 30 MET cc_start: 0.8202 (mtp) cc_final: 0.7974 (mtt) REVERT: D 80 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7377 (mp0) REVERT: D 89 LYS cc_start: 0.8624 (mptt) cc_final: 0.7545 (ptmm) REVERT: D 94 LYS cc_start: 0.7673 (mttp) cc_final: 0.7291 (mttt) REVERT: D 97 LYS cc_start: 0.8919 (mttm) cc_final: 0.8381 (mppt) REVERT: D 221 ASP cc_start: 0.8241 (t0) cc_final: 0.8036 (t0) REVERT: D 238 LYS cc_start: 0.8711 (tttm) cc_final: 0.8477 (tttt) REVERT: E 98 LYS cc_start: 0.7320 (mtpp) cc_final: 0.6904 (mppt) REVERT: E 109 MET cc_start: 0.6971 (ptp) cc_final: 0.6722 (ptm) REVERT: E 126 GLU cc_start: 0.7455 (mp0) cc_final: 0.6983 (tp30) REVERT: E 177 ARG cc_start: 0.8148 (ptt-90) cc_final: 0.7430 (ptp90) REVERT: E 287 LYS cc_start: 0.7809 (mttt) cc_final: 0.7433 (mttp) REVERT: F 77 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7489 (mt-10) REVERT: F 123 MET cc_start: 0.8011 (ptm) cc_final: 0.7785 (ptt) REVERT: F 155 THR cc_start: 0.7896 (m) cc_final: 0.7679 (p) REVERT: F 177 ARG cc_start: 0.7943 (ptp90) cc_final: 0.7625 (ptp90) REVERT: G 97 LYS cc_start: 0.8180 (mttt) cc_final: 0.7723 (mmmt) REVERT: G 279 GLN cc_start: 0.7622 (tp-100) cc_final: 0.7322 (tp40) REVERT: G 289 MET cc_start: 0.4455 (pmm) cc_final: 0.3815 (ppp) REVERT: H 4 ILE cc_start: 0.7529 (pt) cc_final: 0.7168 (mm) REVERT: H 128 ASN cc_start: 0.7667 (t0) cc_final: 0.7320 (t0) REVERT: H 268 ARG cc_start: 0.7156 (mmp80) cc_final: 0.6934 (mmp80) REVERT: H 285 GLU cc_start: 0.8037 (pt0) cc_final: 0.7579 (mt-10) REVERT: I 62 MET cc_start: 0.7600 (tpp) cc_final: 0.7371 (mtt) REVERT: I 66 ILE cc_start: 0.7604 (mt) cc_final: 0.7352 (mm) REVERT: I 151 ARG cc_start: 0.5665 (ttm170) cc_final: 0.5433 (ttt180) REVERT: I 202 LYS cc_start: 0.7679 (mptt) cc_final: 0.7055 (mtpt) REVERT: K 54 MET cc_start: 0.7231 (ptm) cc_final: 0.7003 (ptm) REVERT: K 58 ASN cc_start: 0.7810 (m-40) cc_final: 0.7425 (m110) REVERT: K 84 GLN cc_start: 0.7848 (tp40) cc_final: 0.7525 (tp-100) REVERT: K 88 ASP cc_start: 0.7164 (m-30) cc_final: 0.6758 (m-30) REVERT: M 57 ASP cc_start: 0.5028 (t0) cc_final: 0.4610 (m-30) REVERT: M 76 GLU cc_start: 0.5277 (mp0) cc_final: 0.4984 (mp0) outliers start: 6 outliers final: 2 residues processed: 408 average time/residue: 2.5048 time to fit residues: 1178.6442 Evaluate side-chains 283 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain J residue 117 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 239 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 277 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN E 279 GLN F 76 ASN I 174 ASN I 353 HIS I 414 ASN I 535 ASN K 84 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25849 Z= 0.269 Angle : 0.656 16.880 35177 Z= 0.364 Chirality : 0.048 0.291 3907 Planarity : 0.005 0.065 4447 Dihedral : 17.084 177.789 4120 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.33 % Allowed : 14.57 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3030 helix: 1.67 (0.16), residues: 1021 sheet: 0.48 (0.22), residues: 555 loop : -0.65 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 211 HIS 0.004 0.001 HIS B 239 PHE 0.019 0.001 PHE I 287 TYR 0.013 0.001 TYR M 64 ARG 0.005 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 362 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 302 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8068 (ptpp) cc_final: 0.7739 (ptmm) REVERT: A 200 ASP cc_start: 0.8637 (t0) cc_final: 0.8135 (t70) REVERT: A 211 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6781 (tp30) REVERT: B 1 MET cc_start: 0.0517 (mmt) cc_final: -0.0260 (mmm) REVERT: B 17 GLU cc_start: 0.8034 (tt0) cc_final: 0.7630 (tt0) REVERT: B 103 LYS cc_start: 0.4947 (pttm) cc_final: 0.4515 (mmtt) REVERT: B 177 ARG cc_start: 0.7566 (ptp-110) cc_final: 0.7331 (ptp-110) REVERT: B 240 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7778 (tt0) REVERT: B 256 LYS cc_start: 0.8394 (mttp) cc_final: 0.7881 (mttm) REVERT: B 279 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: C 67 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8505 (mm) REVERT: C 289 MET cc_start: 0.4546 (mpp) cc_final: 0.3673 (pp-130) REVERT: D 30 MET cc_start: 0.8168 (mtp) cc_final: 0.7933 (mtt) REVERT: D 80 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7522 (mm-30) REVERT: D 89 LYS cc_start: 0.8554 (mptt) cc_final: 0.7472 (ptmm) REVERT: D 94 LYS cc_start: 0.7689 (mttp) cc_final: 0.7254 (mttt) REVERT: D 97 LYS cc_start: 0.8903 (mttm) cc_final: 0.8379 (mppt) REVERT: D 133 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7217 (ttm-80) REVERT: E 126 GLU cc_start: 0.7453 (mp0) cc_final: 0.6963 (tp30) REVERT: E 177 ARG cc_start: 0.8290 (ptt-90) cc_final: 0.7539 (ptp90) REVERT: E 287 LYS cc_start: 0.7787 (mttt) cc_final: 0.7381 (mttp) REVERT: F 151 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6854 (tt0) REVERT: F 177 ARG cc_start: 0.8066 (ptp90) cc_final: 0.7190 (ptp90) REVERT: G 15 ASP cc_start: 0.8269 (m-30) cc_final: 0.7817 (p0) REVERT: G 97 LYS cc_start: 0.8144 (mttt) cc_final: 0.7752 (mmmt) REVERT: G 279 GLN cc_start: 0.7647 (tp-100) cc_final: 0.7366 (tp40) REVERT: G 282 GLU cc_start: 0.7954 (pm20) cc_final: 0.7436 (tt0) REVERT: G 289 MET cc_start: 0.4458 (pmm) cc_final: 0.3763 (ppp) REVERT: H 4 ILE cc_start: 0.7469 (pt) cc_final: 0.7141 (mm) REVERT: H 128 ASN cc_start: 0.7618 (t0) cc_final: 0.7361 (t0) REVERT: I 62 MET cc_start: 0.7512 (tpp) cc_final: 0.7127 (mtt) REVERT: I 202 LYS cc_start: 0.7810 (mptt) cc_final: 0.7148 (mtpt) REVERT: I 391 ILE cc_start: 0.8430 (pt) cc_final: 0.8210 (tp) REVERT: I 542 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7545 (tmm) REVERT: K 58 ASN cc_start: 0.7634 (m-40) cc_final: 0.7324 (m110) REVERT: K 84 GLN cc_start: 0.7960 (tp-100) cc_final: 0.7468 (tp-100) REVERT: K 88 ASP cc_start: 0.7162 (m-30) cc_final: 0.6632 (m-30) REVERT: M 53 MET cc_start: 0.7165 (ttt) cc_final: 0.6660 (tmt) REVERT: M 57 ASP cc_start: 0.5569 (t70) cc_final: 0.4855 (m-30) outliers start: 60 outliers final: 24 residues processed: 335 average time/residue: 2.2476 time to fit residues: 892.4340 Evaluate side-chains 299 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 270 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 119 ASP Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain I residue 439 GLN Chi-restraints excluded: chain I residue 542 MET Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 38 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 278 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 223 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN C 112 ASN E 279 GLN I 174 ASN I 414 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25849 Z= 0.287 Angle : 0.620 16.238 35177 Z= 0.336 Chirality : 0.047 0.270 3907 Planarity : 0.005 0.071 4447 Dihedral : 15.552 179.366 4118 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.87 % Allowed : 14.88 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3030 helix: 1.63 (0.16), residues: 1020 sheet: 0.25 (0.21), residues: 574 loop : -0.70 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 211 HIS 0.005 0.001 HIS F 179 PHE 0.017 0.001 PHE J 105 TYR 0.013 0.001 TYR F 68 ARG 0.008 0.000 ARG I 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 350 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 276 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8130 (ptpp) cc_final: 0.7783 (ptmm) REVERT: A 143 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7802 (t0) REVERT: A 178 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7627 (tp) REVERT: B 1 MET cc_start: 0.0528 (mmt) cc_final: -0.0248 (mmm) REVERT: B 17 GLU cc_start: 0.8034 (tt0) cc_final: 0.7640 (tt0) REVERT: B 30 MET cc_start: 0.8388 (mtp) cc_final: 0.8095 (mtp) REVERT: B 103 LYS cc_start: 0.4983 (pttm) cc_final: 0.4546 (mmtt) REVERT: B 177 ARG cc_start: 0.7537 (ptp-110) cc_final: 0.7317 (ptp-110) REVERT: B 240 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7809 (tt0) REVERT: B 256 LYS cc_start: 0.8382 (mttp) cc_final: 0.7862 (mttm) REVERT: B 279 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7848 (mp10) REVERT: C 282 GLU cc_start: 0.7741 (pm20) cc_final: 0.7292 (tp30) REVERT: C 289 MET cc_start: 0.4541 (mpp) cc_final: 0.3660 (pp-130) REVERT: D 9 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8474 (mp0) REVERT: D 30 MET cc_start: 0.8213 (mtp) cc_final: 0.7971 (mtt) REVERT: D 80 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7564 (mm-30) REVERT: D 89 LYS cc_start: 0.8569 (mptt) cc_final: 0.7496 (ptmm) REVERT: D 94 LYS cc_start: 0.7697 (mttp) cc_final: 0.7272 (mttt) REVERT: D 97 LYS cc_start: 0.8892 (mttm) cc_final: 0.8368 (mppt) REVERT: D 133 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7286 (ttm-80) REVERT: D 285 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: E 177 ARG cc_start: 0.8364 (ptt-90) cc_final: 0.7608 (ptp90) REVERT: E 287 LYS cc_start: 0.7768 (mttt) cc_final: 0.7331 (mttp) REVERT: F 9 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8417 (mp0) REVERT: F 151 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6888 (tt0) REVERT: F 177 ARG cc_start: 0.8099 (ptp90) cc_final: 0.7269 (ptp90) REVERT: G 15 ASP cc_start: 0.8166 (m-30) cc_final: 0.7745 (p0) REVERT: G 97 LYS cc_start: 0.8162 (mttt) cc_final: 0.7826 (mmmt) REVERT: G 279 GLN cc_start: 0.7651 (tp-100) cc_final: 0.7383 (tp40) REVERT: G 282 GLU cc_start: 0.7936 (pm20) cc_final: 0.7438 (tt0) REVERT: G 289 MET cc_start: 0.4441 (pmm) cc_final: 0.3758 (ppp) REVERT: H 4 ILE cc_start: 0.7523 (pt) cc_final: 0.7169 (mm) REVERT: H 94 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6595 (ptpt) REVERT: H 128 ASN cc_start: 0.7566 (t0) cc_final: 0.7142 (t0) REVERT: I 202 LYS cc_start: 0.7801 (mptt) cc_final: 0.7156 (mtpt) REVERT: I 413 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8552 (mp) REVERT: I 542 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7566 (ptm) REVERT: K 58 ASN cc_start: 0.7614 (m-40) cc_final: 0.7283 (m110) REVERT: K 84 GLN cc_start: 0.7976 (tp-100) cc_final: 0.7463 (tp-100) REVERT: K 88 ASP cc_start: 0.7313 (m-30) cc_final: 0.6736 (m-30) REVERT: M 53 MET cc_start: 0.7156 (ttt) cc_final: 0.6596 (tmt) REVERT: M 54 ASP cc_start: 0.6325 (t0) cc_final: 0.5946 (t0) REVERT: M 66 ASP cc_start: 0.6845 (t0) cc_final: 0.6212 (m-30) outliers start: 74 outliers final: 41 residues processed: 324 average time/residue: 2.2381 time to fit residues: 850.3650 Evaluate side-chains 314 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 263 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 233 LYS Chi-restraints excluded: chain H residue 94 LYS Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 119 ASP Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 420 SER Chi-restraints excluded: chain I residue 439 GLN Chi-restraints excluded: chain I residue 542 MET Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 38 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 chunk 186 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 295 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN I 174 ASN I 414 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25849 Z= 0.349 Angle : 0.610 15.927 35177 Z= 0.326 Chirality : 0.047 0.288 3907 Planarity : 0.005 0.046 4447 Dihedral : 14.807 175.399 4118 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.15 % Allowed : 15.23 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3030 helix: 1.56 (0.16), residues: 1020 sheet: 0.14 (0.21), residues: 579 loop : -0.82 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 211 HIS 0.006 0.001 HIS I 384 PHE 0.019 0.002 PHE J 105 TYR 0.020 0.002 TYR M 64 ARG 0.004 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 347 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 266 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7509 (pp) REVERT: A 131 LYS cc_start: 0.8153 (ptpp) cc_final: 0.7852 (ptmm) REVERT: A 143 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7836 (t0) REVERT: A 178 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7645 (tp) REVERT: B 1 MET cc_start: 0.0445 (mmt) cc_final: -0.0317 (mmm) REVERT: B 17 GLU cc_start: 0.7997 (tt0) cc_final: 0.7596 (tt0) REVERT: B 30 MET cc_start: 0.8373 (mtp) cc_final: 0.8093 (mtp) REVERT: B 103 LYS cc_start: 0.4918 (pttm) cc_final: 0.4501 (mmtt) REVERT: B 177 ARG cc_start: 0.7574 (ptp-110) cc_final: 0.7347 (ptp-110) REVERT: B 240 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7817 (tt0) REVERT: B 256 LYS cc_start: 0.8347 (mttp) cc_final: 0.7869 (mttm) REVERT: B 279 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7777 (mp10) REVERT: C 261 GLU cc_start: 0.7822 (pm20) cc_final: 0.6647 (tp30) REVERT: C 282 GLU cc_start: 0.7790 (pm20) cc_final: 0.7357 (tp30) REVERT: C 289 MET cc_start: 0.4655 (mpp) cc_final: 0.3687 (pp-130) REVERT: D 9 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8473 (mp0) REVERT: D 30 MET cc_start: 0.8214 (mtp) cc_final: 0.7969 (mtt) REVERT: D 89 LYS cc_start: 0.8592 (mptt) cc_final: 0.7564 (ptmm) REVERT: D 94 LYS cc_start: 0.7706 (mttp) cc_final: 0.7276 (mttt) REVERT: D 97 LYS cc_start: 0.8892 (mttm) cc_final: 0.8369 (mppt) REVERT: D 133 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7286 (ttm-80) REVERT: D 285 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: E 177 ARG cc_start: 0.8384 (ptt-90) cc_final: 0.7596 (ptp90) REVERT: E 191 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8631 (m-80) REVERT: E 287 LYS cc_start: 0.7796 (mttt) cc_final: 0.7332 (mttp) REVERT: F 151 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7109 (tt0) REVERT: F 177 ARG cc_start: 0.8088 (ptp90) cc_final: 0.7633 (ptp90) REVERT: G 15 ASP cc_start: 0.8186 (m-30) cc_final: 0.7702 (p0) REVERT: G 97 LYS cc_start: 0.8191 (mttt) cc_final: 0.7840 (mmmt) REVERT: G 279 GLN cc_start: 0.7618 (tp-100) cc_final: 0.7336 (tp40) REVERT: G 282 GLU cc_start: 0.7906 (pm20) cc_final: 0.7468 (OUTLIER) REVERT: G 289 MET cc_start: 0.4552 (pmm) cc_final: 0.3893 (ppp) REVERT: H 4 ILE cc_start: 0.7527 (pt) cc_final: 0.7192 (mm) REVERT: H 94 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6701 (ptpt) REVERT: H 128 ASN cc_start: 0.7533 (t0) cc_final: 0.7316 (t0) REVERT: I 12 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7456 (ptt90) REVERT: I 202 LYS cc_start: 0.7799 (mptt) cc_final: 0.7149 (mtpt) REVERT: I 346 MET cc_start: 0.7884 (ttm) cc_final: 0.7578 (mtm) REVERT: I 413 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8589 (mp) REVERT: I 542 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7576 (tmm) REVERT: K 58 ASN cc_start: 0.7592 (m-40) cc_final: 0.7308 (m110) REVERT: K 84 GLN cc_start: 0.8018 (tp-100) cc_final: 0.7525 (tp-100) REVERT: K 88 ASP cc_start: 0.7291 (m-30) cc_final: 0.6673 (m-30) REVERT: M 57 ASP cc_start: 0.5429 (t0) cc_final: 0.5104 (p0) REVERT: M 66 ASP cc_start: 0.6755 (t0) cc_final: 0.6113 (m-30) outliers start: 81 outliers final: 47 residues processed: 322 average time/residue: 2.2609 time to fit residues: 853.0078 Evaluate side-chains 318 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 260 time to evaluate : 3.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 233 LYS Chi-restraints excluded: chain H residue 94 LYS Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 119 ASP Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 420 SER Chi-restraints excluded: chain I residue 439 GLN Chi-restraints excluded: chain I residue 542 MET Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 38 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 252 optimal weight: 0.2980 chunk 204 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN I 174 ASN I 414 ASN K 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25849 Z= 0.299 Angle : 0.583 15.898 35177 Z= 0.310 Chirality : 0.046 0.276 3907 Planarity : 0.005 0.043 4447 Dihedral : 14.545 172.025 4118 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.99 % Allowed : 15.54 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3030 helix: 1.57 (0.16), residues: 1026 sheet: 0.09 (0.21), residues: 578 loop : -0.87 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 211 HIS 0.004 0.001 HIS I 384 PHE 0.017 0.001 PHE J 105 TYR 0.013 0.001 TYR F 68 ARG 0.003 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 345 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 268 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7580 (pp) REVERT: A 131 LYS cc_start: 0.8133 (ptpp) cc_final: 0.7818 (ptmm) REVERT: A 143 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7827 (t0) REVERT: A 178 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7646 (tp) REVERT: B 1 MET cc_start: 0.0502 (mmt) cc_final: -0.0273 (mmm) REVERT: B 17 GLU cc_start: 0.7990 (tt0) cc_final: 0.7584 (tt0) REVERT: B 30 MET cc_start: 0.8411 (mtp) cc_final: 0.8148 (mtp) REVERT: B 103 LYS cc_start: 0.5010 (pttm) cc_final: 0.4573 (mmtt) REVERT: B 177 ARG cc_start: 0.7570 (ptp-110) cc_final: 0.7367 (ptp-110) REVERT: B 240 GLN cc_start: 0.8061 (tp-100) cc_final: 0.7832 (tt0) REVERT: B 256 LYS cc_start: 0.8344 (mttp) cc_final: 0.7851 (mttm) REVERT: B 279 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7760 (mp10) REVERT: C 261 GLU cc_start: 0.7839 (pm20) cc_final: 0.6626 (tp30) REVERT: C 282 GLU cc_start: 0.7779 (pm20) cc_final: 0.7366 (tp30) REVERT: C 289 MET cc_start: 0.4576 (mpp) cc_final: 0.3543 (pp-130) REVERT: D 9 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: D 30 MET cc_start: 0.8218 (mtp) cc_final: 0.7973 (mtt) REVERT: D 89 LYS cc_start: 0.8592 (mptt) cc_final: 0.7565 (ptmm) REVERT: D 94 LYS cc_start: 0.7698 (mttp) cc_final: 0.7277 (mttt) REVERT: D 97 LYS cc_start: 0.8893 (mttm) cc_final: 0.8368 (mppt) REVERT: D 133 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7276 (ttm-80) REVERT: D 285 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: E 94 LYS cc_start: 0.8813 (mttt) cc_final: 0.8486 (mppt) REVERT: E 177 ARG cc_start: 0.8373 (ptt-90) cc_final: 0.7616 (ptp90) REVERT: E 191 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8633 (m-80) REVERT: E 287 LYS cc_start: 0.7792 (mttt) cc_final: 0.7318 (mttp) REVERT: F 177 ARG cc_start: 0.8096 (ptp90) cc_final: 0.7840 (ptp90) REVERT: G 15 ASP cc_start: 0.8192 (m-30) cc_final: 0.7717 (p0) REVERT: G 97 LYS cc_start: 0.8195 (mttt) cc_final: 0.7818 (mmmt) REVERT: G 233 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6848 (mtpp) REVERT: G 279 GLN cc_start: 0.7603 (tp-100) cc_final: 0.7317 (tp40) REVERT: G 282 GLU cc_start: 0.7922 (pm20) cc_final: 0.7496 (OUTLIER) REVERT: G 289 MET cc_start: 0.4502 (pmm) cc_final: 0.3819 (ppp) REVERT: H 4 ILE cc_start: 0.7520 (pt) cc_final: 0.7201 (mm) REVERT: H 94 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6680 (ptpt) REVERT: H 128 ASN cc_start: 0.7399 (t0) cc_final: 0.7155 (t0) REVERT: H 191 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: I 202 LYS cc_start: 0.7771 (mptt) cc_final: 0.7123 (mtpt) REVERT: I 346 MET cc_start: 0.7886 (ttm) cc_final: 0.7578 (mtm) REVERT: I 387 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: I 413 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8596 (mp) REVERT: I 542 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7595 (tmm) REVERT: K 58 ASN cc_start: 0.7644 (m-40) cc_final: 0.7346 (m110) REVERT: K 84 GLN cc_start: 0.8055 (tp40) cc_final: 0.7395 (tp-100) REVERT: K 88 ASP cc_start: 0.7307 (m-30) cc_final: 0.6664 (m-30) REVERT: M 57 ASP cc_start: 0.5446 (t0) cc_final: 0.5117 (p0) REVERT: M 66 ASP cc_start: 0.6736 (t0) cc_final: 0.6055 (m-30) outliers start: 77 outliers final: 42 residues processed: 315 average time/residue: 2.2681 time to fit residues: 836.7420 Evaluate side-chains 314 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 259 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 233 LYS Chi-restraints excluded: chain H residue 94 LYS Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 119 ASP Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 377 MET Chi-restraints excluded: chain I residue 387 GLU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 420 SER Chi-restraints excluded: chain I residue 439 GLN Chi-restraints excluded: chain I residue 542 MET Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain M residue 41 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 296 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN I 174 ASN I 414 ASN J 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25849 Z= 0.343 Angle : 0.600 15.942 35177 Z= 0.318 Chirality : 0.046 0.271 3907 Planarity : 0.005 0.044 4447 Dihedral : 14.494 170.711 4118 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.22 % Allowed : 16.01 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3030 helix: 1.49 (0.16), residues: 1026 sheet: 0.04 (0.21), residues: 582 loop : -0.94 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 67 HIS 0.006 0.001 HIS I 384 PHE 0.017 0.002 PHE J 105 TYR 0.030 0.002 TYR M 64 ARG 0.004 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 356 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 273 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7569 (pp) REVERT: A 143 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7846 (t0) REVERT: A 178 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7632 (tp) REVERT: A 200 ASP cc_start: 0.8685 (t0) cc_final: 0.8083 (t70) REVERT: A 207 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8461 (tttm) REVERT: B 1 MET cc_start: 0.0471 (mmt) cc_final: -0.0148 (mmm) REVERT: B 17 GLU cc_start: 0.8011 (tt0) cc_final: 0.7611 (tt0) REVERT: B 30 MET cc_start: 0.8433 (mtp) cc_final: 0.8185 (mtp) REVERT: B 240 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7820 (mt0) REVERT: B 256 LYS cc_start: 0.8377 (mttp) cc_final: 0.7880 (mttm) REVERT: B 279 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7753 (mp10) REVERT: C 261 GLU cc_start: 0.7778 (pm20) cc_final: 0.6530 (tp30) REVERT: C 282 GLU cc_start: 0.7816 (pm20) cc_final: 0.7416 (tp30) REVERT: C 289 MET cc_start: 0.4751 (mpp) cc_final: 0.3604 (pp-130) REVERT: D 9 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: D 89 LYS cc_start: 0.8617 (mptt) cc_final: 0.7582 (ptmm) REVERT: D 94 LYS cc_start: 0.7701 (mttp) cc_final: 0.7301 (mttt) REVERT: D 97 LYS cc_start: 0.8901 (mttm) cc_final: 0.8378 (mppt) REVERT: D 133 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7306 (ttm-80) REVERT: D 285 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: E 94 LYS cc_start: 0.8847 (mttt) cc_final: 0.8509 (mppt) REVERT: E 98 LYS cc_start: 0.6754 (mtpp) cc_final: 0.6552 (ttmm) REVERT: E 177 ARG cc_start: 0.8393 (ptt-90) cc_final: 0.7669 (ptp90) REVERT: E 191 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8640 (m-80) REVERT: E 287 LYS cc_start: 0.7852 (mttt) cc_final: 0.7354 (mttp) REVERT: F 151 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7098 (tt0) REVERT: F 177 ARG cc_start: 0.8101 (ptp90) cc_final: 0.7742 (ptp90) REVERT: G 15 ASP cc_start: 0.8087 (m-30) cc_final: 0.7538 (p0) REVERT: G 97 LYS cc_start: 0.8221 (mttt) cc_final: 0.7835 (mmmt) REVERT: G 233 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6806 (mtpp) REVERT: G 279 GLN cc_start: 0.7595 (tp-100) cc_final: 0.7308 (tp40) REVERT: G 282 GLU cc_start: 0.7943 (pm20) cc_final: 0.7520 (OUTLIER) REVERT: G 289 MET cc_start: 0.4636 (pmm) cc_final: 0.3754 (ppp) REVERT: H 4 ILE cc_start: 0.7607 (pt) cc_final: 0.7338 (mm) REVERT: H 128 ASN cc_start: 0.7374 (t0) cc_final: 0.7159 (t0) REVERT: H 180 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6822 (pp) REVERT: H 191 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: I 12 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7479 (ptt90) REVERT: I 202 LYS cc_start: 0.7786 (mptt) cc_final: 0.7123 (mtpt) REVERT: I 346 MET cc_start: 0.7911 (ttm) cc_final: 0.7644 (mtm) REVERT: I 387 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: I 413 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8649 (mp) REVERT: I 542 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7600 (tmm) REVERT: K 58 ASN cc_start: 0.7620 (m-40) cc_final: 0.7308 (m110) REVERT: K 84 GLN cc_start: 0.8018 (tp40) cc_final: 0.7386 (tp-100) REVERT: K 88 ASP cc_start: 0.7499 (m-30) cc_final: 0.6754 (m-30) REVERT: M 54 ASP cc_start: 0.6244 (t0) cc_final: 0.5683 (t0) REVERT: M 57 ASP cc_start: 0.5301 (t0) cc_final: 0.4952 (p0) outliers start: 83 outliers final: 45 residues processed: 323 average time/residue: 2.2538 time to fit residues: 865.6202 Evaluate side-chains 325 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 265 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 233 LYS Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 119 ASP Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 377 MET Chi-restraints excluded: chain I residue 387 GLU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 420 SER Chi-restraints excluded: chain I residue 439 GLN Chi-restraints excluded: chain I residue 542 MET Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain M residue 41 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 294 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN I 174 ASN I 414 ASN J 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25849 Z= 0.213 Angle : 0.558 15.740 35177 Z= 0.294 Chirality : 0.044 0.251 3907 Planarity : 0.004 0.043 4447 Dihedral : 14.377 173.364 4118 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.60 % Allowed : 16.74 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3030 helix: 1.73 (0.16), residues: 1026 sheet: 0.04 (0.21), residues: 578 loop : -0.89 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 67 HIS 0.004 0.001 HIS B 249 PHE 0.014 0.001 PHE A 126 TYR 0.013 0.001 TYR M 64 ARG 0.007 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 343 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 276 time to evaluate : 3.071 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: A 114 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7550 (pp) REVERT: A 143 ASP cc_start: 0.8268 (m-30) cc_final: 0.7874 (t0) REVERT: A 178 LEU cc_start: 0.7890 (pt) cc_final: 0.7603 (tp) REVERT: B 1 MET cc_start: 0.0516 (mmt) cc_final: -0.0097 (mmm) REVERT: B 17 GLU cc_start: 0.7980 (tt0) cc_final: 0.7584 (tt0) REVERT: B 30 MET cc_start: 0.8395 (mtp) cc_final: 0.8161 (mtp) REVERT: B 240 GLN cc_start: 0.8066 (tp-100) cc_final: 0.7862 (mt0) REVERT: B 256 LYS cc_start: 0.8438 (mttp) cc_final: 0.7937 (mttm) REVERT: B 279 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7791 (mp10) REVERT: C 282 GLU cc_start: 0.7787 (pm20) cc_final: 0.7381 (tp30) REVERT: C 289 MET cc_start: 0.4540 (mpp) cc_final: 0.3780 (pp-130) REVERT: D 9 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: D 80 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7557 (mm-30) REVERT: D 89 LYS cc_start: 0.8542 (mptt) cc_final: 0.7506 (ptmm) REVERT: D 94 LYS cc_start: 0.7724 (mttp) cc_final: 0.7324 (mttt) REVERT: D 97 LYS cc_start: 0.8905 (mttm) cc_final: 0.8375 (mppt) REVERT: D 133 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7289 (ttm-80) REVERT: D 285 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: E 94 LYS cc_start: 0.8848 (mttt) cc_final: 0.8512 (mppt) REVERT: E 177 ARG cc_start: 0.8339 (ptt-90) cc_final: 0.7597 (ptp90) REVERT: E 191 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8636 (m-80) REVERT: E 287 LYS cc_start: 0.7845 (mttt) cc_final: 0.7370 (mttp) REVERT: G 15 ASP cc_start: 0.8045 (m-30) cc_final: 0.7637 (p0) REVERT: G 97 LYS cc_start: 0.8220 (mttt) cc_final: 0.7826 (mmmt) REVERT: G 233 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6799 (mtpp) REVERT: G 279 GLN cc_start: 0.7572 (tp-100) cc_final: 0.7323 (tp40) REVERT: G 282 GLU cc_start: 0.7909 (pm20) cc_final: 0.7309 (tm-30) REVERT: G 289 MET cc_start: 0.4572 (pmm) cc_final: 0.3744 (ppp) REVERT: H 4 ILE cc_start: 0.7601 (pt) cc_final: 0.7345 (mm) REVERT: H 128 ASN cc_start: 0.7359 (t0) cc_final: 0.7134 (t0) REVERT: H 180 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6811 (pp) REVERT: H 191 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8368 (m-80) REVERT: I 12 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7457 (ptt90) REVERT: I 202 LYS cc_start: 0.7824 (mptt) cc_final: 0.7161 (mtpt) REVERT: I 387 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7930 (mt-10) REVERT: I 413 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8705 (mp) REVERT: I 542 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7647 (tmm) REVERT: K 58 ASN cc_start: 0.7613 (m-40) cc_final: 0.7336 (m110) REVERT: K 84 GLN cc_start: 0.7977 (tp40) cc_final: 0.7272 (tp-100) REVERT: K 88 ASP cc_start: 0.7476 (m-30) cc_final: 0.6711 (m-30) REVERT: M 54 ASP cc_start: 0.6195 (t0) cc_final: 0.5587 (t0) REVERT: M 57 ASP cc_start: 0.5482 (t0) cc_final: 0.5065 (p0) outliers start: 67 outliers final: 38 residues processed: 316 average time/residue: 2.1782 time to fit residues: 810.4922 Evaluate side-chains 313 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 263 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 233 LYS Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 119 ASP Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 377 MET Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 414 ASN Chi-restraints excluded: chain I residue 420 SER Chi-restraints excluded: chain I residue 439 GLN Chi-restraints excluded: chain I residue 542 MET Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain M residue 41 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 chunk 268 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 279 GLN I 174 ASN I 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25849 Z= 0.316 Angle : 0.581 15.823 35177 Z= 0.307 Chirality : 0.045 0.258 3907 Planarity : 0.004 0.046 4447 Dihedral : 14.274 175.873 4118 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.60 % Allowed : 17.52 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3030 helix: 1.64 (0.16), residues: 1026 sheet: -0.00 (0.21), residues: 578 loop : -0.94 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 67 HIS 0.005 0.001 HIS I 384 PHE 0.018 0.002 PHE I 126 TYR 0.013 0.001 TYR I 246 ARG 0.014 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 329 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 262 time to evaluate : 3.094 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: A 114 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7593 (pp) REVERT: A 143 ASP cc_start: 0.8276 (m-30) cc_final: 0.7878 (t0) REVERT: A 178 LEU cc_start: 0.7901 (pt) cc_final: 0.7620 (tp) REVERT: A 200 ASP cc_start: 0.8683 (t0) cc_final: 0.8080 (t70) REVERT: A 207 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8458 (tttm) REVERT: B 1 MET cc_start: 0.0716 (mmt) cc_final: 0.0108 (mmm) REVERT: B 17 GLU cc_start: 0.7991 (tt0) cc_final: 0.7585 (tt0) REVERT: B 30 MET cc_start: 0.8433 (mtp) cc_final: 0.8211 (mtp) REVERT: B 240 GLN cc_start: 0.8065 (tp-100) cc_final: 0.7840 (mt0) REVERT: B 256 LYS cc_start: 0.8421 (mttp) cc_final: 0.7960 (mttm) REVERT: B 279 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: C 261 GLU cc_start: 0.7862 (pm20) cc_final: 0.6639 (tp30) REVERT: C 282 GLU cc_start: 0.7813 (pm20) cc_final: 0.7402 (tp30) REVERT: C 289 MET cc_start: 0.4690 (mpp) cc_final: 0.3882 (pp-130) REVERT: D 9 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8448 (mp0) REVERT: D 89 LYS cc_start: 0.8612 (mptt) cc_final: 0.7589 (ptmm) REVERT: D 94 LYS cc_start: 0.7672 (mttp) cc_final: 0.7271 (mttt) REVERT: D 97 LYS cc_start: 0.8908 (mttm) cc_final: 0.8397 (mppt) REVERT: D 133 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7292 (ttm-80) REVERT: D 285 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: E 94 LYS cc_start: 0.8868 (mttt) cc_final: 0.8523 (mppt) REVERT: E 177 ARG cc_start: 0.8346 (ptt-90) cc_final: 0.7601 (ptp90) REVERT: E 191 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8638 (m-80) REVERT: E 287 LYS cc_start: 0.7798 (mttt) cc_final: 0.7399 (mttp) REVERT: G 15 ASP cc_start: 0.8033 (m-30) cc_final: 0.7593 (p0) REVERT: G 97 LYS cc_start: 0.8235 (mttt) cc_final: 0.7829 (mmmt) REVERT: G 233 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6818 (mtpp) REVERT: G 279 GLN cc_start: 0.7577 (tp-100) cc_final: 0.7332 (tp40) REVERT: G 282 GLU cc_start: 0.7950 (pm20) cc_final: 0.7330 (tm-30) REVERT: G 289 MET cc_start: 0.4637 (pmm) cc_final: 0.3780 (ppp) REVERT: H 4 ILE cc_start: 0.7610 (pt) cc_final: 0.7351 (mm) REVERT: H 180 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6807 (pp) REVERT: H 191 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8441 (m-80) REVERT: I 12 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7439 (ptt90) REVERT: I 202 LYS cc_start: 0.7840 (mptt) cc_final: 0.7162 (mtpt) REVERT: I 387 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8022 (mt-10) REVERT: I 542 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7638 (tmm) REVERT: K 58 ASN cc_start: 0.7610 (m-40) cc_final: 0.7343 (m110) REVERT: K 84 GLN cc_start: 0.7944 (tp40) cc_final: 0.7229 (tp-100) REVERT: K 88 ASP cc_start: 0.7495 (m-30) cc_final: 0.6714 (m-30) REVERT: M 54 ASP cc_start: 0.6176 (t0) cc_final: 0.5573 (t0) REVERT: M 57 ASP cc_start: 0.5511 (t0) cc_final: 0.5112 (p0) outliers start: 67 outliers final: 44 residues processed: 303 average time/residue: 2.2370 time to fit residues: 796.1226 Evaluate side-chains 313 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 258 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 128 ASN Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 233 LYS Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 119 ASP Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 377 MET Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 420 SER Chi-restraints excluded: chain I residue 439 GLN Chi-restraints excluded: chain I residue 542 MET Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain M residue 41 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 274 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 273 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25849 Z= 0.235 Angle : 0.559 15.747 35177 Z= 0.293 Chirality : 0.044 0.248 3907 Planarity : 0.004 0.050 4447 Dihedral : 14.159 178.626 4118 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.45 % Allowed : 17.72 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3030 helix: 1.76 (0.16), residues: 1026 sheet: 0.04 (0.22), residues: 570 loop : -0.92 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 67 HIS 0.004 0.001 HIS B 249 PHE 0.015 0.001 PHE I 105 TYR 0.012 0.001 TYR E 68 ARG 0.014 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 331 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 268 time to evaluate : 3.048 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: A 114 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7519 (pp) REVERT: A 178 LEU cc_start: 0.7846 (pt) cc_final: 0.7579 (tp) REVERT: B 1 MET cc_start: 0.0718 (mmt) cc_final: 0.0113 (mmm) REVERT: B 17 GLU cc_start: 0.7978 (tt0) cc_final: 0.7583 (tt0) REVERT: B 30 MET cc_start: 0.8424 (mtp) cc_final: 0.8199 (mtp) REVERT: B 240 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7768 (mt0) REVERT: B 256 LYS cc_start: 0.8501 (mttp) cc_final: 0.8028 (mttm) REVERT: B 279 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7792 (mp10) REVERT: C 261 GLU cc_start: 0.7767 (pm20) cc_final: 0.6447 (tp30) REVERT: C 289 MET cc_start: 0.4578 (mpp) cc_final: 0.3801 (pp-130) REVERT: D 9 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8474 (mt-10) REVERT: D 72 LYS cc_start: 0.7480 (tptp) cc_final: 0.6782 (tppt) REVERT: D 80 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7658 (mm-30) REVERT: D 89 LYS cc_start: 0.8552 (mptt) cc_final: 0.7508 (ptmm) REVERT: D 94 LYS cc_start: 0.7654 (mttp) cc_final: 0.7255 (mttt) REVERT: D 97 LYS cc_start: 0.8906 (mttm) cc_final: 0.8375 (mppt) REVERT: D 133 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7260 (ttm-80) REVERT: D 285 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: E 94 LYS cc_start: 0.8861 (mttt) cc_final: 0.8516 (mppt) REVERT: E 177 ARG cc_start: 0.8352 (ptt-90) cc_final: 0.7575 (ptp90) REVERT: E 191 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: E 287 LYS cc_start: 0.7800 (mttt) cc_final: 0.7392 (mttp) REVERT: G 15 ASP cc_start: 0.8026 (m-30) cc_final: 0.7579 (p0) REVERT: G 97 LYS cc_start: 0.8243 (mttt) cc_final: 0.7884 (mmmt) REVERT: G 233 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6807 (mtpp) REVERT: G 279 GLN cc_start: 0.7560 (tp-100) cc_final: 0.7312 (tp40) REVERT: G 282 GLU cc_start: 0.7944 (pm20) cc_final: 0.7263 (tm-30) REVERT: G 289 MET cc_start: 0.4622 (pmm) cc_final: 0.3767 (ppp) REVERT: H 4 ILE cc_start: 0.7629 (pt) cc_final: 0.7388 (mm) REVERT: H 180 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6803 (pp) REVERT: H 191 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8379 (m-80) REVERT: I 12 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7446 (ptt90) REVERT: I 202 LYS cc_start: 0.7846 (mptt) cc_final: 0.7164 (mtpt) REVERT: I 287 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.5535 (p90) REVERT: I 351 ARG cc_start: 0.7281 (ptt180) cc_final: 0.7025 (ptp-110) REVERT: I 387 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: I 542 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7630 (tmm) REVERT: K 58 ASN cc_start: 0.7592 (m-40) cc_final: 0.7332 (m110) REVERT: K 84 GLN cc_start: 0.7964 (tp40) cc_final: 0.7237 (tp-100) REVERT: K 88 ASP cc_start: 0.7524 (m-30) cc_final: 0.6770 (m-30) REVERT: M 54 ASP cc_start: 0.6171 (t0) cc_final: 0.5572 (t0) REVERT: M 57 ASP cc_start: 0.5510 (t0) cc_final: 0.5125 (p0) outliers start: 63 outliers final: 39 residues processed: 304 average time/residue: 2.3083 time to fit residues: 825.5079 Evaluate side-chains 311 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 233 LYS Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 119 ASP Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 377 MET Chi-restraints excluded: chain I residue 387 GLU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 420 SER Chi-restraints excluded: chain I residue 439 GLN Chi-restraints excluded: chain I residue 514 GLU Chi-restraints excluded: chain I residue 542 MET Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain M residue 41 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 304 optimal weight: 9.9990 chunk 280 optimal weight: 0.9980 chunk 242 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN I 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25849 Z= 0.209 Angle : 0.554 15.739 35177 Z= 0.290 Chirality : 0.044 0.246 3907 Planarity : 0.004 0.056 4447 Dihedral : 14.078 178.299 4118 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.21 % Allowed : 18.03 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3030 helix: 1.84 (0.16), residues: 1026 sheet: 0.07 (0.22), residues: 570 loop : -0.89 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 67 HIS 0.004 0.001 HIS B 249 PHE 0.024 0.001 PHE I 126 TYR 0.012 0.001 TYR E 68 ARG 0.014 0.000 ARG B 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 324 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 267 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7479 (pp) REVERT: A 178 LEU cc_start: 0.7845 (pt) cc_final: 0.7577 (tp) REVERT: B 1 MET cc_start: 0.0806 (mmt) cc_final: 0.0179 (mmm) REVERT: B 17 GLU cc_start: 0.7990 (tt0) cc_final: 0.7594 (tt0) REVERT: B 30 MET cc_start: 0.8418 (mtp) cc_final: 0.8190 (mtp) REVERT: B 240 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7762 (mt0) REVERT: B 256 LYS cc_start: 0.8494 (mttp) cc_final: 0.8022 (mttm) REVERT: B 279 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.7791 (mp10) REVERT: C 261 GLU cc_start: 0.7742 (pm20) cc_final: 0.6422 (tp30) REVERT: C 289 MET cc_start: 0.4593 (mpp) cc_final: 0.3811 (pp-130) REVERT: D 72 LYS cc_start: 0.7442 (tptp) cc_final: 0.6751 (tppt) REVERT: D 80 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7574 (mt-10) REVERT: D 89 LYS cc_start: 0.8547 (mptt) cc_final: 0.7486 (ptmm) REVERT: D 94 LYS cc_start: 0.7635 (mttp) cc_final: 0.7232 (mttt) REVERT: D 97 LYS cc_start: 0.8904 (mttm) cc_final: 0.8374 (mppt) REVERT: D 133 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7226 (ttm-80) REVERT: D 285 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: E 94 LYS cc_start: 0.8818 (mttt) cc_final: 0.8486 (mppt) REVERT: E 177 ARG cc_start: 0.8349 (ptt-90) cc_final: 0.7570 (ptp90) REVERT: E 191 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8624 (m-80) REVERT: E 287 LYS cc_start: 0.7803 (mttt) cc_final: 0.7416 (mttp) REVERT: F 151 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7109 (tt0) REVERT: G 15 ASP cc_start: 0.7987 (m-30) cc_final: 0.7614 (p0) REVERT: G 97 LYS cc_start: 0.8243 (mttt) cc_final: 0.7883 (mmmt) REVERT: G 233 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6772 (mtpp) REVERT: G 279 GLN cc_start: 0.7545 (tp-100) cc_final: 0.7297 (tp40) REVERT: G 282 GLU cc_start: 0.7947 (pm20) cc_final: 0.7263 (tm-30) REVERT: G 289 MET cc_start: 0.4598 (pmm) cc_final: 0.3790 (ppp) REVERT: H 4 ILE cc_start: 0.7648 (pt) cc_final: 0.7407 (mm) REVERT: H 180 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6798 (pp) REVERT: H 191 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: I 12 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7439 (ptt90) REVERT: I 202 LYS cc_start: 0.7842 (mptt) cc_final: 0.7163 (mtpt) REVERT: I 287 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.5511 (p90) REVERT: I 343 MET cc_start: 0.7317 (ppp) cc_final: 0.7108 (ppp) REVERT: I 351 ARG cc_start: 0.7248 (ptt180) cc_final: 0.7017 (ptp-110) REVERT: I 387 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7908 (mt-10) REVERT: I 413 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8701 (mp) REVERT: I 542 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7653 (tmm) REVERT: K 58 ASN cc_start: 0.7667 (m-40) cc_final: 0.7387 (m110) REVERT: K 84 GLN cc_start: 0.7977 (tp40) cc_final: 0.7318 (tp-100) REVERT: K 88 ASP cc_start: 0.7518 (m-30) cc_final: 0.6761 (m-30) REVERT: M 54 ASP cc_start: 0.6154 (t0) cc_final: 0.5569 (t0) REVERT: M 57 ASP cc_start: 0.5517 (t0) cc_final: 0.5122 (p0) outliers start: 57 outliers final: 36 residues processed: 301 average time/residue: 2.2845 time to fit residues: 803.9614 Evaluate side-chains 314 residues out of total 2574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 233 LYS Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 12 ARG Chi-restraints excluded: chain I residue 119 ASP Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 377 MET Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 439 GLN Chi-restraints excluded: chain I residue 542 MET Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 117 PHE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain M residue 41 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 223 optimal weight: 0.0060 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 249 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.100295 restraints weight = 100277.707| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.17 r_work: 0.3118 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25849 Z= 0.210 Angle : 0.545 15.735 35177 Z= 0.286 Chirality : 0.043 0.246 3907 Planarity : 0.004 0.080 4447 Dihedral : 13.982 177.994 4118 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.10 % Allowed : 18.18 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 3030 helix: 1.87 (0.16), residues: 1027 sheet: 0.10 (0.21), residues: 576 loop : -0.85 (0.17), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 67 HIS 0.004 0.001 HIS B 249 PHE 0.016 0.001 PHE A 126 TYR 0.012 0.001 TYR I 246 ARG 0.014 0.000 ARG B 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14084.43 seconds wall clock time: 241 minutes 43.73 seconds (14503.73 seconds total)