Starting phenix.real_space_refine on Mon Mar 25 15:12:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfs_27412/03_2024/8dfs_27412.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfs_27412/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfs_27412/03_2024/8dfs_27412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfs_27412/03_2024/8dfs_27412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfs_27412/03_2024/8dfs_27412.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfs_27412/03_2024/8dfs_27412.pdb" } 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 Residue "C GLU 126": "OE1" <-> "OE2" Residue "G PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 36": "OE1" <-> "OE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "M GLU 14": "OE1" <-> "OE2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "M GLU 81": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 20.77, per 1000 atoms: 0.42 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 - 3.50 Amino acid : False - 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: 38.13 Conformation dependent library (CDL) restraints added in 4.9 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: 21.13 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: 19.07 Time building geometry restraints manager: 39.72 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: 23.73 - 45.81: 2 45.81 - 67.88: 0 67.88 - 89.96: 1 89.96 - 112.03: 57866 112.03 - 134.10: 33149 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 1.850 nonbonded pdb=" HE ARG G 7 " pdb=" OE2 GLU G 9 " model vdw 1.537 1.850 nonbonded pdb=" O ASP K 69 " pdb="HH12 ARG K 72 " model vdw 1.543 1.850 ... (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 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: 4.600 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: 0.710 Extract box with map and model: 18.670 Check model and map are aligned: 0.650 Set scattering table: 0.430 Process input model: 163.620 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 205.350 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 6 poor density : 405 time to evaluate : 3.560 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: 3.0584 time to fit residues: 1436.4637 Evaluate side-chains 283 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 281 time to evaluate : 3.931 ------------------------------------------------------------------------------- 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: 0.5980 chunk 239 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 ASN E 279 GLN F 76 ASN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN I 353 HIS I 414 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25849 Z= 0.289 Angle : 0.643 17.316 35177 Z= 0.358 Chirality : 0.048 0.290 3907 Planarity : 0.004 0.047 4447 Dihedral : 17.567 178.517 4120 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.56 % Allowed : 14.65 % Favored : 82.79 % 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: 0.47 (0.15), residues: 3030 helix: 1.62 (0.16), residues: 1033 sheet: 0.41 (0.21), residues: 568 loop : -0.68 (0.17), residues: 1429 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 0.020 0.002 PHE I 287 TYR 0.015 0.001 TYR M 64 ARG 0.003 0.000 ARG H 133 *********************** 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 357 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 291 time to evaluate : 3.728 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: 0.8090 (ptpp) cc_final: 0.7768 (ptmm) REVERT: A 211 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6726 (tp30) REVERT: B 1 MET cc_start: 0.0515 (mmt) cc_final: -0.0259 (mmm) REVERT: B 17 GLU cc_start: 0.8053 (tt0) cc_final: 0.7636 (tt0) REVERT: B 103 LYS cc_start: 0.4937 (pttm) cc_final: 0.4529 (mmtt) REVERT: B 177 ARG cc_start: 0.7753 (ptp-110) cc_final: 0.7355 (ptp-110) REVERT: B 240 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7720 (tt0) REVERT: B 256 LYS cc_start: 0.8402 (mttp) cc_final: 0.7885 (mttm) REVERT: B 279 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: B 289 MET cc_start: 0.8072 (mmt) cc_final: 0.7828 (mmm) REVERT: C 63 GLU cc_start: 0.8163 (tt0) cc_final: 0.7762 (mm-30) REVERT: C 100 GLU cc_start: 0.7034 (mp0) cc_final: 0.6804 (tp30) REVERT: C 282 GLU cc_start: 0.7714 (pm20) cc_final: 0.7279 (tp30) REVERT: C 289 MET cc_start: 0.4587 (mpp) cc_final: 0.3690 (pp-130) REVERT: D 30 MET cc_start: 0.8188 (mtp) cc_final: 0.7965 (mtt) REVERT: D 80 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7397 (mm-30) REVERT: D 89 LYS cc_start: 0.8578 (mptt) cc_final: 0.7482 (ptmm) REVERT: D 94 LYS cc_start: 0.7688 (mttp) cc_final: 0.7266 (mttt) REVERT: D 97 LYS cc_start: 0.8895 (mttm) cc_final: 0.8393 (mppt) REVERT: D 133 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7159 (ttm-80) REVERT: E 126 GLU cc_start: 0.7484 (mp0) cc_final: 0.6847 (tp30) REVERT: E 177 ARG cc_start: 0.8297 (ptt-90) cc_final: 0.7541 (ptp90) REVERT: E 287 LYS cc_start: 0.7790 (mttt) cc_final: 0.7379 (mttp) REVERT: F 151 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6899 (tt0) REVERT: F 155 THR cc_start: 0.7450 (m) cc_final: 0.7177 (p) REVERT: F 177 ARG cc_start: 0.8021 (ptp90) cc_final: 0.7367 (ptp90) REVERT: G 97 LYS cc_start: 0.8149 (mttt) cc_final: 0.7754 (mmmt) REVERT: G 279 GLN cc_start: 0.7609 (tp-100) cc_final: 0.7347 (tp40) REVERT: G 287 LYS cc_start: 0.7226 (ptmt) cc_final: 0.7005 (pttt) REVERT: G 289 MET cc_start: 0.4442 (pmm) cc_final: 0.3740 (ppp) REVERT: H 4 ILE cc_start: 0.7469 (pt) cc_final: 0.7136 (mm) REVERT: H 70 GLN cc_start: 0.6837 (tp40) cc_final: 0.6621 (tp-100) REVERT: H 128 ASN cc_start: 0.7692 (t0) cc_final: 0.7462 (t0) REVERT: I 62 MET cc_start: 0.7477 (tpp) cc_final: 0.7093 (mtt) REVERT: I 202 LYS cc_start: 0.7769 (mptt) cc_final: 0.7098 (mtpt) REVERT: I 542 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7550 (tmm) REVERT: K 58 ASN cc_start: 0.7812 (m-40) cc_final: 0.7481 (m110) REVERT: K 84 GLN cc_start: 0.7900 (tp40) cc_final: 0.7459 (tp-100) REVERT: K 88 ASP cc_start: 0.7283 (m-30) cc_final: 0.6730 (m-30) REVERT: M 53 MET cc_start: 0.6980 (ttt) cc_final: 0.6454 (tmt) REVERT: M 57 ASP cc_start: 0.4997 (t70) cc_final: 0.4610 (m-30) outliers start: 66 outliers final: 33 residues processed: 330 average time/residue: 2.7407 time to fit residues: 1060.7456 Evaluate side-chains 302 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 265 time to evaluate : 3.866 ------------------------------------------------------------------------------- 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 174 THR Chi-restraints excluded: chain B residue 279 GLN 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 223 SER 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 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 229 MET Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 241 ASN 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 287 PHE 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 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 K residue 100 ASP Chi-restraints excluded: chain M residue 2 ILE 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: 0.7980 chunk 231 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 chunk 278 optimal weight: 5.9990 chunk 300 optimal weight: 7.9990 chunk 247 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN E 279 GLN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN I 414 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25849 Z= 0.249 Angle : 0.603 15.787 35177 Z= 0.334 Chirality : 0.047 0.308 3907 Planarity : 0.004 0.075 4447 Dihedral : 16.632 175.457 4118 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.72 % Allowed : 15.38 % Favored : 81.90 % 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: 0.54 (0.15), residues: 3030 helix: 1.75 (0.16), residues: 1020 sheet: 0.24 (0.21), residues: 610 loop : -0.60 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 211 HIS 0.005 0.001 HIS M 6 PHE 0.016 0.001 PHE J 105 TYR 0.012 0.001 TYR M 64 ARG 0.003 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 346 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 276 time to evaluate : 4.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.8129 (ptpp) cc_final: 0.7792 (ptmm) REVERT: A 143 ASP cc_start: 0.8220 (m-30) cc_final: 0.7791 (t0) REVERT: A 178 LEU cc_start: 0.7945 (pt) cc_final: 0.7649 (tp) REVERT: B 1 MET cc_start: 0.0562 (mmt) cc_final: -0.0207 (mmm) REVERT: B 17 GLU cc_start: 0.8020 (tt0) cc_final: 0.7615 (tt0) REVERT: B 103 LYS cc_start: 0.4926 (pttm) cc_final: 0.4525 (mmtt) REVERT: B 177 ARG cc_start: 0.7801 (ptp-110) cc_final: 0.7370 (ptp-110) REVERT: B 240 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7707 (tt0) REVERT: B 256 LYS cc_start: 0.8375 (mttp) cc_final: 0.7866 (mttm) REVERT: B 279 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7848 (mp10) REVERT: B 289 MET cc_start: 0.8085 (mmt) cc_final: 0.7817 (mmm) REVERT: C 77 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6157 (mp0) REVERT: C 231 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8513 (m) REVERT: C 282 GLU cc_start: 0.7719 (pm20) cc_final: 0.7276 (tp30) REVERT: C 289 MET cc_start: 0.4504 (mpp) cc_final: 0.3629 (pp-130) REVERT: D 30 MET cc_start: 0.8164 (mtp) cc_final: 0.7939 (mtt) REVERT: D 80 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7526 (mm-30) REVERT: D 89 LYS cc_start: 0.8571 (mptt) cc_final: 0.7497 (ptmm) REVERT: D 94 LYS cc_start: 0.7650 (mttp) cc_final: 0.7225 (mttt) REVERT: D 97 LYS cc_start: 0.8883 (mttm) cc_final: 0.8363 (mppt) REVERT: D 133 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7221 (ttm-80) REVERT: D 285 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: E 94 LYS cc_start: 0.8688 (mttt) cc_final: 0.8384 (mppt) REVERT: E 126 GLU cc_start: 0.7491 (mp0) cc_final: 0.7150 (tp30) REVERT: E 177 ARG cc_start: 0.8339 (ptt-90) cc_final: 0.7567 (ptp90) REVERT: E 287 LYS cc_start: 0.7820 (mttt) cc_final: 0.7411 (mttp) REVERT: F 151 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6852 (tt0) REVERT: F 155 THR cc_start: 0.7686 (m) cc_final: 0.7394 (p) REVERT: F 177 ARG cc_start: 0.8011 (ptp90) cc_final: 0.7367 (ptp90) REVERT: G 97 LYS cc_start: 0.8145 (mttt) cc_final: 0.7755 (mtpt) REVERT: G 229 MET cc_start: 0.8498 (mtm) cc_final: 0.8182 (mtm) REVERT: G 279 GLN cc_start: 0.7594 (tp-100) cc_final: 0.7316 (tp40) REVERT: G 289 MET cc_start: 0.4351 (pmm) cc_final: 0.3684 (ppp) REVERT: H 4 ILE cc_start: 0.7524 (pt) cc_final: 0.7180 (mm) REVERT: H 74 ILE cc_start: 0.7372 (mp) cc_final: 0.7146 (mt) REVERT: H 128 ASN cc_start: 0.7643 (t0) cc_final: 0.7294 (t0) REVERT: H 180 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6774 (pp) REVERT: I 202 LYS cc_start: 0.7739 (mptt) cc_final: 0.7087 (mtpt) REVERT: I 413 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8392 (mp) REVERT: I 542 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7562 (ptm) REVERT: I 586 SER cc_start: 0.7623 (OUTLIER) cc_final: 0.7210 (p) REVERT: K 54 MET cc_start: 0.7231 (ptm) cc_final: 0.7000 (ptm) REVERT: K 58 ASN cc_start: 0.7778 (m-40) cc_final: 0.7453 (m110) REVERT: K 84 GLN cc_start: 0.7986 (tp40) cc_final: 0.7466 (tp-100) REVERT: K 88 ASP cc_start: 0.7300 (m-30) cc_final: 0.6662 (m-30) REVERT: M 53 MET cc_start: 0.6997 (ttt) cc_final: 0.6522 (tmt) REVERT: M 57 ASP cc_start: 0.5353 (t0) cc_final: 0.4908 (m-30) REVERT: M 66 ASP cc_start: 0.6829 (t0) cc_final: 0.6202 (m-30) outliers start: 70 outliers final: 43 residues processed: 324 average time/residue: 2.8667 time to fit residues: 1102.9747 Evaluate side-chains 318 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 266 time to evaluate : 3.980 ------------------------------------------------------------------------------- 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 211 GLU Chi-restraints excluded: chain B residue 9 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 174 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 241 ASN 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 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 H residue 129 CYS Chi-restraints excluded: chain H residue 180 ILE 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 246 TYR Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 413 LEU 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 I residue 586 SER 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 38 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain M residue 24 ASP Chi-restraints excluded: chain M residue 46 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 295 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 264 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 70 GLN F 39 HIS ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25849 Z= 0.359 Angle : 0.615 15.981 35177 Z= 0.335 Chirality : 0.048 0.312 3907 Planarity : 0.005 0.046 4447 Dihedral : 15.975 177.653 4118 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.11 % Allowed : 15.62 % Favored : 81.27 % 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: 0.31 (0.15), residues: 3030 helix: 1.56 (0.16), residues: 1020 sheet: 0.25 (0.21), residues: 569 loop : -0.80 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 211 HIS 0.007 0.001 HIS I 384 PHE 0.020 0.002 PHE J 105 TYR 0.019 0.002 TYR M 64 ARG 0.004 0.000 ARG I 498 *********************** 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 346 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 266 time to evaluate : 3.741 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 114 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7466 (pp) REVERT: A 131 LYS cc_start: 0.8168 (ptpp) cc_final: 0.7874 (ptmm) REVERT: A 143 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7821 (t0) REVERT: A 178 LEU cc_start: 0.7927 (pt) cc_final: 0.7632 (tp) REVERT: A 207 LYS cc_start: 0.8802 (ttmm) cc_final: 0.8448 (tttm) REVERT: B 1 MET cc_start: 0.0488 (mmt) cc_final: -0.0266 (mmm) REVERT: B 9 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: B 17 GLU cc_start: 0.8018 (tt0) cc_final: 0.7605 (tt0) REVERT: B 103 LYS cc_start: 0.4857 (pttm) cc_final: 0.4466 (mmtt) REVERT: B 240 GLN cc_start: 0.8038 (tp-100) cc_final: 0.7735 (tt0) REVERT: B 256 LYS cc_start: 0.8379 (mttp) cc_final: 0.7904 (mttm) REVERT: B 279 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: C 77 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6229 (mp0) REVERT: C 282 GLU cc_start: 0.7788 (pm20) cc_final: 0.7350 (tp30) REVERT: C 289 MET cc_start: 0.4685 (mpp) cc_final: 0.3712 (pp-130) REVERT: D 30 MET cc_start: 0.8194 (mtp) cc_final: 0.7966 (mtt) REVERT: D 89 LYS cc_start: 0.8620 (mptt) cc_final: 0.7537 (ptmm) REVERT: D 94 LYS cc_start: 0.7661 (mttp) cc_final: 0.7228 (mttt) REVERT: D 97 LYS cc_start: 0.8893 (mttm) cc_final: 0.8388 (mppt) REVERT: D 133 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7267 (ttm-80) REVERT: D 285 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: E 177 ARG cc_start: 0.8371 (ptt-90) cc_final: 0.7597 (ptp90) REVERT: E 287 LYS cc_start: 0.7783 (mttt) cc_final: 0.7320 (mttp) REVERT: F 151 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7059 (tt0) REVERT: F 177 ARG cc_start: 0.8013 (ptp90) cc_final: 0.7727 (ptp90) REVERT: G 97 LYS cc_start: 0.8173 (mttt) cc_final: 0.7828 (mmmt) REVERT: G 279 GLN cc_start: 0.7587 (tp-100) cc_final: 0.7315 (tp40) REVERT: G 289 MET cc_start: 0.4378 (pmm) cc_final: 0.3655 (ppp) REVERT: H 4 ILE cc_start: 0.7529 (pt) cc_final: 0.7189 (mm) REVERT: H 74 ILE cc_start: 0.7390 (mp) cc_final: 0.7180 (mt) REVERT: H 94 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6654 (ptpt) REVERT: H 128 ASN cc_start: 0.7644 (t0) cc_final: 0.7239 (t0) REVERT: H 180 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6762 (pp) REVERT: I 12 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7388 (ptt90) REVERT: I 202 LYS cc_start: 0.7773 (mptt) cc_final: 0.7112 (mtpt) REVERT: I 346 MET cc_start: 0.7878 (ttm) cc_final: 0.7588 (mtm) REVERT: I 413 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8569 (mp) REVERT: I 542 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7572 (tmm) REVERT: I 586 SER cc_start: 0.7617 (OUTLIER) cc_final: 0.7183 (p) REVERT: K 58 ASN cc_start: 0.7671 (m-40) cc_final: 0.7391 (m110) REVERT: K 84 GLN cc_start: 0.7940 (tp40) cc_final: 0.7322 (tp-100) REVERT: K 88 ASP cc_start: 0.7388 (m-30) cc_final: 0.6725 (m-30) REVERT: M 1 MET cc_start: 0.3705 (tpp) cc_final: 0.2735 (tpp) REVERT: M 57 ASP cc_start: 0.5273 (t0) cc_final: 0.4796 (m-30) REVERT: M 60 SER cc_start: 0.5707 (m) cc_final: 0.5499 (m) REVERT: M 66 ASP cc_start: 0.6833 (t0) cc_final: 0.6170 (m-30) outliers start: 80 outliers final: 51 residues processed: 321 average time/residue: 2.7248 time to fit residues: 1026.7825 Evaluate side-chains 323 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 259 time to evaluate : 3.709 ------------------------------------------------------------------------------- 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 113 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 9 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 174 THR Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 231 SER 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 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 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 104 ARG Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 241 ASN Chi-restraints excluded: chain G residue 282 GLU Chi-restraints excluded: chain H residue 94 LYS Chi-restraints excluded: chain H residue 180 ILE 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 246 TYR 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 514 GLU Chi-restraints excluded: chain I residue 542 MET Chi-restraints excluded: chain I residue 586 SER 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 Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain M residue 24 ASP Chi-restraints excluded: chain M residue 46 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.0040 chunk 167 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 220 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 204 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25849 Z= 0.188 Angle : 0.553 15.734 35177 Z= 0.296 Chirality : 0.044 0.270 3907 Planarity : 0.004 0.041 4447 Dihedral : 15.482 170.621 4118 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.72 % Allowed : 16.16 % Favored : 81.12 % 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: 0.53 (0.15), residues: 3030 helix: 1.79 (0.16), residues: 1026 sheet: 0.13 (0.21), residues: 612 loop : -0.60 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 67 HIS 0.003 0.001 HIS B 249 PHE 0.014 0.001 PHE I 105 TYR 0.021 0.001 TYR M 64 ARG 0.002 0.000 ARG H 268 *********************** 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 fitting. rotamer outliers: 70 poor density : 275 time to evaluate : 4.472 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: 0.8126 (ptpp) cc_final: 0.7761 (ptmm) REVERT: A 143 ASP cc_start: 0.8273 (m-30) cc_final: 0.7860 (t0) REVERT: A 178 LEU cc_start: 0.7907 (pt) cc_final: 0.7609 (tp) REVERT: B 1 MET cc_start: 0.0495 (mmt) cc_final: -0.0254 (mmm) REVERT: B 17 GLU cc_start: 0.7983 (tt0) cc_final: 0.7582 (tt0) REVERT: B 103 LYS cc_start: 0.4857 (pttm) cc_final: 0.4490 (mmtt) REVERT: B 240 GLN cc_start: 0.8013 (tp-100) cc_final: 0.7765 (tt0) REVERT: B 256 LYS cc_start: 0.8383 (mttp) cc_final: 0.7935 (mttm) REVERT: B 279 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7827 (mp10) REVERT: C 231 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8510 (m) REVERT: C 282 GLU cc_start: 0.7735 (pm20) cc_final: 0.7295 (tp30) REVERT: C 289 MET cc_start: 0.4535 (mpp) cc_final: 0.3536 (pp-130) REVERT: D 30 MET cc_start: 0.8193 (mtp) cc_final: 0.7958 (mtt) REVERT: D 80 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7544 (mm-30) REVERT: D 89 LYS cc_start: 0.8601 (mptt) cc_final: 0.7527 (ptmm) REVERT: D 94 LYS cc_start: 0.7642 (mttp) cc_final: 0.7208 (mttt) REVERT: D 97 LYS cc_start: 0.8884 (mttm) cc_final: 0.8361 (mppt) REVERT: D 133 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7278 (ttm-80) REVERT: D 285 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: E 94 LYS cc_start: 0.8681 (mttt) cc_final: 0.8385 (mppt) REVERT: E 177 ARG cc_start: 0.8324 (ptt-90) cc_final: 0.7570 (ptp90) REVERT: E 191 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8607 (m-80) REVERT: E 287 LYS cc_start: 0.7777 (mttt) cc_final: 0.7365 (mttp) REVERT: G 97 LYS cc_start: 0.8170 (mttt) cc_final: 0.7820 (mmmt) REVERT: G 279 GLN cc_start: 0.7561 (tp-100) cc_final: 0.7284 (tp40) REVERT: G 289 MET cc_start: 0.4405 (pmm) cc_final: 0.3570 (ppp) REVERT: H 4 ILE cc_start: 0.7526 (pt) cc_final: 0.7206 (mm) REVERT: H 94 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6715 (ptpt) REVERT: H 180 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6790 (pp) REVERT: H 191 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8342 (m-80) REVERT: I 202 LYS cc_start: 0.7729 (mptt) cc_final: 0.7093 (mtpt) REVERT: I 346 MET cc_start: 0.7868 (ttm) cc_final: 0.7504 (mtm) REVERT: I 413 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8576 (mp) REVERT: I 542 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7605 (tmm) REVERT: K 58 ASN cc_start: 0.7603 (m-40) cc_final: 0.7289 (m110) REVERT: K 84 GLN cc_start: 0.7969 (tp40) cc_final: 0.7298 (tp-100) REVERT: K 88 ASP cc_start: 0.7490 (m-30) cc_final: 0.6849 (m-30) REVERT: M 57 ASP cc_start: 0.5219 (t0) cc_final: 0.4725 (p0) REVERT: M 66 ASP cc_start: 0.6724 (t0) cc_final: 0.6094 (m-30) outliers start: 70 outliers final: 36 residues processed: 319 average time/residue: 2.7820 time to fit residues: 1043.2069 Evaluate side-chains 308 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 262 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 217 MET Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 241 ASN 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 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 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 241 ASN Chi-restraints excluded: chain H residue 94 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 119 ASP Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 246 TYR 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 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 117 PHE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain M residue 24 ASP 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: 3.9990 chunk 58 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 25849 Z= 0.399 Angle : 0.616 16.030 35177 Z= 0.331 Chirality : 0.048 0.309 3907 Planarity : 0.005 0.064 4447 Dihedral : 15.057 172.059 4118 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.19 % Allowed : 16.63 % Favored : 80.19 % 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: 0.20 (0.15), residues: 3030 helix: 1.53 (0.16), residues: 1026 sheet: 0.13 (0.21), residues: 587 loop : -0.90 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 67 HIS 0.008 0.001 HIS I 384 PHE 0.020 0.002 PHE J 105 TYR 0.015 0.002 TYR F 68 ARG 0.007 0.000 ARG I 209 *********************** 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 345 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 263 time to evaluate : 3.714 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 143 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7896 (t0) REVERT: A 178 LEU cc_start: 0.7875 (pt) cc_final: 0.7586 (tp) REVERT: A 207 LYS cc_start: 0.8808 (ttmm) cc_final: 0.8483 (tttm) REVERT: B 1 MET cc_start: 0.0544 (mmt) cc_final: -0.0228 (mmm) REVERT: B 9 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: B 17 GLU cc_start: 0.8023 (tt0) cc_final: 0.7612 (tt0) REVERT: B 103 LYS cc_start: 0.4940 (pttm) cc_final: 0.4522 (mmtt) REVERT: B 240 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7723 (tt0) REVERT: B 256 LYS cc_start: 0.8350 (mttp) cc_final: 0.7882 (mttm) REVERT: B 279 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7697 (mp10) REVERT: C 77 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6219 (mp0) REVERT: C 279 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.6528 (mm-40) REVERT: C 282 GLU cc_start: 0.7839 (pm20) cc_final: 0.7440 (tp30) REVERT: C 289 MET cc_start: 0.4845 (mpp) cc_final: 0.3804 (pp-130) REVERT: D 89 LYS cc_start: 0.8627 (mptt) cc_final: 0.7599 (ptmm) REVERT: D 94 LYS cc_start: 0.7624 (mttp) cc_final: 0.7167 (mttt) REVERT: D 97 LYS cc_start: 0.8902 (mttm) cc_final: 0.8396 (mppt) REVERT: D 133 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7274 (ttm-80) REVERT: D 285 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: E 137 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: E 177 ARG cc_start: 0.8395 (ptt-90) cc_final: 0.7636 (ptp90) REVERT: E 191 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8655 (m-80) REVERT: E 287 LYS cc_start: 0.7840 (mttt) cc_final: 0.7344 (mttp) REVERT: G 97 LYS cc_start: 0.8185 (mttt) cc_final: 0.7815 (mmmt) REVERT: G 279 GLN cc_start: 0.7564 (tp-100) cc_final: 0.7296 (tp40) REVERT: G 289 MET cc_start: 0.4393 (pmm) cc_final: 0.3625 (ppp) REVERT: H 4 ILE cc_start: 0.7522 (pt) cc_final: 0.7200 (mm) REVERT: H 128 ASN cc_start: 0.7514 (t0) cc_final: 0.7193 (t0) REVERT: H 180 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6790 (pp) REVERT: H 191 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8460 (m-80) REVERT: I 12 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7438 (ptt90) REVERT: I 202 LYS cc_start: 0.7734 (mptt) cc_final: 0.7082 (mtpt) REVERT: I 346 MET cc_start: 0.7882 (ttm) cc_final: 0.7619 (mtm) REVERT: I 413 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8578 (mp) REVERT: I 542 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7596 (tmm) REVERT: I 586 SER cc_start: 0.7665 (OUTLIER) cc_final: 0.7215 (p) REVERT: K 53 HIS cc_start: 0.6442 (OUTLIER) cc_final: 0.5635 (p-80) REVERT: K 58 ASN cc_start: 0.7606 (m-40) cc_final: 0.7324 (m110) REVERT: K 84 GLN cc_start: 0.7948 (tp40) cc_final: 0.7424 (tp-100) REVERT: K 88 ASP cc_start: 0.7508 (m-30) cc_final: 0.6934 (m-30) REVERT: M 57 ASP cc_start: 0.5261 (t0) cc_final: 0.4817 (p0) outliers start: 82 outliers final: 48 residues processed: 315 average time/residue: 2.7749 time to fit residues: 1035.8666 Evaluate side-chains 317 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 253 time to evaluate : 3.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 131 GLN 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 77 GLU Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 279 GLN 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 285 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 137 GLN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain F residue 9 GLU 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 241 ASN Chi-restraints excluded: chain G residue 282 GLU 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 124 LEU Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 341 ASP 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 514 GLU Chi-restraints excluded: chain I residue 542 MET Chi-restraints excluded: chain I residue 586 SER 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 36 ILE Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 53 HIS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 64 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 ASN E 76 ASN I 174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25849 Z= 0.236 Angle : 0.560 15.735 35177 Z= 0.298 Chirality : 0.045 0.269 3907 Planarity : 0.004 0.043 4447 Dihedral : 14.974 171.039 4118 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.56 % Allowed : 17.44 % Favored : 79.99 % 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: 1.68 (0.16), residues: 1026 sheet: 0.03 (0.20), residues: 612 loop : -0.75 (0.17), residues: 1392 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 0.013 0.001 PHE J 105 TYR 0.012 0.001 TYR M 64 ARG 0.005 0.000 ARG I 209 *********************** 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 332 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 266 time to evaluate : 3.989 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 114 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7635 (pp) REVERT: A 143 ASP cc_start: 0.8276 (m-30) cc_final: 0.7882 (t0) REVERT: A 178 LEU cc_start: 0.7853 (pt) cc_final: 0.7562 (tp) REVERT: A 207 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8470 (tttm) REVERT: B 1 MET cc_start: 0.0549 (mmt) cc_final: -0.0222 (mmm) REVERT: B 17 GLU cc_start: 0.7969 (tt0) cc_final: 0.7559 (tt0) REVERT: B 103 LYS cc_start: 0.4943 (pttm) cc_final: 0.4525 (mmtt) REVERT: B 240 GLN cc_start: 0.7982 (tp-100) cc_final: 0.7714 (tt0) REVERT: B 256 LYS cc_start: 0.8350 (mttp) cc_final: 0.7869 (mttm) REVERT: B 279 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: C 77 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6219 (mp0) REVERT: C 282 GLU cc_start: 0.7821 (pm20) cc_final: 0.7382 (tp30) REVERT: C 289 MET cc_start: 0.4562 (mpp) cc_final: 0.3431 (pp-130) REVERT: D 80 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7552 (mm-30) REVERT: D 88 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7785 (mp) REVERT: D 89 LYS cc_start: 0.8585 (mptt) cc_final: 0.7514 (ptmm) REVERT: D 94 LYS cc_start: 0.7614 (mttp) cc_final: 0.7164 (mttt) REVERT: D 97 LYS cc_start: 0.8898 (mttm) cc_final: 0.8393 (mppt) REVERT: D 133 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7324 (ttm-80) REVERT: D 285 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: E 137 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: E 177 ARG cc_start: 0.8347 (ptt-90) cc_final: 0.7612 (ptp90) REVERT: E 191 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8618 (m-80) REVERT: E 287 LYS cc_start: 0.7903 (mttt) cc_final: 0.7447 (mttp) REVERT: F 30 MET cc_start: 0.7905 (mtp) cc_final: 0.7602 (mmm) REVERT: G 97 LYS cc_start: 0.8198 (mttt) cc_final: 0.7820 (mmmt) REVERT: G 279 GLN cc_start: 0.7547 (tp-100) cc_final: 0.7278 (tp40) REVERT: G 289 MET cc_start: 0.4346 (pmm) cc_final: 0.3608 (ppp) REVERT: H 4 ILE cc_start: 0.7606 (pt) cc_final: 0.7339 (mm) REVERT: H 128 ASN cc_start: 0.7462 (t0) cc_final: 0.7210 (t0) REVERT: H 180 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6794 (pp) REVERT: H 191 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: I 202 LYS cc_start: 0.7710 (mptt) cc_final: 0.7060 (mtpt) REVERT: I 413 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8598 (mp) REVERT: I 542 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7629 (tmm) REVERT: K 58 ASN cc_start: 0.7589 (m-40) cc_final: 0.7308 (m110) REVERT: K 84 GLN cc_start: 0.8055 (tp40) cc_final: 0.7357 (tp-100) REVERT: K 88 ASP cc_start: 0.7556 (m-30) cc_final: 0.6972 (m-30) REVERT: M 57 ASP cc_start: 0.5331 (t0) cc_final: 0.5088 (p0) outliers start: 66 outliers final: 41 residues processed: 306 average time/residue: 2.6612 time to fit residues: 959.8193 Evaluate side-chains 310 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 257 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 114 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 279 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 88 LEU 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 223 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 137 GLN Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain F residue 9 GLU 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 241 ASN 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 119 ASP Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 345 ASP 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 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 117 PHE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain M residue 24 ASP Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 64 TYR 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: 2.9990 chunk 176 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.7327 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25849 Z= 0.309 Angle : 0.576 15.822 35177 Z= 0.307 Chirality : 0.045 0.274 3907 Planarity : 0.004 0.043 4447 Dihedral : 14.881 172.546 4118 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.80 % Allowed : 17.56 % Favored : 79.64 % 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: 0.25 (0.15), residues: 3030 helix: 1.61 (0.16), residues: 1027 sheet: -0.04 (0.20), residues: 631 loop : -0.82 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 67 HIS 0.006 0.001 HIS I 384 PHE 0.021 0.002 PHE I 126 TYR 0.014 0.001 TYR F 68 ARG 0.005 0.000 ARG I 209 *********************** 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 fitting. rotamer outliers: 72 poor density : 257 time to evaluate : 3.943 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 114 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.7667 (pp) REVERT: A 143 ASP cc_start: 0.8281 (m-30) cc_final: 0.7895 (t0) REVERT: A 178 LEU cc_start: 0.7859 (pt) cc_final: 0.7562 (tp) REVERT: A 207 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8470 (tttm) REVERT: B 1 MET cc_start: 0.0713 (mmt) cc_final: -0.0033 (mmm) REVERT: B 17 GLU cc_start: 0.8001 (tt0) cc_final: 0.7589 (tt0) REVERT: B 240 GLN cc_start: 0.7982 (tp-100) cc_final: 0.7667 (tt0) REVERT: B 256 LYS cc_start: 0.8501 (mttp) cc_final: 0.8072 (mttm) REVERT: B 279 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: C 77 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: C 282 GLU cc_start: 0.7853 (pm20) cc_final: 0.7449 (tp30) REVERT: C 289 MET cc_start: 0.4717 (mpp) cc_final: 0.3935 (pp-130) REVERT: D 88 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7839 (mp) REVERT: D 89 LYS cc_start: 0.8611 (mptt) cc_final: 0.7581 (ptmm) REVERT: D 94 LYS cc_start: 0.7620 (mttp) cc_final: 0.7176 (mttt) REVERT: D 97 LYS cc_start: 0.8897 (mttm) cc_final: 0.8387 (mppt) REVERT: D 133 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7319 (ttm-80) REVERT: D 285 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: E 137 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7915 (pt0) REVERT: E 177 ARG cc_start: 0.8353 (ptt-90) cc_final: 0.7563 (ptp90) REVERT: E 191 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8628 (m-80) REVERT: E 287 LYS cc_start: 0.7786 (mttt) cc_final: 0.7369 (mttp) REVERT: F 30 MET cc_start: 0.7913 (mtp) cc_final: 0.7603 (mmm) REVERT: G 97 LYS cc_start: 0.8213 (mttt) cc_final: 0.7835 (mmmt) REVERT: G 279 GLN cc_start: 0.7557 (tp-100) cc_final: 0.7277 (tp40) REVERT: G 289 MET cc_start: 0.4376 (pmm) cc_final: 0.3693 (ppp) REVERT: H 4 ILE cc_start: 0.7634 (pt) cc_final: 0.7333 (mm) REVERT: H 128 ASN cc_start: 0.7482 (t0) cc_final: 0.7210 (t0) REVERT: H 138 MET cc_start: 0.7905 (ptp) cc_final: 0.7364 (ptp) REVERT: H 180 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6792 (pp) REVERT: H 191 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8407 (m-80) REVERT: I 202 LYS cc_start: 0.7803 (mptt) cc_final: 0.7133 (mtpt) REVERT: I 413 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8613 (mp) REVERT: I 542 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7625 (tmm) REVERT: K 58 ASN cc_start: 0.7586 (m-40) cc_final: 0.7337 (m110) REVERT: K 84 GLN cc_start: 0.8012 (tp40) cc_final: 0.7349 (tp-100) REVERT: K 88 ASP cc_start: 0.7610 (m-30) cc_final: 0.7061 (m-30) REVERT: M 57 ASP cc_start: 0.5392 (t0) cc_final: 0.5155 (p0) outliers start: 72 outliers final: 43 residues processed: 302 average time/residue: 2.7103 time to fit residues: 962.9380 Evaluate side-chains 308 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 253 time to evaluate : 3.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 204 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 279 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 88 LEU 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 285 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 137 GLN 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 9 GLU 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 241 ASN 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 I residue 3 LEU Chi-restraints excluded: chain I residue 119 ASP Chi-restraints excluded: chain I residue 246 TYR 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 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 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 24 ASP Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 64 TYR 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: 1.9990 chunk 274 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 215 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 259 optimal weight: 1.9990 chunk 273 optimal weight: 0.5980 chunk 180 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25849 Z= 0.214 Angle : 0.545 15.692 35177 Z= 0.289 Chirality : 0.044 0.267 3907 Planarity : 0.004 0.043 4447 Dihedral : 14.773 172.640 4118 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.37 % Allowed : 18.03 % Favored : 79.60 % 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: 1.79 (0.16), residues: 1027 sheet: 0.00 (0.20), residues: 612 loop : -0.73 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 67 HIS 0.004 0.001 HIS B 249 PHE 0.016 0.001 PHE I 105 TYR 0.011 0.001 TYR F 68 ARG 0.005 0.000 ARG I 209 *********************** 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 329 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 268 time to evaluate : 3.867 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 114 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7624 (pp) REVERT: A 178 LEU cc_start: 0.7812 (pt) cc_final: 0.7525 (tp) REVERT: A 207 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8472 (tttm) REVERT: B 1 MET cc_start: 0.0798 (mmt) cc_final: 0.0035 (mmm) REVERT: B 17 GLU cc_start: 0.7960 (tt0) cc_final: 0.7546 (tt0) REVERT: B 30 MET cc_start: 0.8308 (mtp) cc_final: 0.8094 (mtp) REVERT: B 240 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7623 (tt0) REVERT: B 256 LYS cc_start: 0.8499 (mttp) cc_final: 0.8073 (mttm) REVERT: B 279 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: C 77 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6221 (mp0) REVERT: C 231 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8474 (m) REVERT: C 282 GLU cc_start: 0.7822 (pm20) cc_final: 0.7422 (tp30) REVERT: C 289 MET cc_start: 0.4574 (mpp) cc_final: 0.3411 (pp-130) REVERT: D 80 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7560 (mt-10) REVERT: D 89 LYS cc_start: 0.8598 (mptt) cc_final: 0.7533 (ptmm) REVERT: D 94 LYS cc_start: 0.7609 (mttp) cc_final: 0.7168 (mttt) REVERT: D 97 LYS cc_start: 0.8903 (mttm) cc_final: 0.8396 (mppt) REVERT: D 133 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7289 (ttm-80) REVERT: D 285 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: E 137 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7752 (pt0) REVERT: E 177 ARG cc_start: 0.8327 (ptt-90) cc_final: 0.7560 (ptp90) REVERT: E 191 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8604 (m-80) REVERT: E 287 LYS cc_start: 0.7840 (mttt) cc_final: 0.7449 (mttp) REVERT: F 30 MET cc_start: 0.7906 (mtp) cc_final: 0.7595 (mmm) REVERT: G 97 LYS cc_start: 0.8215 (mttt) cc_final: 0.7880 (mmmt) REVERT: G 279 GLN cc_start: 0.7595 (tp-100) cc_final: 0.7354 (tp40) REVERT: G 289 MET cc_start: 0.4342 (pmm) cc_final: 0.3617 (ppp) REVERT: H 4 ILE cc_start: 0.7690 (pt) cc_final: 0.7371 (mm) REVERT: H 128 ASN cc_start: 0.7450 (t0) cc_final: 0.7207 (t0) REVERT: H 180 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6790 (pp) REVERT: H 191 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8444 (m-80) REVERT: I 202 LYS cc_start: 0.7811 (mptt) cc_final: 0.7132 (mtpt) REVERT: I 287 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.5680 (p90) REVERT: I 413 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8604 (mp) REVERT: I 542 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7653 (tmm) REVERT: K 58 ASN cc_start: 0.7536 (m-40) cc_final: 0.7301 (m110) REVERT: K 84 GLN cc_start: 0.8002 (tp40) cc_final: 0.7336 (tp-100) REVERT: K 88 ASP cc_start: 0.7609 (m-30) cc_final: 0.7044 (m-30) REVERT: M 53 MET cc_start: 0.6865 (ttt) cc_final: 0.6313 (tmt) REVERT: M 57 ASP cc_start: 0.5399 (t0) cc_final: 0.5164 (p0) outliers start: 61 outliers final: 38 residues processed: 305 average time/residue: 2.7731 time to fit residues: 993.1064 Evaluate side-chains 309 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 258 time to evaluate : 3.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 204 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 C residue 77 GLU Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 231 SER 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 191 PHE Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 137 GLN 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 9 GLU 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 241 ASN 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 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 246 TYR 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 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 117 PHE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain M residue 24 ASP Chi-restraints excluded: chain M residue 64 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 304 optimal weight: 0.7980 chunk 280 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25849 Z= 0.211 Angle : 0.540 15.684 35177 Z= 0.286 Chirality : 0.044 0.267 3907 Planarity : 0.004 0.073 4447 Dihedral : 14.717 173.857 4118 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.18 % Allowed : 18.38 % Favored : 79.45 % 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: 0.48 (0.15), residues: 3030 helix: 1.88 (0.16), residues: 1027 sheet: 0.04 (0.21), residues: 604 loop : -0.72 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 67 HIS 0.004 0.001 HIS B 249 PHE 0.023 0.001 PHE I 126 TYR 0.012 0.001 TYR F 68 ARG 0.012 0.000 ARG K 113 ********************** 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 321 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 265 time to evaluate : 3.926 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 114 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7619 (pp) REVERT: A 178 LEU cc_start: 0.7811 (pt) cc_final: 0.7519 (tp) REVERT: A 207 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8471 (tttm) REVERT: B 1 MET cc_start: 0.0800 (mmt) cc_final: 0.0036 (mmm) REVERT: B 17 GLU cc_start: 0.7966 (tt0) cc_final: 0.7547 (tt0) REVERT: B 30 MET cc_start: 0.8302 (mtp) cc_final: 0.8085 (mtp) REVERT: B 240 GLN cc_start: 0.7943 (tp-100) cc_final: 0.7623 (mt0) REVERT: B 256 LYS cc_start: 0.8510 (mttp) cc_final: 0.8092 (mttm) REVERT: B 279 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7755 (mp10) REVERT: C 77 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6235 (mp0) REVERT: C 231 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8470 (m) REVERT: C 282 GLU cc_start: 0.7780 (pm20) cc_final: 0.7392 (tp30) REVERT: C 289 MET cc_start: 0.4561 (mpp) cc_final: 0.3792 (pp-130) REVERT: D 72 LYS cc_start: 0.7288 (tptp) cc_final: 0.6532 (tppt) REVERT: D 80 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7551 (mt-10) REVERT: D 89 LYS cc_start: 0.8598 (mptt) cc_final: 0.7533 (ptmm) REVERT: D 94 LYS cc_start: 0.7607 (mttp) cc_final: 0.7161 (mttt) REVERT: D 97 LYS cc_start: 0.8901 (mttm) cc_final: 0.8395 (mppt) REVERT: D 133 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7272 (ttm-80) REVERT: D 285 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: E 137 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7801 (pt0) REVERT: E 177 ARG cc_start: 0.8327 (ptt-90) cc_final: 0.7552 (ptp90) REVERT: E 191 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8620 (m-80) REVERT: E 287 LYS cc_start: 0.7825 (mttt) cc_final: 0.7452 (mttp) REVERT: F 30 MET cc_start: 0.7878 (mtp) cc_final: 0.7576 (mmm) REVERT: G 15 ASP cc_start: 0.8206 (m-30) cc_final: 0.7687 (p0) REVERT: G 97 LYS cc_start: 0.8211 (mttt) cc_final: 0.7878 (mmmt) REVERT: G 276 THR cc_start: 0.7223 (m) cc_final: 0.6771 (p) REVERT: G 279 GLN cc_start: 0.7582 (tp-100) cc_final: 0.7343 (tp40) REVERT: G 289 MET cc_start: 0.4405 (pmm) cc_final: 0.3797 (ppp) REVERT: H 4 ILE cc_start: 0.7702 (pt) cc_final: 0.7377 (mm) REVERT: H 128 ASN cc_start: 0.7410 (t0) cc_final: 0.7149 (t0) REVERT: H 180 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6780 (pp) REVERT: H 191 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8383 (m-80) REVERT: I 12 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7432 (ptt90) REVERT: I 202 LYS cc_start: 0.7821 (mptt) cc_final: 0.7136 (mtpt) REVERT: I 287 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.5667 (p90) REVERT: I 351 ARG cc_start: 0.7237 (ptt180) cc_final: 0.6998 (ptp-110) REVERT: I 413 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8611 (mp) REVERT: I 542 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7636 (tmm) REVERT: K 58 ASN cc_start: 0.7527 (m-40) cc_final: 0.7290 (m110) REVERT: K 84 GLN cc_start: 0.8006 (tp40) cc_final: 0.7375 (tp-100) REVERT: K 88 ASP cc_start: 0.7580 (m-30) cc_final: 0.7008 (m-30) REVERT: M 53 MET cc_start: 0.6863 (ttt) cc_final: 0.6306 (tmt) REVERT: M 57 ASP cc_start: 0.5198 (t0) cc_final: 0.4950 (p0) outliers start: 56 outliers final: 39 residues processed: 301 average time/residue: 2.9369 time to fit residues: 1042.8205 Evaluate side-chains 317 residues out of total 2574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 264 time to evaluate : 3.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 204 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 77 GLU Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 231 SER 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 223 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain E residue 9 GLU Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 137 GLN 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 9 GLU 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 241 ASN 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 246 TYR 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 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 117 PHE Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain M residue 24 ASP Chi-restraints excluded: chain M residue 64 TYR 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: 3.9990 chunk 223 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.134246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100213 restraints weight = 100095.810| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.85 r_work: 0.3118 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25849 Z= 0.251 Angle : 0.556 15.736 35177 Z= 0.293 Chirality : 0.044 0.275 3907 Planarity : 0.004 0.056 4447 Dihedral : 14.689 174.757 4118 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.33 % Allowed : 18.30 % Favored : 79.37 % 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: 0.44 (0.15), residues: 3030 helix: 1.84 (0.16), residues: 1027 sheet: 0.01 (0.20), residues: 611 loop : -0.74 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 67 HIS 0.005 0.001 HIS I 384 PHE 0.019 0.001 PHE A 126 TYR 0.013 0.001 TYR F 68 ARG 0.008 0.000 ARG K 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17737.19 seconds wall clock time: 310 minutes 38.35 seconds (18638.35 seconds total)