Starting phenix.real_space_refine on Wed Jul 24 15:26:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd2_29000/07_2024/8fd2_29000.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd2_29000/07_2024/8fd2_29000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd2_29000/07_2024/8fd2_29000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd2_29000/07_2024/8fd2_29000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd2_29000/07_2024/8fd2_29000.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fd2_29000/07_2024/8fd2_29000.cif" } resolution = 3.65 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 408 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 63 5.49 5 S 94 5.16 5 C 16320 2.51 5 N 4376 2.21 5 O 4944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 18": "OE1" <-> "OE2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E GLU 257": "OE1" <-> "OE2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "F GLU 251": "OE1" <-> "OE2" Residue "G GLU 257": "OE1" <-> "OE2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "J GLU 6": "OE1" <-> "OE2" Residue "J GLU 7": "OE1" <-> "OE2" Residue "J GLU 35": "OE1" <-> "OE2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 25797 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1745 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "B" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1727 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 202} Chain: "C" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "D" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2345 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 10, 'TRANS': 277} Chain breaks: 1 Chain: "F" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "G" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2351 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 1 Chain: "H" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2420 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 1 Chain: "I" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4147 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "L" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1342 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 10, 'rna3p_pur': 18, 'rna3p_pyr': 20} Link IDs: {'rna2p': 25, 'rna3p': 37} Time building chain proxies: 13.13, per 1000 atoms: 0.51 Number of scatterers: 25797 At special positions: 0 Unit cell: (102.238, 119.102, 196.044, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 P 63 15.00 O 4944 8.00 N 4376 7.00 C 16320 6.00 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: 10.65 Conformation dependent library (CDL) restraints added in 4.9 seconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5590 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 51 sheets defined 39.4% alpha, 23.4% beta 2 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 9.50 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.584A pdb=" N TRP A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 40 through 45 removed outlier: 4.325A pdb=" N GLU B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 45 " --> pdb=" O PRO B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.817A pdb=" N MET B 204 " --> pdb=" O ARG B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.618A pdb=" N THR B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 56 through 71 removed outlier: 3.730A pdb=" N ILE C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 196 through 206 removed outlier: 3.573A pdb=" N MET C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.645A pdb=" N SER C 214 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.552A pdb=" N GLY C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.662A pdb=" N ASP C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 318 Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 56 through 71 removed outlier: 3.577A pdb=" N ILE D 60 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.522A pdb=" N MET D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.784A pdb=" N GLY D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 277 through 284 removed outlier: 4.084A pdb=" N ASP D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 301 through 318 Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.598A pdb=" N ILE E 60 " --> pdb=" O GLY E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 189 through 191 No H-bonds generated for 'chain 'E' and resid 189 through 191' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 196 through 206 removed outlier: 3.522A pdb=" N MET E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.883A pdb=" N GLY E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 277 through 284 removed outlier: 4.093A pdb=" N ASP E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 296 Processing helix chain 'E' and resid 301 through 318 Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.644A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 105 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 196 through 206 removed outlier: 3.773A pdb=" N MET F 200 " --> pdb=" O ARG F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.826A pdb=" N GLY F 265 " --> pdb=" O GLU F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.956A pdb=" N ASP F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 301 through 318 Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 56 through 71 removed outlier: 3.747A pdb=" N ILE G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 105 Processing helix chain 'G' and resid 189 through 191 No H-bonds generated for 'chain 'G' and resid 189 through 191' Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 196 through 206 removed outlier: 3.644A pdb=" N MET G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 264 Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 277 through 284 removed outlier: 4.009A pdb=" N ASP G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 318 Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 56 through 71 removed outlier: 3.531A pdb=" N ILE H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 104 Processing helix chain 'H' and resid 109 through 112 Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 196 through 206 removed outlier: 3.573A pdb=" N MET H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.679A pdb=" N GLY H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 270 No H-bonds generated for 'chain 'H' and resid 268 through 270' Processing helix chain 'H' and resid 277 through 285 removed outlier: 3.920A pdb=" N ASP H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 296 removed outlier: 3.603A pdb=" N LYS H 295 " --> pdb=" O PRO H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 317 Processing helix chain 'I' and resid 19 through 40 Processing helix chain 'I' and resid 46 through 50 removed outlier: 3.747A pdb=" N ILE I 50 " --> pdb=" O GLY I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.585A pdb=" N ALA I 70 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 113 Processing helix chain 'I' and resid 116 through 118 No H-bonds generated for 'chain 'I' and resid 116 through 118' Processing helix chain 'I' and resid 148 through 157 removed outlier: 5.400A pdb=" N ALA I 153 " --> pdb=" O HIS I 149 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLU I 154 " --> pdb=" O GLN I 150 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS I 155 " --> pdb=" O THR I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 187 removed outlier: 3.505A pdb=" N GLN I 187 " --> pdb=" O ALA I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 238 through 250 Processing helix chain 'I' and resid 251 through 252 No H-bonds generated for 'chain 'I' and resid 251 through 252' Processing helix chain 'I' and resid 253 through 256 Processing helix chain 'I' and resid 261 through 270 removed outlier: 3.538A pdb=" N TYR I 270 " --> pdb=" O GLY I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 325 Processing helix chain 'I' and resid 342 through 355 Processing helix chain 'I' and resid 361 through 367 removed outlier: 3.667A pdb=" N LYS I 365 " --> pdb=" O ASN I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 382 removed outlier: 4.030A pdb=" N GLN I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU I 379 " --> pdb=" O LEU I 375 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE I 380 " --> pdb=" O PHE I 376 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER I 381 " --> pdb=" O ASN I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 392 Processing helix chain 'I' and resid 397 through 421 removed outlier: 3.686A pdb=" N ILE I 417 " --> pdb=" O ASN I 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 443 removed outlier: 3.835A pdb=" N LYS I 432 " --> pdb=" O PRO I 428 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N CYS I 443 " --> pdb=" O GLU I 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 460 Processing helix chain 'I' and resid 463 through 469 Processing helix chain 'I' and resid 469 through 480 Processing helix chain 'I' and resid 481 through 495 Processing helix chain 'J' and resid 6 through 33 Processing helix chain 'J' and resid 41 through 53 Processing helix chain 'J' and resid 58 through 72 removed outlier: 5.965A pdb=" N TYR J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 81 Processing helix chain 'J' and resid 81 through 91 removed outlier: 3.716A pdb=" N ILE J 85 " --> pdb=" O HIS J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 107 Processing helix chain 'J' and resid 108 through 112 removed outlier: 3.525A pdb=" N LYS J 111 " --> pdb=" O TYR J 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 33 Processing helix chain 'K' and resid 41 through 54 removed outlier: 3.816A pdb=" N VAL K 45 " --> pdb=" O ILE K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 73 removed outlier: 3.605A pdb=" N GLY K 73 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 81 Processing helix chain 'K' and resid 82 through 91 Processing helix chain 'K' and resid 93 through 107 Processing helix chain 'L' and resid 5 through 33 Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.769A pdb=" N CYS L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 73 removed outlier: 3.806A pdb=" N GLY L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 81 Processing helix chain 'L' and resid 81 through 92 Processing helix chain 'L' and resid 93 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 75 removed outlier: 3.914A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 13.523A pdb=" N LEU A 57 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N ARG A 165 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE A 59 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG A 186 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 150 removed outlier: 6.589A pdb=" N PHE A 13 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER A 97 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 50 removed outlier: 4.026A pdb=" N ARG B 19 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B 100 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 50 removed outlier: 4.358A pdb=" N LEU B 109 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N GLU B 10 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N LYS B 107 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N VAL B 12 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N ASP B 105 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 150 removed outlier: 5.582A pdb=" N VAL B 179 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ARG B 118 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE B 181 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TYR B 116 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.658A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.658A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR C 180 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR C 15 " --> pdb=" O TRP C 230 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP C 230 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYR C 17 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE C 228 " --> pdb=" O TYR C 17 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR C 19 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU C 226 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU C 21 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 276 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.662A pdb=" N GLY C 25 " --> pdb=" O THR C 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB3, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB4, first strand: chain 'C' and resid 155 through 160 removed outlier: 3.546A pdb=" N SER C 169 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AB6, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.648A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.648A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR D 180 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.541A pdb=" N GLY D 25 " --> pdb=" O THR D 178 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.996A pdb=" N THR D 39 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 77 through 79 Processing sheet with id=AC2, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AC3, first strand: chain 'D' and resid 242 through 244 Processing sheet with id=AC4, first strand: chain 'E' and resid 42 through 47 removed outlier: 4.451A pdb=" N GLN E 42 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER E 53 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 42 through 47 removed outlier: 4.451A pdb=" N GLN E 42 " --> pdb=" O PHE E 54 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER E 53 " --> pdb=" O SER E 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC8, first strand: chain 'E' and resid 106 through 107 Processing sheet with id=AC9, first strand: chain 'E' and resid 242 through 244 Processing sheet with id=AD1, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.720A pdb=" N LYS F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 43 through 46 removed outlier: 3.720A pdb=" N LYS F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR F 180 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 25 through 26 removed outlier: 3.512A pdb=" N GLY F 25 " --> pdb=" O THR F 178 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR F 178 " --> pdb=" O GLY F 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.531A pdb=" N GLU F 174 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AD6, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.521A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.521A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR G 180 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY G 276 " --> pdb=" O TYR G 299 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 25 through 27 Processing sheet with id=AD9, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AE1, first strand: chain 'G' and resid 77 through 80 removed outlier: 3.633A pdb=" N ILE G 85 " --> pdb=" O ASP G 80 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 106 through 107 removed outlier: 3.673A pdb=" N PHE G 106 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AE4, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.583A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.583A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR H 180 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR H 15 " --> pdb=" O TRP H 230 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TRP H 230 " --> pdb=" O TYR H 15 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR H 17 " --> pdb=" O PHE H 228 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE H 228 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR H 19 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU H 226 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU H 21 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY H 276 " --> pdb=" O TYR H 299 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE7, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AE8, first strand: chain 'H' and resid 77 through 80 Processing sheet with id=AE9, first strand: chain 'H' and resid 105 through 107 Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.570A pdb=" N ILE I 9 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 79 through 81 Processing sheet with id=AF3, first strand: chain 'I' and resid 120 through 131 removed outlier: 6.476A pdb=" N GLN I 121 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER I 143 " --> pdb=" O GLY I 123 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE I 125 " --> pdb=" O TYR I 141 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR I 141 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN I 127 " --> pdb=" O TYR I 139 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR I 139 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU I 129 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL I 137 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AF5, first strand: chain 'I' and resid 258 through 259 removed outlier: 8.255A pdb=" N VAL I 259 " --> pdb=" O TYR I 211 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU I 213 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG I 228 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER I 304 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU I 302 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 329 through 333 1109 hydrogen bonds defined for protein. 3105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 6 hydrogen bonds 12 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 10.04 Time building geometry restraints manager: 11.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7226 1.33 - 1.45: 5111 1.45 - 1.57: 13951 1.57 - 1.69: 125 1.69 - 1.81: 149 Bond restraints: 26562 Sorted by residual: bond pdb=" CA SER F 28 " pdb=" C SER F 28 " ideal model delta sigma weight residual 1.532 1.507 0.026 1.21e-02 6.83e+03 4.52e+00 bond pdb=" CA SER E 28 " pdb=" C SER E 28 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.61e-02 3.86e+03 2.33e+00 bond pdb=" CA LYS G 250 " pdb=" CB LYS G 250 " ideal model delta sigma weight residual 1.526 1.553 -0.026 1.76e-02 3.23e+03 2.26e+00 bond pdb=" O5' U M 34 " pdb=" C5' U M 34 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.85e+00 bond pdb=" C3' G M 48 " pdb=" O3' G M 48 " ideal model delta sigma weight residual 1.427 1.447 -0.020 1.50e-02 4.44e+03 1.78e+00 ... (remaining 26557 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.49: 1026 106.49 - 113.37: 13915 113.37 - 120.26: 9597 120.26 - 127.14: 11220 127.14 - 134.03: 414 Bond angle restraints: 36172 Sorted by residual: angle pdb=" N SER E 28 " pdb=" CA SER E 28 " pdb=" C SER E 28 " ideal model delta sigma weight residual 110.44 103.37 7.07 1.20e+00 6.94e-01 3.47e+01 angle pdb=" N LEU E 29 " pdb=" CA LEU E 29 " pdb=" C LEU E 29 " ideal model delta sigma weight residual 111.03 117.40 -6.37 1.11e+00 8.12e-01 3.30e+01 angle pdb=" N TYR H 244 " pdb=" CA TYR H 244 " pdb=" C TYR H 244 " ideal model delta sigma weight residual 114.56 108.29 6.27 1.27e+00 6.20e-01 2.44e+01 angle pdb=" C ARG E 35 " pdb=" CA ARG E 35 " pdb=" CB ARG E 35 " ideal model delta sigma weight residual 117.23 111.01 6.22 1.36e+00 5.41e-01 2.09e+01 angle pdb=" N SER I 260 " pdb=" CA SER I 260 " pdb=" C SER I 260 " ideal model delta sigma weight residual 113.61 107.25 6.36 1.50e+00 4.44e-01 1.80e+01 ... (remaining 36167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 15226 35.83 - 71.67: 643 71.67 - 107.50: 42 107.50 - 143.34: 1 143.34 - 179.17: 5 Dihedral angle restraints: 15917 sinusoidal: 7192 harmonic: 8725 Sorted by residual: dihedral pdb=" O4' U M 60 " pdb=" C1' U M 60 " pdb=" N1 U M 60 " pdb=" C2 U M 60 " ideal model delta sinusoidal sigma weight residual 200.00 44.58 155.42 1 1.50e+01 4.44e-03 8.15e+01 dihedral pdb=" O4' U M 20 " pdb=" C1' U M 20 " pdb=" N1 U M 20 " pdb=" C2 U M 20 " ideal model delta sinusoidal sigma weight residual 200.00 73.30 126.70 1 1.50e+01 4.44e-03 6.82e+01 dihedral pdb=" O4' C M 50 " pdb=" C1' C M 50 " pdb=" N1 C M 50 " pdb=" C2 C M 50 " ideal model delta sinusoidal sigma weight residual -128.00 51.17 -179.17 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2770 0.036 - 0.072: 774 0.072 - 0.108: 250 0.108 - 0.145: 64 0.145 - 0.181: 11 Chirality restraints: 3869 Sorted by residual: chirality pdb=" CA PRO F 247 " pdb=" N PRO F 247 " pdb=" C PRO F 247 " pdb=" CB PRO F 247 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA TYR I 334 " pdb=" N TYR I 334 " pdb=" C TYR I 334 " pdb=" CB TYR I 334 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" C1' U M 20 " pdb=" O4' U M 20 " pdb=" C2' U M 20 " pdb=" N1 U M 20 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.17 2.00e-01 2.50e+01 7.57e-01 ... (remaining 3866 not shown) Planarity restraints: 4399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " -0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C PHE J 61 " 0.064 2.00e-02 2.50e+03 pdb=" O PHE J 61 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS J 62 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " -0.060 5.00e-02 4.00e+02 9.20e-02 1.35e+01 pdb=" N PRO F 247 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO F 247 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 247 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 209 " -0.042 5.00e-02 4.00e+02 6.46e-02 6.69e+00 pdb=" N PRO B 210 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " -0.036 5.00e-02 4.00e+02 ... (remaining 4396 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 785 2.69 - 3.24: 24850 3.24 - 3.79: 42277 3.79 - 4.35: 58691 4.35 - 4.90: 95244 Nonbonded interactions: 221847 Sorted by model distance: nonbonded pdb=" O LEU B 184 " pdb=" ND2 ASN B 185 " model vdw 2.136 2.520 nonbonded pdb=" N GLU G 257 " pdb=" OE1 GLU G 257 " model vdw 2.194 2.520 nonbonded pdb=" OG1 THR A 15 " pdb=" NE2 GLN A 143 " model vdw 2.202 2.520 nonbonded pdb=" N GLU J 83 " pdb=" OE1 GLU J 83 " model vdw 2.206 2.520 nonbonded pdb=" OG1 THR E 19 " pdb=" O SER E 239 " model vdw 2.220 2.440 ... (remaining 221842 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 'C' selection = chain 'D' selection = (chain 'E' and (resid 12 through 109 or resid 133 through 319)) selection = chain 'F' selection = (chain 'G' and (resid 12 through 109 or resid 133 through 319)) selection = (chain 'H' and (resid 12 through 109 or resid 133 through 319)) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.660 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 73.780 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.120 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26562 Z= 0.173 Angle : 0.572 11.789 36172 Z= 0.309 Chirality : 0.040 0.181 3869 Planarity : 0.004 0.092 4399 Dihedral : 17.940 179.170 10327 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.40 % Favored : 94.26 % Rotamer: Outliers : 2.84 % Allowed : 20.68 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 (0.16), residues: 2943 helix: 1.66 (0.17), residues: 1015 sheet: -0.68 (0.22), residues: 596 loop : -0.22 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 488 HIS 0.005 0.001 HIS I 106 PHE 0.016 0.001 PHE J 26 TYR 0.020 0.001 TYR I 334 ARG 0.009 0.000 ARG I 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 793 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1 MET cc_start: 0.3180 (mmm) cc_final: 0.2348 (tmm) REVERT: A 184 ASN cc_start: 0.5000 (m-40) cc_final: 0.2906 (m-40) REVERT: A 197 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6355 (mmm160) REVERT: B 61 ASN cc_start: 0.6906 (m-40) cc_final: 0.6614 (t0) REVERT: B 130 ASN cc_start: 0.8901 (m-40) cc_final: 0.8645 (m-40) REVERT: B 142 LEU cc_start: 0.7697 (mt) cc_final: 0.6685 (tt) REVERT: C 61 ARG cc_start: 0.6823 (mtt-85) cc_final: 0.6610 (ttm170) REVERT: C 245 CYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7307 (p) REVERT: D 15 TYR cc_start: 0.6014 (m-80) cc_final: 0.5623 (m-10) REVERT: F 57 SER cc_start: 0.6764 (OUTLIER) cc_final: 0.6408 (t) REVERT: G 57 SER cc_start: 0.7268 (p) cc_final: 0.6711 (t) REVERT: G 161 SER cc_start: 0.4287 (OUTLIER) cc_final: 0.3835 (m) REVERT: G 215 ASN cc_start: 0.7514 (p0) cc_final: 0.7226 (p0) REVERT: G 254 LEU cc_start: 0.8216 (tp) cc_final: 0.7990 (tp) REVERT: H 32 ASP cc_start: 0.5641 (t0) cc_final: 0.5216 (t0) REVERT: H 146 VAL cc_start: 0.8450 (m) cc_final: 0.8177 (p) REVERT: H 171 HIS cc_start: 0.6545 (p-80) cc_final: 0.6306 (p90) REVERT: H 242 PHE cc_start: 0.6630 (m-80) cc_final: 0.6400 (m-10) REVERT: H 248 LYS cc_start: 0.7911 (mttp) cc_final: 0.7340 (mttp) REVERT: I 109 ILE cc_start: 0.6496 (mt) cc_final: 0.6134 (tp) REVERT: I 261 SER cc_start: 0.5542 (OUTLIER) cc_final: 0.5311 (p) REVERT: I 321 VAL cc_start: 0.7563 (t) cc_final: 0.6876 (t) REVERT: I 482 TRP cc_start: 0.7030 (p-90) cc_final: 0.6654 (p-90) REVERT: J 26 PHE cc_start: 0.7836 (m-80) cc_final: 0.7136 (m-80) REVERT: K 6 GLU cc_start: 0.8210 (tp30) cc_final: 0.7858 (tp30) outliers start: 75 outliers final: 12 residues processed: 837 average time/residue: 0.4386 time to fit residues: 550.2511 Evaluate side-chains 482 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 465 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 245 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 261 SER Chi-restraints excluded: chain J residue 80 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 151 optimal weight: 0.0870 chunk 119 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 172 optimal weight: 0.4980 chunk 268 optimal weight: 0.9980 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN C 13 ASN C 52 HIS ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN E 86 ASN E 232 ASN F 30 ASN F 86 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 ASN F 233 HIS ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN G 287 ASN I 104 HIS ** I 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 GLN ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 HIS K 4 ASN ** K 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** K 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26562 Z= 0.230 Angle : 0.683 12.285 36172 Z= 0.356 Chirality : 0.043 0.241 3869 Planarity : 0.005 0.081 4399 Dihedral : 14.984 179.896 4287 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.20 % Favored : 94.53 % Rotamer: Outliers : 4.69 % Allowed : 23.86 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: 0.15 (0.16), residues: 2943 helix: 1.17 (0.16), residues: 1027 sheet: -0.63 (0.21), residues: 596 loop : -0.28 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 363 HIS 0.016 0.001 HIS F 190 PHE 0.035 0.002 PHE L 61 TYR 0.023 0.002 TYR I 399 ARG 0.008 0.001 ARG L 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 491 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.6223 (mmm160) REVERT: B 61 ASN cc_start: 0.7052 (m-40) cc_final: 0.6595 (t0) REVERT: B 142 LEU cc_start: 0.7848 (mt) cc_final: 0.6804 (tt) REVERT: C 46 TRP cc_start: 0.7308 (t-100) cc_final: 0.6866 (t-100) REVERT: C 61 ARG cc_start: 0.7248 (mtt-85) cc_final: 0.6683 (ttp-170) REVERT: D 45 TYR cc_start: 0.7598 (m-80) cc_final: 0.7273 (m-10) REVERT: D 305 MET cc_start: 0.7195 (ttm) cc_final: 0.6880 (ttt) REVERT: E 33 ILE cc_start: 0.7880 (mm) cc_final: 0.7398 (tp) REVERT: E 54 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6756 (m-80) REVERT: E 152 ASP cc_start: 0.7720 (p0) cc_final: 0.7165 (p0) REVERT: F 57 SER cc_start: 0.7050 (p) cc_final: 0.6386 (t) REVERT: G 35 ARG cc_start: 0.2654 (OUTLIER) cc_final: 0.2340 (mmm160) REVERT: G 224 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7244 (t0) REVERT: I 228 ARG cc_start: 0.5071 (mpt180) cc_final: 0.4861 (mmt-90) REVERT: I 320 GLN cc_start: 0.7777 (tm130) cc_final: 0.7135 (tm-30) REVERT: I 321 VAL cc_start: 0.7473 (t) cc_final: 0.7098 (t) REVERT: I 410 MET cc_start: 0.6306 (ptm) cc_final: 0.5802 (ttp) REVERT: I 451 GLU cc_start: 0.8453 (tt0) cc_final: 0.8164 (tm-30) REVERT: J 26 PHE cc_start: 0.7793 (m-80) cc_final: 0.7421 (m-80) REVERT: J 34 GLU cc_start: 0.3251 (pm20) cc_final: 0.2633 (mp0) REVERT: J 80 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7113 (pt0) REVERT: J 84 GLU cc_start: 0.8607 (pm20) cc_final: 0.8247 (pm20) REVERT: J 108 TYR cc_start: 0.5313 (OUTLIER) cc_final: 0.3557 (t80) REVERT: K 10 GLN cc_start: 0.7272 (mt0) cc_final: 0.6646 (mt0) REVERT: L 112 ASP cc_start: 0.6262 (OUTLIER) cc_final: 0.5886 (p0) outliers start: 124 outliers final: 52 residues processed: 579 average time/residue: 0.4087 time to fit residues: 357.8282 Evaluate side-chains 462 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 403 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 54 PHE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 171 HIS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 177 LEU Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 374 TYR Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 22 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 112 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 223 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 269 optimal weight: 6.9990 chunk 290 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 267 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 229 GLN E 229 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN F 256 GLN G 181 GLN ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN G 297 HIS ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS I 104 HIS ** I 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 250 GLN I 313 ASN ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 26562 Z= 0.420 Angle : 0.841 12.781 36172 Z= 0.437 Chirality : 0.046 0.250 3869 Planarity : 0.006 0.097 4399 Dihedral : 15.231 179.535 4278 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 31.40 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.91 % Favored : 93.75 % Rotamer: Outliers : 6.16 % Allowed : 23.14 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.37 (0.15), residues: 2943 helix: 0.53 (0.15), residues: 1020 sheet: -0.64 (0.21), residues: 578 loop : -0.54 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP H 46 HIS 0.010 0.002 HIS F 190 PHE 0.034 0.003 PHE D 221 TYR 0.030 0.003 TYR F 15 ARG 0.010 0.001 ARG I 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 427 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7369 (ptp) REVERT: A 197 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.5813 (mmm160) REVERT: B 61 ASN cc_start: 0.7142 (m-40) cc_final: 0.6653 (t0) REVERT: B 90 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8094 (tp-100) REVERT: B 131 PHE cc_start: 0.8364 (t80) cc_final: 0.8019 (m-80) REVERT: D 305 MET cc_start: 0.7443 (ttm) cc_final: 0.7191 (ttt) REVERT: F 57 SER cc_start: 0.7525 (OUTLIER) cc_final: 0.6731 (m) REVERT: F 272 LEU cc_start: 0.8160 (tp) cc_final: 0.7778 (mm) REVERT: G 224 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7480 (t0) REVERT: H 41 LEU cc_start: 0.8111 (tp) cc_final: 0.7823 (tp) REVERT: H 88 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7592 (tp) REVERT: H 100 ASP cc_start: 0.5999 (OUTLIER) cc_final: 0.5253 (t70) REVERT: I 361 ASN cc_start: 0.5675 (OUTLIER) cc_final: 0.5374 (p0) REVERT: J 22 MET cc_start: 0.8126 (ppp) cc_final: 0.7564 (ppp) REVERT: J 80 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8048 (mt-10) REVERT: J 99 ILE cc_start: 0.8474 (mt) cc_final: 0.8117 (mt) REVERT: J 108 TYR cc_start: 0.6080 (OUTLIER) cc_final: 0.4230 (t80) REVERT: K 23 LYS cc_start: 0.7527 (tppt) cc_final: 0.7217 (tppt) REVERT: K 58 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5823 (tt0) REVERT: K 100 TRP cc_start: 0.8431 (m-10) cc_final: 0.8160 (m-10) REVERT: L 88 LEU cc_start: 0.8703 (tp) cc_final: 0.8435 (tp) REVERT: L 90 LYS cc_start: 0.7639 (tptp) cc_final: 0.7176 (tptp) REVERT: L 101 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8485 (p) REVERT: L 105 ILE cc_start: 0.7854 (mt) cc_final: 0.7636 (mt) REVERT: L 112 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.6202 (p0) outliers start: 163 outliers final: 86 residues processed: 554 average time/residue: 0.3903 time to fit residues: 331.7501 Evaluate side-chains 474 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 376 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain E residue 15 TYR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 171 HIS Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 38 LYS Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 300 ARG Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 261 SER Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 361 ASN Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 22 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 112 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 0.0870 chunk 202 optimal weight: 9.9990 chunk 139 optimal weight: 0.0050 chunk 29 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 270 optimal weight: 0.6980 chunk 286 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 HIS D 13 ASN D 84 HIS E 256 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN G 84 HIS G 215 ASN I 104 HIS I 117 ASN ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 GLN ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 26562 Z= 0.198 Angle : 0.675 13.748 36172 Z= 0.345 Chirality : 0.043 0.251 3869 Planarity : 0.005 0.082 4399 Dihedral : 15.050 179.296 4278 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.20 % Favored : 94.50 % Rotamer: Outliers : 4.23 % Allowed : 24.88 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.14 (0.16), residues: 2943 helix: 0.79 (0.16), residues: 1026 sheet: -0.61 (0.22), residues: 571 loop : -0.43 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP H 46 HIS 0.007 0.001 HIS I 104 PHE 0.021 0.002 PHE I 119 TYR 0.029 0.002 TYR H 244 ARG 0.010 0.001 ARG L 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 419 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7271 (ptp) REVERT: B 131 PHE cc_start: 0.8278 (t80) cc_final: 0.8031 (m-80) REVERT: D 305 MET cc_start: 0.7317 (ttm) cc_final: 0.6994 (ttt) REVERT: E 144 MET cc_start: 0.8466 (mmm) cc_final: 0.8158 (mmm) REVERT: E 152 ASP cc_start: 0.8157 (p0) cc_final: 0.7602 (p0) REVERT: G 224 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7498 (t0) REVERT: H 221 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.6244 (m-80) REVERT: I 62 PHE cc_start: 0.0029 (OUTLIER) cc_final: -0.0435 (m-80) REVERT: I 231 VAL cc_start: 0.4886 (OUTLIER) cc_final: 0.4671 (t) REVERT: I 310 ILE cc_start: -0.0799 (OUTLIER) cc_final: -0.1349 (mp) REVERT: I 320 GLN cc_start: 0.7692 (tm-30) cc_final: 0.6739 (tm-30) REVERT: J 80 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: J 82 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7602 (mm-40) REVERT: J 100 TRP cc_start: 0.8632 (OUTLIER) cc_final: 0.8346 (m-90) REVERT: J 108 TYR cc_start: 0.5976 (OUTLIER) cc_final: 0.5149 (t80) REVERT: J 111 LYS cc_start: 0.5500 (tmtt) cc_final: 0.4991 (tmtt) REVERT: K 47 ARG cc_start: 0.8701 (tpp-160) cc_final: 0.8472 (tpp-160) REVERT: K 53 ASN cc_start: 0.8094 (p0) cc_final: 0.7835 (p0) REVERT: K 57 ASP cc_start: 0.6129 (t0) cc_final: 0.5106 (t0) REVERT: L 38 ASP cc_start: 0.5737 (OUTLIER) cc_final: 0.5499 (p0) REVERT: L 112 ASP cc_start: 0.6405 (OUTLIER) cc_final: 0.6126 (p0) outliers start: 112 outliers final: 57 residues processed: 503 average time/residue: 0.3889 time to fit residues: 303.6494 Evaluate side-chains 438 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 370 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 300 ARG Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 281 ASP Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 253 GLU Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 100 TRP Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 112 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 146 optimal weight: 0.9980 chunk 256 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 136 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS G 233 HIS I 104 HIS ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 26562 Z= 0.390 Angle : 0.804 13.564 36172 Z= 0.413 Chirality : 0.046 0.227 3869 Planarity : 0.006 0.165 4399 Dihedral : 15.331 179.249 4273 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 32.61 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.86 % Favored : 92.83 % Rotamer: Outliers : 5.94 % Allowed : 24.39 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.49 (0.16), residues: 2943 helix: 0.47 (0.16), residues: 1021 sheet: -0.85 (0.21), residues: 606 loop : -0.56 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP H 46 HIS 0.020 0.002 HIS A 20 PHE 0.033 0.003 PHE J 26 TYR 0.029 0.003 TYR B 29 ARG 0.008 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 368 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7493 (ptp) REVERT: B 77 HIS cc_start: 0.6912 (OUTLIER) cc_final: 0.6659 (p-80) REVERT: C 55 VAL cc_start: 0.7883 (t) cc_final: 0.7627 (t) REVERT: D 305 MET cc_start: 0.7624 (ttm) cc_final: 0.7334 (ttt) REVERT: E 152 ASP cc_start: 0.8430 (p0) cc_final: 0.8120 (p0) REVERT: E 206 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7391 (t0) REVERT: E 286 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6776 (p0) REVERT: G 13 ASN cc_start: 0.5350 (OUTLIER) cc_final: 0.5129 (p0) REVERT: G 224 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7758 (t0) REVERT: H 88 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7823 (tt) REVERT: H 221 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6341 (m-80) REVERT: H 250 LYS cc_start: 0.6091 (OUTLIER) cc_final: 0.5731 (ptpp) REVERT: I 62 PHE cc_start: -0.0034 (OUTLIER) cc_final: -0.0931 (m-80) REVERT: I 465 TYR cc_start: 0.6925 (OUTLIER) cc_final: 0.4960 (m-80) REVERT: J 58 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6643 (mp0) REVERT: J 62 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8751 (mtmm) REVERT: J 80 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: J 100 TRP cc_start: 0.8600 (OUTLIER) cc_final: 0.8189 (m-90) REVERT: J 108 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.4991 (t80) REVERT: K 100 TRP cc_start: 0.8258 (m-10) cc_final: 0.7893 (m-10) REVERT: L 112 ASP cc_start: 0.6528 (OUTLIER) cc_final: 0.6221 (p0) outliers start: 157 outliers final: 87 residues processed: 485 average time/residue: 0.3771 time to fit residues: 285.9531 Evaluate side-chains 442 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 339 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 300 ARG Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 281 ASP Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 253 GLU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 66 SER Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 100 TRP Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 112 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 286 optimal weight: 1.9990 chunk 237 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26562 Z= 0.239 Angle : 0.704 15.654 36172 Z= 0.358 Chirality : 0.043 0.239 3869 Planarity : 0.005 0.125 4399 Dihedral : 15.242 179.139 4273 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 25.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.84 % Favored : 93.88 % Rotamer: Outliers : 4.91 % Allowed : 26.28 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.38 (0.16), residues: 2943 helix: 0.52 (0.16), residues: 1023 sheet: -0.70 (0.22), residues: 540 loop : -0.54 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP H 46 HIS 0.012 0.001 HIS C 190 PHE 0.019 0.002 PHE E 217 TYR 0.031 0.002 TYR H 244 ARG 0.024 0.001 ARG F 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 375 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3071 (tpt) cc_final: 0.0986 (tmm) REVERT: C 205 MET cc_start: 0.7608 (tpp) cc_final: 0.7367 (tpp) REVERT: D 57 SER cc_start: 0.7276 (OUTLIER) cc_final: 0.6690 (m) REVERT: D 157 LEU cc_start: 0.8814 (mm) cc_final: 0.8338 (mt) REVERT: D 170 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8439 (pt) REVERT: D 305 MET cc_start: 0.7530 (ttm) cc_final: 0.7135 (ttt) REVERT: E 152 ASP cc_start: 0.8033 (p0) cc_final: 0.7833 (p0) REVERT: F 254 LEU cc_start: 0.8127 (tp) cc_final: 0.7863 (tt) REVERT: G 13 ASN cc_start: 0.5236 (OUTLIER) cc_final: 0.5036 (p0) REVERT: G 224 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7693 (t0) REVERT: H 221 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.6208 (m-80) REVERT: I 62 PHE cc_start: 0.0024 (OUTLIER) cc_final: -0.0894 (m-80) REVERT: I 109 ILE cc_start: 0.7422 (mt) cc_final: 0.7083 (mt) REVERT: I 228 ARG cc_start: 0.5804 (mpt180) cc_final: 0.5181 (mmt-90) REVERT: I 310 ILE cc_start: -0.0364 (OUTLIER) cc_final: -0.0843 (mp) REVERT: I 451 GLU cc_start: 0.8524 (tt0) cc_final: 0.8281 (tm-30) REVERT: I 465 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.5413 (m-80) REVERT: J 26 PHE cc_start: 0.8244 (m-80) cc_final: 0.7841 (m-80) REVERT: J 62 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8691 (mtmm) REVERT: J 80 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7810 (pt0) REVERT: J 82 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7945 (mm-40) REVERT: J 100 TRP cc_start: 0.8492 (m-10) cc_final: 0.8157 (m-90) REVERT: J 108 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.5543 (t80) REVERT: K 100 TRP cc_start: 0.8186 (m-10) cc_final: 0.7830 (m-10) REVERT: L 20 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.7117 (tp-100) REVERT: L 75 ASN cc_start: 0.7350 (t0) cc_final: 0.6936 (t0) REVERT: L 90 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6916 (tptt) REVERT: L 112 ASP cc_start: 0.6531 (OUTLIER) cc_final: 0.5475 (t70) outliers start: 130 outliers final: 66 residues processed: 469 average time/residue: 0.3827 time to fit residues: 281.7610 Evaluate side-chains 421 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 341 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 171 HIS Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 281 ASP Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 253 GLU Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 108 TYR Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 54 TYR Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain L residue 20 GLN Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 112 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 285 optimal weight: 10.0000 chunk 178 optimal weight: 0.0070 chunk 173 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN F 190 HIS ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26562 Z= 0.200 Angle : 0.689 15.692 36172 Z= 0.348 Chirality : 0.043 0.241 3869 Planarity : 0.005 0.087 4399 Dihedral : 15.121 177.996 4272 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.91 % Favored : 93.82 % Rotamer: Outliers : 4.20 % Allowed : 26.77 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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 (0.16), residues: 2943 helix: 0.50 (0.16), residues: 1027 sheet: -0.66 (0.23), residues: 528 loop : -0.50 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP L 100 HIS 0.008 0.001 HIS C 190 PHE 0.025 0.002 PHE K 26 TYR 0.034 0.002 TYR E 182 ARG 0.009 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 383 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2778 (tpt) cc_final: 0.0716 (tmm) REVERT: B 130 ASN cc_start: 0.8561 (m-40) cc_final: 0.8251 (m-40) REVERT: D 157 LEU cc_start: 0.8767 (mm) cc_final: 0.8355 (mt) REVERT: D 170 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8392 (pt) REVERT: D 305 MET cc_start: 0.7471 (ttm) cc_final: 0.7066 (ttt) REVERT: E 152 ASP cc_start: 0.7808 (p0) cc_final: 0.7272 (p0) REVERT: E 206 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7419 (t0) REVERT: F 254 LEU cc_start: 0.8083 (tp) cc_final: 0.7831 (tt) REVERT: G 13 ASN cc_start: 0.5336 (OUTLIER) cc_final: 0.5099 (p0) REVERT: G 305 MET cc_start: 0.6496 (ttt) cc_final: 0.5920 (ttt) REVERT: H 146 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8444 (m) REVERT: H 200 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7710 (ttm) REVERT: H 221 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6234 (m-80) REVERT: I 62 PHE cc_start: -0.0448 (OUTLIER) cc_final: -0.1389 (m-80) REVERT: I 228 ARG cc_start: 0.5873 (mpt180) cc_final: 0.5556 (mmt-90) REVERT: I 231 VAL cc_start: 0.5277 (OUTLIER) cc_final: 0.5000 (t) REVERT: I 310 ILE cc_start: -0.0345 (OUTLIER) cc_final: -0.0707 (mp) REVERT: I 451 GLU cc_start: 0.8495 (tt0) cc_final: 0.8265 (tm-30) REVERT: I 465 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.5300 (m-80) REVERT: J 22 MET cc_start: 0.7795 (ppp) cc_final: 0.7520 (ppp) REVERT: J 26 PHE cc_start: 0.8194 (m-80) cc_final: 0.7941 (m-80) REVERT: J 34 GLU cc_start: 0.3360 (pm20) cc_final: 0.2756 (mp0) REVERT: J 80 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: J 100 TRP cc_start: 0.8473 (m-10) cc_final: 0.8123 (m-90) REVERT: K 22 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6446 (ppp) REVERT: K 94 TRP cc_start: 0.8233 (p-90) cc_final: 0.7939 (p-90) REVERT: L 20 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7117 (tp-100) REVERT: L 75 ASN cc_start: 0.7600 (t0) cc_final: 0.7282 (t0) outliers start: 111 outliers final: 69 residues processed: 463 average time/residue: 0.3680 time to fit residues: 268.4691 Evaluate side-chains 433 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 351 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 171 HIS Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 38 LYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 166 HIS Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 253 GLU Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 374 TYR Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 22 MET Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 20 GLN Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 90 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS ** I 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.7814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 26562 Z= 0.374 Angle : 0.805 16.088 36172 Z= 0.414 Chirality : 0.046 0.313 3869 Planarity : 0.006 0.169 4399 Dihedral : 15.432 179.689 4271 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 32.83 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.93 % Favored : 92.80 % Rotamer: Outliers : 5.22 % Allowed : 27.03 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.65 (0.15), residues: 2943 helix: 0.21 (0.16), residues: 1025 sheet: -0.69 (0.22), residues: 548 loop : -0.70 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP L 100 HIS 0.008 0.002 HIS C 190 PHE 0.032 0.003 PHE D 221 TYR 0.032 0.003 TYR H 17 ARG 0.007 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 348 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2927 (tpt) cc_final: 0.0899 (tmm) REVERT: B 46 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.6980 (tptt) REVERT: D 157 LEU cc_start: 0.8847 (mm) cc_final: 0.8407 (mt) REVERT: D 170 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8412 (pt) REVERT: D 207 LEU cc_start: 0.8284 (mt) cc_final: 0.8037 (mp) REVERT: D 305 MET cc_start: 0.7707 (ttm) cc_final: 0.7402 (ttt) REVERT: E 152 ASP cc_start: 0.8417 (p0) cc_final: 0.8012 (p0) REVERT: E 206 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7543 (t0) REVERT: E 209 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8930 (tttt) REVERT: G 13 ASN cc_start: 0.5526 (OUTLIER) cc_final: 0.5276 (p0) REVERT: H 221 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6277 (m-80) REVERT: H 304 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7204 (pt0) REVERT: I 62 PHE cc_start: -0.0592 (OUTLIER) cc_final: -0.1589 (m-80) REVERT: I 338 PHE cc_start: 0.6235 (m-80) cc_final: 0.5771 (m-80) REVERT: I 451 GLU cc_start: 0.8496 (tt0) cc_final: 0.8286 (tm-30) REVERT: I 465 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.5231 (m-80) REVERT: J 62 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8688 (mtmm) REVERT: J 80 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: J 100 TRP cc_start: 0.8605 (m-10) cc_final: 0.8172 (m-90) REVERT: J 108 TYR cc_start: 0.5392 (t80) cc_final: 0.5120 (t80) REVERT: K 22 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6493 (ppp) REVERT: K 53 ASN cc_start: 0.8641 (p0) cc_final: 0.8043 (t0) REVERT: L 75 ASN cc_start: 0.7556 (t0) cc_final: 0.7301 (t0) REVERT: L 112 ASP cc_start: 0.6581 (OUTLIER) cc_final: 0.5625 (t70) outliers start: 138 outliers final: 96 residues processed: 449 average time/residue: 0.3810 time to fit residues: 268.2859 Evaluate side-chains 439 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 330 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 171 HIS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 209 LYS Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 226 LEU Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain H residue 281 ASP Chi-restraints excluded: chain H residue 304 GLU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 253 GLU Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 282 TYR Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 295 LYS Chi-restraints excluded: chain I residue 303 MET Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 366 LEU Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 22 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 54 TYR Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 90 LYS Chi-restraints excluded: chain L residue 112 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 208 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 251 optimal weight: 0.9980 chunk 264 optimal weight: 0.9980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS B 61 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN I 104 HIS ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.7943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26562 Z= 0.259 Angle : 0.756 16.510 36172 Z= 0.382 Chirality : 0.044 0.268 3869 Planarity : 0.005 0.096 4399 Dihedral : 15.384 179.819 4271 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 28.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.98 % Favored : 93.78 % Rotamer: Outliers : 3.97 % Allowed : 28.17 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.55 (0.16), residues: 2943 helix: 0.33 (0.16), residues: 1014 sheet: -0.72 (0.23), residues: 524 loop : -0.63 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP H 46 HIS 0.008 0.001 HIS A 52 PHE 0.028 0.002 PHE L 61 TYR 0.047 0.002 TYR H 244 ARG 0.009 0.001 ARG I 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 349 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2746 (tpt) cc_final: 0.0800 (tmm) REVERT: A 41 LEU cc_start: 0.7269 (pp) cc_final: 0.6707 (mt) REVERT: B 46 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.6902 (tptt) REVERT: D 157 LEU cc_start: 0.8788 (mm) cc_final: 0.8398 (mt) REVERT: D 170 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8536 (pt) REVERT: D 305 MET cc_start: 0.7664 (ttm) cc_final: 0.7253 (ttt) REVERT: E 152 ASP cc_start: 0.8251 (p0) cc_final: 0.7800 (p0) REVERT: E 163 ARG cc_start: 0.4227 (mmm-85) cc_final: 0.3873 (mtt180) REVERT: E 206 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7410 (t0) REVERT: G 13 ASN cc_start: 0.5763 (OUTLIER) cc_final: 0.5490 (p0) REVERT: H 221 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6156 (m-80) REVERT: I 31 MET cc_start: 0.5765 (tpt) cc_final: 0.4631 (tpt) REVERT: I 62 PHE cc_start: -0.0476 (OUTLIER) cc_final: -0.1570 (m-80) REVERT: I 228 ARG cc_start: 0.6827 (mpt180) cc_final: 0.6620 (mpt180) REVERT: I 247 TRP cc_start: 0.6310 (m-90) cc_final: 0.5900 (m-90) REVERT: I 320 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7643 (tm-30) REVERT: I 338 PHE cc_start: 0.6369 (m-80) cc_final: 0.5831 (m-80) REVERT: I 347 LEU cc_start: 0.8668 (mm) cc_final: 0.8462 (mp) REVERT: I 451 GLU cc_start: 0.8460 (tt0) cc_final: 0.8244 (tm-30) REVERT: I 465 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.5494 (m-80) REVERT: J 18 PHE cc_start: 0.9116 (t80) cc_final: 0.8801 (t80) REVERT: J 62 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8658 (mtmm) REVERT: J 80 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: J 100 TRP cc_start: 0.8527 (m-10) cc_final: 0.8153 (m-90) REVERT: J 108 TYR cc_start: 0.5340 (t80) cc_final: 0.5067 (t80) REVERT: K 22 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6272 (ppp) REVERT: K 43 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8454 (ptpp) REVERT: K 53 ASN cc_start: 0.8511 (p0) cc_final: 0.7917 (t0) REVERT: L 8 ASP cc_start: 0.7801 (m-30) cc_final: 0.7435 (m-30) REVERT: L 61 PHE cc_start: 0.7832 (t80) cc_final: 0.7531 (t80) REVERT: L 71 ARG cc_start: 0.8264 (mtm180) cc_final: 0.7689 (ptm160) outliers start: 105 outliers final: 78 residues processed: 426 average time/residue: 0.3753 time to fit residues: 249.5241 Evaluate side-chains 425 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 336 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 282 TYR Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 303 MET Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 374 TYR Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 22 MET Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 90 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 5.9990 chunk 281 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 294 optimal weight: 20.0000 chunk 271 optimal weight: 4.9990 chunk 234 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.8078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26562 Z= 0.253 Angle : 0.757 16.768 36172 Z= 0.382 Chirality : 0.044 0.287 3869 Planarity : 0.005 0.095 4399 Dihedral : 15.380 179.887 4271 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 27.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.52 % Favored : 93.24 % Rotamer: Outliers : 3.52 % Allowed : 28.51 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.56 (0.16), residues: 2943 helix: 0.34 (0.16), residues: 1018 sheet: -0.75 (0.23), residues: 531 loop : -0.64 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.003 TRP H 46 HIS 0.006 0.001 HIS A 52 PHE 0.027 0.002 PHE K 26 TYR 0.055 0.002 TYR H 244 ARG 0.014 0.001 ARG I 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 355 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3140 (tpt) cc_final: 0.1122 (tmm) REVERT: A 41 LEU cc_start: 0.7236 (pp) cc_final: 0.6712 (mt) REVERT: A 78 LYS cc_start: 0.6986 (ttpt) cc_final: 0.6704 (mmtm) REVERT: B 46 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6780 (tptt) REVERT: C 137 MET cc_start: 0.7542 (tpp) cc_final: 0.7332 (tpt) REVERT: D 157 LEU cc_start: 0.8698 (mm) cc_final: 0.8330 (tp) REVERT: D 170 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8475 (pt) REVERT: D 305 MET cc_start: 0.7666 (ttm) cc_final: 0.7280 (ttt) REVERT: E 152 ASP cc_start: 0.8184 (p0) cc_final: 0.7718 (p0) REVERT: E 163 ARG cc_start: 0.4279 (mmm-85) cc_final: 0.4041 (mtt180) REVERT: E 206 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7420 (t0) REVERT: G 13 ASN cc_start: 0.6126 (OUTLIER) cc_final: 0.5858 (p0) REVERT: G 305 MET cc_start: 0.6888 (ttt) cc_final: 0.6654 (ttt) REVERT: H 221 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.6148 (m-80) REVERT: I 62 PHE cc_start: -0.0610 (OUTLIER) cc_final: -0.1652 (m-80) REVERT: I 228 ARG cc_start: 0.6799 (mpt180) cc_final: 0.6509 (mpt180) REVERT: I 247 TRP cc_start: 0.6319 (m-90) cc_final: 0.5939 (m-90) REVERT: I 338 PHE cc_start: 0.6153 (m-80) cc_final: 0.5604 (m-80) REVERT: I 451 GLU cc_start: 0.8456 (tt0) cc_final: 0.8238 (tm-30) REVERT: I 465 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.5512 (m-80) REVERT: J 18 PHE cc_start: 0.9159 (t80) cc_final: 0.8867 (t80) REVERT: J 34 GLU cc_start: 0.3330 (pm20) cc_final: 0.2860 (mp0) REVERT: J 62 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8616 (mtmm) REVERT: J 64 TYR cc_start: 0.7494 (t80) cc_final: 0.7267 (t80) REVERT: J 80 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: J 100 TRP cc_start: 0.8516 (m-10) cc_final: 0.8135 (m-90) REVERT: J 108 TYR cc_start: 0.5484 (t80) cc_final: 0.5128 (t80) REVERT: K 34 GLU cc_start: 0.0393 (tp30) cc_final: -0.0099 (tp30) REVERT: K 43 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8351 (ptpp) REVERT: K 49 ARG cc_start: 0.8967 (ttp-110) cc_final: 0.8709 (ttp-110) REVERT: K 53 ASN cc_start: 0.8435 (p0) cc_final: 0.7899 (t0) REVERT: L 8 ASP cc_start: 0.7573 (m-30) cc_final: 0.7223 (m-30) REVERT: L 75 ASN cc_start: 0.7151 (t0) cc_final: 0.6932 (t0) outliers start: 93 outliers final: 70 residues processed: 424 average time/residue: 0.3934 time to fit residues: 262.8629 Evaluate side-chains 420 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 340 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 284 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 LYS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 47 ASN Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 238 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 139 TYR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 210 HIS Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 262 LEU Chi-restraints excluded: chain I residue 282 TYR Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 303 MET Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 348 ILE Chi-restraints excluded: chain I residue 374 TYR Chi-restraints excluded: chain I residue 384 GLU Chi-restraints excluded: chain I residue 443 CYS Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 465 TYR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 90 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 4.9990 chunk 250 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 241 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN ** I 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 ASN ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.098431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.078392 restraints weight = 123785.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.080276 restraints weight = 74593.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.081373 restraints weight = 51811.213| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.8352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 26562 Z= 0.289 Angle : 0.772 17.325 36172 Z= 0.391 Chirality : 0.045 0.245 3869 Planarity : 0.005 0.106 4399 Dihedral : 15.433 179.566 4271 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 29.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.59 % Favored : 93.17 % Rotamer: Outliers : 3.63 % Allowed : 28.32 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % 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: -0.63 (0.16), residues: 2943 helix: 0.30 (0.16), residues: 1013 sheet: -0.78 (0.23), residues: 524 loop : -0.70 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.003 TRP H 46 HIS 0.006 0.001 HIS A 52 PHE 0.037 0.002 PHE K 68 TYR 0.057 0.002 TYR H 244 ARG 0.012 0.001 ARG K 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6212.31 seconds wall clock time: 112 minutes 59.55 seconds (6779.55 seconds total)