Starting phenix.real_space_refine on Tue Jun 24 01:32:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ff5_29040/06_2025/8ff5_29040.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ff5_29040/06_2025/8ff5_29040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ff5_29040/06_2025/8ff5_29040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ff5_29040/06_2025/8ff5_29040.map" model { file = "/net/cci-nas-00/data/ceres_data/8ff5_29040/06_2025/8ff5_29040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ff5_29040/06_2025/8ff5_29040.cif" } resolution = 3.13 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= 0.005 sd= 0.023 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 859 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 136 5.49 5 S 94 5.16 5 C 16944 2.51 5 N 4614 2.21 5 O 5336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.61s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27124 Number of models: 1 Model: "" Number of chains: 15 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: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1702 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 199} 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: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2330 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 10, 'TRANS': 275} 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: 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: "H" 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: "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': 17, 'rna2p_pyr': 9, 'rna3p_pur': 16, 'rna3p_pyr': 21} Link IDs: {'rna2p': 26, 'rna3p': 36} Chain: "N" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1079 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "O" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 1 Time building chain proxies: 16.24, per 1000 atoms: 0.60 Number of scatterers: 27124 At special positions: 0 Unit cell: (110.67, 129.642, 219.232, 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 136 15.00 O 5336 8.00 N 4614 7.00 C 16944 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.60 Conformation dependent library (CDL) restraints added in 3.3 seconds 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5546 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 44 sheets defined 39.3% alpha, 21.2% beta 47 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 10.96 Creating SS restraints... Processing helix chain 'A' and resid 32 through 44 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 40 through 44 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 142 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.635A 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: 3.617A 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 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' 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: 3.873A pdb=" N MET C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.898A 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 285 removed outlier: 3.611A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 317 removed outlier: 3.535A pdb=" N MET C 305 " --> pdb=" O ASN C 301 " (cutoff:3.500A) 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 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: 3.645A pdb=" N MET D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.752A 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: 4.018A 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 removed outlier: 3.612A pdb=" N MET D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.586A 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: 3.772A pdb=" N MET E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 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 285 removed outlier: 3.911A 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 removed outlier: 3.645A pdb=" N MET E 305 " --> pdb=" O ASN E 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.634A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.554A 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: 3.933A pdb=" N MET F 200 " --> pdb=" O ARG F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.532A 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: 3.716A pdb=" N ASP F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 301 through 318 removed outlier: 3.542A pdb=" N MET F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) 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 72 removed outlier: 3.749A pdb=" N ILE G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 104 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: 3.671A pdb=" N MET G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 265 removed outlier: 3.518A pdb=" N ILE G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) 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: 3.950A pdb=" N ASP G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 296 Processing helix chain 'G' and resid 301 through 317 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: 3.526A 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 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: 3.672A pdb=" N MET H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.886A 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 284 removed outlier: 3.946A pdb=" N ASP H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 296 Processing helix chain 'H' and resid 301 through 318 Processing helix chain 'I' and resid 19 through 40 Processing helix chain 'I' and resid 42 through 50 removed outlier: 5.246A pdb=" N GLY I 47 " --> pdb=" O ARG I 44 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY I 48 " --> pdb=" O GLN I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.940A 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 152 through 157 Processing helix chain 'I' and resid 183 through 187 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 253 through 257 removed outlier: 3.572A pdb=" N PHE I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 253 through 257' Processing helix chain 'I' and resid 261 through 270 Processing helix chain 'I' and resid 312 through 325 Processing helix chain 'I' and resid 342 through 355 removed outlier: 3.642A pdb=" N SER I 346 " --> pdb=" O ASN I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 367 Processing helix chain 'I' and resid 373 through 393 removed outlier: 3.956A pdb=" N GLN I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU I 384 " --> pdb=" O PHE I 380 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLY I 385 " --> pdb=" O SER I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 421 removed outlier: 4.545A pdb=" N TYR I 399 " --> pdb=" O GLU I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 443 Processing helix chain 'I' and resid 445 through 461 removed outlier: 3.755A pdb=" N GLY I 461 " --> pdb=" O LEU I 457 " (cutoff:3.500A) 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 5 through 33 Processing helix chain 'J' and resid 41 through 54 Processing helix chain 'J' and resid 58 through 73 removed outlier: 6.086A pdb=" N TYR J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY J 73 " --> pdb=" O LEU J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 81 Processing helix chain 'J' and resid 81 through 91 Processing helix chain 'J' and resid 93 through 108 Processing helix chain 'J' and resid 109 through 112 Processing helix chain 'K' and resid 5 through 33 Processing helix chain 'K' and resid 41 through 54 Processing helix chain 'K' and resid 58 through 73 removed outlier: 6.029A pdb=" N TYR K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 81 removed outlier: 3.769A pdb=" N HIS K 81 " --> pdb=" O TYR K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 91 removed outlier: 4.059A pdb=" N ILE K 85 " --> pdb=" O HIS K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 109 removed outlier: 4.606A pdb=" N LYS K 109 " --> pdb=" O ILE K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 33 Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 57 through 73 removed outlier: 3.800A pdb=" N GLY L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 81 removed outlier: 3.550A pdb=" N HIS L 81 " --> pdb=" O TYR L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 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: 3.984A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 13.568A pdb=" N LEU A 57 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N ARG A 165 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE A 59 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 160 " --> pdb=" O MET A 195 " (cutoff:3.500A) removed outlier: 6.915A 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: 6.994A pdb=" N ILE A 6 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TRP A 104 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR A 8 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 102 " --> pdb=" O TYR A 8 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP A 10 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A 100 " --> pdb=" O ASP A 10 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.489A pdb=" N LYS B 72 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.489A pdb=" N LYS B 72 " --> pdb=" O HIS B 51 " (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: 6.294A pdb=" N PHE B 177 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B 119 " --> pdb=" O PHE B 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.555A 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: 5.555A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 3.665A 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 Processing sheet with id=AB2, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB4, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 225 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY D 276 " --> pdb=" O TYR D 299 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 25 through 27 Processing sheet with id=AB7, first strand: chain 'D' and resid 77 through 79 Processing sheet with id=AB8, first strand: chain 'D' and resid 155 through 156 Processing sheet with id=AB9, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC1, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AC2, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.620A pdb=" N SER E 225 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY E 276 " --> pdb=" O TYR E 299 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AC4, first strand: chain 'E' and resid 43 through 47 removed outlier: 6.565A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC6, first strand: chain 'E' and resid 155 through 159 Processing sheet with id=AC7, first strand: chain 'F' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR F 180 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR F 182 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR F 15 " --> pdb=" O TRP F 230 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TRP F 230 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR F 17 " --> pdb=" O PHE F 228 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE F 228 " --> pdb=" O TYR F 17 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR F 19 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU F 226 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU F 21 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY F 276 " --> pdb=" O TYR F 299 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.690A pdb=" N GLU F 174 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AD3, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.398A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR G 183 " --> pdb=" O ASN G 143 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA G 145 " --> pdb=" O GLN G 181 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLN G 181 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR G 180 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 225 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 25 through 27 removed outlier: 3.782A pdb=" N GLY G 25 " --> pdb=" O THR G 178 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD6, first strand: chain 'G' and resid 77 through 80 Processing sheet with id=AD7, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AD8, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.307A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.307A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR H 180 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 6.422A 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: 6.904A pdb=" N TYR H 17 " --> pdb=" O PHE H 228 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE H 228 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR H 19 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU H 226 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU H 21 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY H 276 " --> pdb=" O TYR H 299 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE2, first strand: chain 'H' and resid 77 through 80 Processing sheet with id=AE3, first strand: chain 'I' and resid 9 through 12 removed outlier: 4.081A pdb=" N ILE I 9 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU I 61 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU I 11 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 79 through 81 Processing sheet with id=AE5, first strand: chain 'I' and resid 120 through 131 removed outlier: 6.592A pdb=" N GLN I 121 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER I 143 " --> pdb=" O GLY I 123 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE I 125 " --> pdb=" O TYR I 141 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR I 141 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN I 127 " --> pdb=" O TYR I 139 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR I 139 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU I 129 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL I 137 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AE7, first strand: chain 'I' and resid 258 through 259 removed outlier: 8.376A pdb=" N VAL I 259 " --> pdb=" O TYR I 211 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU I 213 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG I 228 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER I 304 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU I 302 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 332 through 333 1087 hydrogen bonds defined for protein. 3009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 12.35 Time building geometry restraints manager: 7.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8138 1.34 - 1.46: 7686 1.46 - 1.59: 11827 1.59 - 1.71: 266 1.71 - 1.84: 149 Bond restraints: 28066 Sorted by residual: bond pdb=" CA ASP D 246 " pdb=" C ASP D 246 " ideal model delta sigma weight residual 1.524 1.508 0.016 8.10e-03 1.52e+04 3.84e+00 bond pdb=" O3' DC N 50 " pdb=" P DT N 51 " ideal model delta sigma weight residual 1.607 1.635 -0.028 1.50e-02 4.44e+03 3.51e+00 bond pdb=" C PRO A 200 " pdb=" N PRO A 201 " ideal model delta sigma weight residual 1.329 1.350 -0.020 1.25e-02 6.40e+03 2.60e+00 bond pdb=" CA VAL I 205 " pdb=" C VAL I 205 " ideal model delta sigma weight residual 1.520 1.534 -0.014 8.80e-03 1.29e+04 2.49e+00 bond pdb=" C LEU I 379 " pdb=" O LEU I 379 " ideal model delta sigma weight residual 1.236 1.219 0.018 1.15e-02 7.56e+03 2.45e+00 ... (remaining 28061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 37684 2.02 - 4.03: 725 4.03 - 6.05: 87 6.05 - 8.06: 16 8.06 - 10.08: 2 Bond angle restraints: 38514 Sorted by residual: angle pdb=" C THR B 157 " pdb=" N PRO B 158 " pdb=" CA PRO B 158 " ideal model delta sigma weight residual 119.76 115.31 4.45 1.03e+00 9.43e-01 1.87e+01 angle pdb=" N GLY I 355 " pdb=" CA GLY I 355 " pdb=" C GLY I 355 " ideal model delta sigma weight residual 115.21 109.83 5.38 1.30e+00 5.92e-01 1.71e+01 angle pdb=" C ILE B 50 " pdb=" N HIS B 51 " pdb=" CA HIS B 51 " ideal model delta sigma weight residual 120.49 126.34 -5.85 1.42e+00 4.96e-01 1.70e+01 angle pdb=" C PRO A 200 " pdb=" N PRO A 201 " pdb=" CA PRO A 201 " ideal model delta sigma weight residual 120.14 115.79 4.35 1.06e+00 8.90e-01 1.68e+01 angle pdb=" N GLN I 45 " pdb=" CA GLN I 45 " pdb=" C GLN I 45 " ideal model delta sigma weight residual 112.23 107.18 5.05 1.26e+00 6.30e-01 1.61e+01 ... (remaining 38509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 15733 35.81 - 71.62: 822 71.62 - 107.43: 60 107.43 - 143.24: 4 143.24 - 179.04: 5 Dihedral angle restraints: 16624 sinusoidal: 7965 harmonic: 8659 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 20.96 179.04 1 1.50e+01 4.44e-03 8.53e+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 60.29 139.71 1 1.50e+01 4.44e-03 7.52e+01 dihedral pdb=" O4' U M 32 " pdb=" C1' U M 32 " pdb=" N1 U M 32 " pdb=" C2 U M 32 " ideal model delta sinusoidal sigma weight residual 232.00 66.54 165.46 1 1.70e+01 3.46e-03 6.54e+01 ... (remaining 16621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3317 0.046 - 0.091: 623 0.091 - 0.137: 174 0.137 - 0.183: 14 0.183 - 0.228: 5 Chirality restraints: 4133 Sorted by residual: chirality pdb=" C3' A M 38 " pdb=" C4' A M 38 " pdb=" O3' A M 38 " pdb=" C2' A M 38 " both_signs ideal model delta sigma weight residual False -2.74 -2.52 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE J 13 " pdb=" CA ILE J 13 " pdb=" CG1 ILE J 13 " pdb=" CG2 ILE J 13 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA MET A 1 " pdb=" N MET A 1 " pdb=" C MET A 1 " pdb=" CB MET A 1 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 4130 not shown) Planarity restraints: 4439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " 0.058 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO F 247 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO F 247 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 247 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C PHE J 61 " 0.056 2.00e-02 2.50e+03 pdb=" O PHE J 61 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS J 62 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 246 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO E 247 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO E 247 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 247 " 0.041 5.00e-02 4.00e+02 ... (remaining 4436 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 190 2.49 - 3.09: 19801 3.09 - 3.69: 44453 3.69 - 4.30: 65577 4.30 - 4.90: 104498 Nonbonded interactions: 234519 Sorted by model distance: nonbonded pdb=" C5' DG O 10 " pdb=" O6 DG O 11 " model vdw 1.886 3.440 nonbonded pdb=" O4 U M 35 " pdb=" N6 A M 36 " model vdw 2.163 3.120 nonbonded pdb=" O4 U M 23 " pdb=" N6 A M 24 " model vdw 2.164 3.120 nonbonded pdb=" C5' DG O 10 " pdb=" C6 DG O 11 " model vdw 2.185 3.660 nonbonded pdb=" OG SER E 28 " pdb=" O GLU E 174 " model vdw 2.211 3.040 ... (remaining 234514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 12 through 109 or resid 133 through 319)) selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.030 Extract box with map and model: 1.050 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 70.400 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 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 0.060 28066 Z= 0.165 Angle : 0.657 10.079 38514 Z= 0.377 Chirality : 0.040 0.228 4133 Planarity : 0.005 0.088 4439 Dihedral : 19.538 179.045 11078 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.16 % Favored : 92.16 % Rotamer: Outliers : 0.95 % Allowed : 20.05 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.16), residues: 2921 helix: 1.34 (0.16), residues: 1001 sheet: -0.86 (0.20), residues: 619 loop : -0.87 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP I 63 HIS 0.005 0.001 HIS H 171 PHE 0.019 0.001 PHE G 234 TYR 0.038 0.001 TYR C 244 ARG 0.004 0.000 ARG B 213 Details of bonding type rmsd hydrogen bonds : bond 0.18246 ( 1150) hydrogen bonds : angle 6.85381 ( 3233) covalent geometry : bond 0.00323 (28066) covalent geometry : angle 0.65709 (38514) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 368 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASN cc_start: 0.8214 (m-40) cc_final: 0.7879 (p0) REVERT: C 155 VAL cc_start: 0.8718 (p) cc_final: 0.8509 (p) REVERT: C 172 PHE cc_start: 0.6419 (m-10) cc_final: 0.5925 (m-10) REVERT: E 15 TYR cc_start: 0.8489 (m-80) cc_final: 0.8186 (m-80) REVERT: E 108 LEU cc_start: 0.8204 (tt) cc_final: 0.7872 (tt) REVERT: E 248 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7475 (mptt) REVERT: F 48 ASN cc_start: 0.8678 (m-40) cc_final: 0.8408 (t0) REVERT: F 144 MET cc_start: 0.8830 (mtm) cc_final: 0.8242 (mtm) REVERT: F 205 MET cc_start: 0.8489 (mmp) cc_final: 0.8078 (mmm) REVERT: G 135 GLN cc_start: 0.8447 (pt0) cc_final: 0.8182 (pt0) REVERT: I 310 ILE cc_start: 0.7768 (mt) cc_final: 0.6967 (mm) REVERT: I 443 CYS cc_start: 0.8878 (m) cc_final: 0.8653 (m) REVERT: J 38 ASP cc_start: 0.6373 (t0) cc_final: 0.6117 (m-30) REVERT: J 53 ASN cc_start: 0.7992 (t0) cc_final: 0.7588 (m-40) REVERT: K 38 ASP cc_start: 0.8389 (t0) cc_final: 0.8141 (t0) REVERT: K 47 ARG cc_start: 0.8730 (ttt90) cc_final: 0.8433 (ttt90) REVERT: L 43 LYS cc_start: 0.8861 (mtpt) cc_final: 0.8659 (tppt) REVERT: L 51 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7974 (mm-30) REVERT: L 80 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8273 (mt-10) REVERT: L 96 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8363 (mp0) outliers start: 25 outliers final: 3 residues processed: 387 average time/residue: 0.4415 time to fit residues: 258.5275 Evaluate side-chains 218 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 214 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain I residue 358 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 122 optimal weight: 0.0170 chunk 236 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 176 optimal weight: 6.9990 chunk 274 optimal weight: 6.9990 overall best weight: 2.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN B 193 GLN B 195 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS C 229 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 ASN ** J 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.101949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.073658 restraints weight = 97562.050| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.13 r_work: 0.3297 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 28066 Z= 0.210 Angle : 0.659 7.391 38514 Z= 0.353 Chirality : 0.042 0.240 4133 Planarity : 0.005 0.092 4439 Dihedral : 19.348 175.434 5061 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.88 % Favored : 92.61 % Rotamer: Outliers : 3.28 % Allowed : 17.99 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.09 (0.16), residues: 2921 helix: 1.59 (0.16), residues: 1009 sheet: -0.68 (0.22), residues: 558 loop : -0.76 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 73 HIS 0.010 0.001 HIS H 171 PHE 0.021 0.002 PHE G 234 TYR 0.026 0.002 TYR A 175 ARG 0.010 0.001 ARG J 98 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 1150) hydrogen bonds : angle 4.96396 ( 3233) covalent geometry : bond 0.00466 (28066) covalent geometry : angle 0.65949 (38514) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 215 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.7626 (t0) cc_final: 0.7152 (t70) REVERT: A 167 ASN cc_start: 0.8335 (m-40) cc_final: 0.7888 (p0) REVERT: B 98 PHE cc_start: 0.4745 (OUTLIER) cc_final: 0.4396 (t80) REVERT: B 116 TYR cc_start: 0.0336 (OUTLIER) cc_final: -0.0032 (t80) REVERT: F 144 MET cc_start: 0.9102 (mtm) cc_final: 0.8876 (mtp) REVERT: F 205 MET cc_start: 0.8453 (mmp) cc_final: 0.8118 (mmm) REVERT: G 32 ASP cc_start: 0.8255 (p0) cc_final: 0.8048 (p0) REVERT: G 77 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8772 (ttp-170) REVERT: G 137 MET cc_start: 0.8628 (tpp) cc_final: 0.8300 (tpp) REVERT: G 170 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7366 (pt) REVERT: G 221 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.7876 (t80) REVERT: H 205 MET cc_start: 0.8881 (mmm) cc_final: 0.8619 (mmp) REVERT: I 74 LEU cc_start: 0.9570 (tp) cc_final: 0.9291 (pp) REVERT: I 187 GLN cc_start: 0.8858 (pm20) cc_final: 0.8409 (pp30) REVERT: I 323 LYS cc_start: 0.8287 (mmmt) cc_final: 0.7809 (mmtt) REVERT: J 38 ASP cc_start: 0.6506 (t0) cc_final: 0.6121 (m-30) REVERT: K 38 ASP cc_start: 0.8460 (t0) cc_final: 0.8155 (t0) REVERT: K 47 ARG cc_start: 0.8870 (ttt90) cc_final: 0.8515 (ttt90) REVERT: L 51 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8288 (mm-30) REVERT: L 97 ILE cc_start: 0.9316 (mm) cc_final: 0.9019 (mt) outliers start: 86 outliers final: 20 residues processed: 294 average time/residue: 0.4285 time to fit residues: 195.7721 Evaluate side-chains 207 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 32 LYS Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 109 optimal weight: 6.9990 chunk 300 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 263 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 283 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 GLN F 30 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 HIS ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN I 88 HIS ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 ASN J 81 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.101085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.072382 restraints weight = 97685.700| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.07 r_work: 0.3299 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 28066 Z= 0.186 Angle : 0.611 8.600 38514 Z= 0.328 Chirality : 0.041 0.193 4133 Planarity : 0.005 0.094 4439 Dihedral : 19.261 172.224 5055 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.74 % Favored : 92.71 % Rotamer: Outliers : 2.32 % Allowed : 18.45 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.16 (0.16), residues: 2921 helix: 1.60 (0.16), residues: 1016 sheet: -0.67 (0.22), residues: 548 loop : -0.67 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 104 HIS 0.007 0.001 HIS H 171 PHE 0.026 0.001 PHE J 78 TYR 0.024 0.002 TYR K 77 ARG 0.008 0.000 ARG J 98 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 1150) hydrogen bonds : angle 4.73465 ( 3233) covalent geometry : bond 0.00420 (28066) covalent geometry : angle 0.61066 (38514) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 3.947 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: A 166 ASP cc_start: 0.7658 (t0) cc_final: 0.7170 (t0) REVERT: A 167 ASN cc_start: 0.8212 (m-40) cc_final: 0.7769 (p0) REVERT: B 98 PHE cc_start: 0.4713 (OUTLIER) cc_final: 0.4364 (t80) REVERT: D 137 MET cc_start: 0.8087 (tpp) cc_final: 0.7882 (tmm) REVERT: E 152 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8139 (p0) REVERT: F 108 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8611 (tt) REVERT: F 205 MET cc_start: 0.8426 (mmp) cc_final: 0.8164 (mmm) REVERT: G 77 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8489 (ttp-170) REVERT: G 137 MET cc_start: 0.8616 (tpp) cc_final: 0.8278 (tpp) REVERT: G 170 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7418 (pt) REVERT: G 219 TYR cc_start: 0.8550 (t80) cc_final: 0.8344 (t80) REVERT: I 323 LYS cc_start: 0.8415 (mmmt) cc_final: 0.7963 (mmtt) REVERT: I 359 TRP cc_start: 0.5819 (t-100) cc_final: 0.5611 (t-100) REVERT: J 38 ASP cc_start: 0.6411 (t0) cc_final: 0.6006 (m-30) REVERT: K 38 ASP cc_start: 0.8578 (t0) cc_final: 0.8287 (t0) REVERT: L 51 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8146 (mm-30) outliers start: 61 outliers final: 25 residues processed: 244 average time/residue: 0.4480 time to fit residues: 171.4987 Evaluate side-chains 206 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 233 HIS Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain J residue 32 LYS Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 50 optimal weight: 10.0000 chunk 270 optimal weight: 0.8980 chunk 282 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 123 optimal weight: 0.0670 chunk 232 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 overall best weight: 4.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 GLN ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.099060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.070218 restraints weight = 97951.020| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.08 r_work: 0.3229 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 28066 Z= 0.253 Angle : 0.648 9.601 38514 Z= 0.347 Chirality : 0.042 0.198 4133 Planarity : 0.005 0.093 4439 Dihedral : 19.210 168.172 5053 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.29 % Favored : 92.19 % Rotamer: Outliers : 3.09 % Allowed : 17.87 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -0.03 (0.16), residues: 2921 helix: 1.42 (0.16), residues: 1014 sheet: -0.86 (0.21), residues: 585 loop : -0.70 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.006 0.001 HIS H 171 PHE 0.021 0.002 PHE G 234 TYR 0.022 0.002 TYR A 37 ARG 0.008 0.001 ARG K 71 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 1150) hydrogen bonds : angle 4.76475 ( 3233) covalent geometry : bond 0.00564 (28066) covalent geometry : angle 0.64797 (38514) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 184 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.7217 (tpp) REVERT: A 113 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8875 (mm-40) REVERT: A 166 ASP cc_start: 0.7927 (t0) cc_final: 0.7473 (t0) REVERT: A 167 ASN cc_start: 0.8305 (m-40) cc_final: 0.7854 (p0) REVERT: B 98 PHE cc_start: 0.4707 (OUTLIER) cc_final: 0.4416 (t80) REVERT: C 295 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8659 (tptp) REVERT: D 137 MET cc_start: 0.8178 (tpp) cc_final: 0.7933 (tmm) REVERT: E 152 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8321 (p0) REVERT: F 166 ASP cc_start: 0.8242 (t0) cc_final: 0.8029 (t0) REVERT: F 283 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8930 (mp10) REVERT: G 77 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8619 (ttp-170) REVERT: G 137 MET cc_start: 0.8731 (tpp) cc_final: 0.8412 (tpp) REVERT: G 170 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7435 (pt) REVERT: G 302 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8187 (mtt90) REVERT: I 21 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6615 (ttm) REVERT: I 303 MET cc_start: 0.8170 (mmm) cc_final: 0.7891 (mmm) REVERT: I 323 LYS cc_start: 0.8423 (mmmt) cc_final: 0.8003 (mmtt) REVERT: I 439 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8011 (tp30) REVERT: J 38 ASP cc_start: 0.6414 (t0) cc_final: 0.5949 (m-30) REVERT: J 67 ASP cc_start: 0.7692 (m-30) cc_final: 0.7388 (t0) REVERT: J 71 ARG cc_start: 0.8374 (mtt180) cc_final: 0.7693 (mtt-85) REVERT: K 38 ASP cc_start: 0.8589 (t0) cc_final: 0.8291 (t0) REVERT: L 47 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8674 (tpt-90) outliers start: 81 outliers final: 39 residues processed: 251 average time/residue: 0.4120 time to fit residues: 162.0505 Evaluate side-chains 218 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 233 HIS Chi-restraints excluded: chain G residue 302 ARG Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 47 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 243 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 chunk 250 optimal weight: 8.9990 chunk 253 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 284 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.100446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.072089 restraints weight = 97894.880| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.04 r_work: 0.3271 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28066 Z= 0.141 Angle : 0.582 9.475 38514 Z= 0.313 Chirality : 0.040 0.216 4133 Planarity : 0.004 0.092 4439 Dihedral : 19.160 166.919 5053 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.71 % Favored : 92.81 % Rotamer: Outliers : 2.55 % Allowed : 18.33 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.03 (0.16), residues: 2921 helix: 1.48 (0.16), residues: 1020 sheet: -0.81 (0.21), residues: 587 loop : -0.69 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP I 73 HIS 0.007 0.001 HIS H 171 PHE 0.011 0.001 PHE G 234 TYR 0.022 0.001 TYR G 182 ARG 0.011 0.000 ARG K 71 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 1150) hydrogen bonds : angle 4.57780 ( 3233) covalent geometry : bond 0.00318 (28066) covalent geometry : angle 0.58234 (38514) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 181 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6960 (tpp) REVERT: A 61 MET cc_start: 0.8647 (mmt) cc_final: 0.8317 (mmt) REVERT: A 113 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8926 (mm-40) REVERT: A 140 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7696 (tp30) REVERT: A 166 ASP cc_start: 0.7851 (t0) cc_final: 0.7406 (t0) REVERT: A 167 ASN cc_start: 0.8270 (m-40) cc_final: 0.7827 (p0) REVERT: B 98 PHE cc_start: 0.4567 (OUTLIER) cc_final: 0.4327 (t80) REVERT: F 108 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8723 (tt) REVERT: F 166 ASP cc_start: 0.8055 (t0) cc_final: 0.7787 (t0) REVERT: F 200 MET cc_start: 0.8602 (mmm) cc_final: 0.8361 (mtp) REVERT: F 283 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8963 (mp10) REVERT: G 77 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7793 (mtm-85) REVERT: G 137 MET cc_start: 0.8698 (tpp) cc_final: 0.8409 (tpp) REVERT: G 170 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7397 (pt) REVERT: G 302 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8257 (mtt90) REVERT: I 74 LEU cc_start: 0.9573 (tp) cc_final: 0.9277 (pp) REVERT: I 187 GLN cc_start: 0.8945 (pm20) cc_final: 0.8469 (pp30) REVERT: I 303 MET cc_start: 0.8424 (mmm) cc_final: 0.8076 (mmm) REVERT: I 323 LYS cc_start: 0.8465 (mmmt) cc_final: 0.8063 (mmtt) REVERT: I 439 GLU cc_start: 0.8601 (mm-30) cc_final: 0.7993 (tp30) REVERT: J 38 ASP cc_start: 0.6585 (t0) cc_final: 0.6139 (m-30) REVERT: J 67 ASP cc_start: 0.7777 (m-30) cc_final: 0.7525 (t0) REVERT: J 71 ARG cc_start: 0.8498 (mtt180) cc_final: 0.7876 (mtt-85) REVERT: K 38 ASP cc_start: 0.8582 (t0) cc_final: 0.8282 (t0) outliers start: 67 outliers final: 35 residues processed: 234 average time/residue: 0.4243 time to fit residues: 153.0453 Evaluate side-chains 209 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 233 HIS Chi-restraints excluded: chain G residue 302 ARG Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain L residue 41 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 288 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 260 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN F 30 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.099126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.070745 restraints weight = 98551.275| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.06 r_work: 0.3248 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28066 Z= 0.202 Angle : 0.611 9.596 38514 Z= 0.327 Chirality : 0.041 0.191 4133 Planarity : 0.005 0.092 4439 Dihedral : 19.145 168.712 5053 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.05 % Favored : 92.47 % Rotamer: Outliers : 2.44 % Allowed : 18.75 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.00 (0.16), residues: 2921 helix: 1.38 (0.16), residues: 1025 sheet: -0.77 (0.21), residues: 579 loop : -0.68 (0.18), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 73 HIS 0.006 0.001 HIS H 171 PHE 0.013 0.001 PHE E 242 TYR 0.016 0.002 TYR G 182 ARG 0.012 0.000 ARG K 71 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 1150) hydrogen bonds : angle 4.60991 ( 3233) covalent geometry : bond 0.00457 (28066) covalent geometry : angle 0.61078 (38514) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 175 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8624 (mmt) cc_final: 0.8254 (mmt) REVERT: A 113 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8878 (mm-40) REVERT: A 166 ASP cc_start: 0.8016 (t0) cc_final: 0.7556 (t0) REVERT: A 167 ASN cc_start: 0.8074 (m-40) cc_final: 0.7747 (p0) REVERT: B 98 PHE cc_start: 0.4746 (OUTLIER) cc_final: 0.4451 (t80) REVERT: F 166 ASP cc_start: 0.8170 (t0) cc_final: 0.7860 (t0) REVERT: G 77 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.7702 (mtm-85) REVERT: G 137 MET cc_start: 0.8678 (tpp) cc_final: 0.8369 (tpp) REVERT: G 170 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7363 (pt) REVERT: G 302 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8166 (mtt90) REVERT: I 187 GLN cc_start: 0.9024 (pm20) cc_final: 0.8621 (pp30) REVERT: I 323 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8122 (mmtt) REVERT: I 439 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7966 (tp30) REVERT: J 38 ASP cc_start: 0.6432 (t0) cc_final: 0.5997 (m-30) REVERT: J 67 ASP cc_start: 0.7779 (m-30) cc_final: 0.7566 (t0) REVERT: J 71 ARG cc_start: 0.8456 (mtt180) cc_final: 0.7857 (mtt-85) REVERT: J 112 ASP cc_start: 0.4067 (OUTLIER) cc_final: 0.2772 (p0) REVERT: K 38 ASP cc_start: 0.8599 (t0) cc_final: 0.8289 (t0) REVERT: L 47 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8515 (tpt-90) outliers start: 64 outliers final: 42 residues processed: 228 average time/residue: 0.4542 time to fit residues: 166.6294 Evaluate side-chains 212 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 302 ARG Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 245 optimal weight: 20.0000 chunk 55 optimal weight: 40.0000 chunk 227 optimal weight: 0.0570 chunk 204 optimal weight: 6.9990 chunk 177 optimal weight: 0.0770 chunk 10 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 overall best weight: 1.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.099885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.071595 restraints weight = 97747.313| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.06 r_work: 0.3264 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28066 Z= 0.151 Angle : 0.585 9.448 38514 Z= 0.313 Chirality : 0.040 0.198 4133 Planarity : 0.004 0.091 4439 Dihedral : 19.118 170.255 5053 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.78 % Favored : 92.74 % Rotamer: Outliers : 2.55 % Allowed : 18.90 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.08 (0.16), residues: 2921 helix: 1.46 (0.16), residues: 1027 sheet: -0.72 (0.21), residues: 582 loop : -0.65 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 73 HIS 0.007 0.001 HIS H 171 PHE 0.014 0.001 PHE G 234 TYR 0.020 0.001 TYR A 37 ARG 0.014 0.000 ARG K 71 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 1150) hydrogen bonds : angle 4.52718 ( 3233) covalent geometry : bond 0.00341 (28066) covalent geometry : angle 0.58458 (38514) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 171 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8907 (mm-40) REVERT: A 140 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7669 (tp30) REVERT: A 166 ASP cc_start: 0.7923 (t0) cc_final: 0.7481 (t0) REVERT: A 167 ASN cc_start: 0.7937 (m-40) cc_final: 0.7624 (p0) REVERT: B 98 PHE cc_start: 0.4759 (OUTLIER) cc_final: 0.4484 (t80) REVERT: F 108 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8762 (tt) REVERT: F 166 ASP cc_start: 0.8073 (t0) cc_final: 0.7737 (t0) REVERT: G 77 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.7764 (mtm-85) REVERT: G 137 MET cc_start: 0.8657 (tpp) cc_final: 0.8383 (tpp) REVERT: G 170 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7343 (pt) REVERT: G 302 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8138 (mtt90) REVERT: H 302 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.6942 (mtm180) REVERT: I 323 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8109 (mmtt) REVERT: I 324 TYR cc_start: 0.8426 (m-80) cc_final: 0.8183 (m-80) REVERT: I 439 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8001 (tp30) REVERT: J 22 MET cc_start: 0.7560 (ppp) cc_final: 0.7163 (ppp) REVERT: J 38 ASP cc_start: 0.6411 (t0) cc_final: 0.6026 (m-30) REVERT: J 56 TYR cc_start: 0.8599 (p90) cc_final: 0.8216 (p90) REVERT: J 71 ARG cc_start: 0.8527 (mtt180) cc_final: 0.7918 (mtt-85) REVERT: J 112 ASP cc_start: 0.3894 (OUTLIER) cc_final: 0.2710 (p0) REVERT: K 38 ASP cc_start: 0.8521 (t0) cc_final: 0.8217 (t0) REVERT: L 47 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8559 (tpt-90) outliers start: 67 outliers final: 43 residues processed: 224 average time/residue: 0.4599 time to fit residues: 161.6034 Evaluate side-chains 216 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 233 HIS Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain G residue 302 ARG Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 47 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 291 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 294 optimal weight: 50.0000 chunk 81 optimal weight: 0.0980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** I 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.098098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.069753 restraints weight = 98006.215| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.98 r_work: 0.3213 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28066 Z= 0.239 Angle : 0.642 9.477 38514 Z= 0.341 Chirality : 0.042 0.221 4133 Planarity : 0.005 0.091 4439 Dihedral : 19.142 171.691 5053 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.19 % Favored : 92.33 % Rotamer: Outliers : 2.29 % Allowed : 19.74 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -0.08 (0.16), residues: 2921 helix: 1.32 (0.16), residues: 1028 sheet: -0.78 (0.21), residues: 587 loop : -0.74 (0.18), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 273 HIS 0.007 0.001 HIS H 171 PHE 0.025 0.002 PHE F 234 TYR 0.029 0.002 TYR G 182 ARG 0.014 0.001 ARG K 71 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 1150) hydrogen bonds : angle 4.66284 ( 3233) covalent geometry : bond 0.00541 (28066) covalent geometry : angle 0.64181 (38514) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7208 (tpp) REVERT: A 166 ASP cc_start: 0.8144 (t0) cc_final: 0.7726 (t0) REVERT: A 167 ASN cc_start: 0.8007 (m-40) cc_final: 0.7636 (p0) REVERT: B 98 PHE cc_start: 0.4688 (OUTLIER) cc_final: 0.4439 (t80) REVERT: C 224 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8040 (p0) REVERT: F 166 ASP cc_start: 0.8212 (t0) cc_final: 0.7858 (t0) REVERT: G 77 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.7723 (mtm-85) REVERT: G 137 MET cc_start: 0.8640 (tpp) cc_final: 0.8404 (tpp) REVERT: G 170 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7385 (pt) REVERT: G 302 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8247 (mtt90) REVERT: H 302 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.6857 (mtm180) REVERT: I 323 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8116 (mmtt) REVERT: I 324 TYR cc_start: 0.8346 (m-80) cc_final: 0.8072 (m-80) REVERT: I 439 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8017 (tp30) REVERT: J 22 MET cc_start: 0.7465 (ppp) cc_final: 0.7052 (ppp) REVERT: J 71 ARG cc_start: 0.8561 (mtt180) cc_final: 0.8228 (mtt90) REVERT: J 112 ASP cc_start: 0.4317 (OUTLIER) cc_final: 0.2804 (p0) REVERT: K 38 ASP cc_start: 0.8614 (t0) cc_final: 0.8321 (t0) REVERT: L 47 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8680 (tpt-90) outliers start: 60 outliers final: 41 residues processed: 219 average time/residue: 0.4388 time to fit residues: 149.7489 Evaluate side-chains 213 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain G residue 302 ARG Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 117 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 280 optimal weight: 1.9990 chunk 204 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 chunk 293 optimal weight: 30.0000 chunk 162 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 GLN ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.098932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.070583 restraints weight = 98406.833| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.08 r_work: 0.3252 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28066 Z= 0.175 Angle : 0.608 9.351 38514 Z= 0.324 Chirality : 0.040 0.234 4133 Planarity : 0.005 0.089 4439 Dihedral : 19.116 172.056 5053 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.12 % Favored : 92.40 % Rotamer: Outliers : 2.13 % Allowed : 20.05 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: -0.03 (0.16), residues: 2921 helix: 1.38 (0.16), residues: 1027 sheet: -0.79 (0.21), residues: 587 loop : -0.71 (0.18), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 358 HIS 0.007 0.001 HIS H 171 PHE 0.017 0.001 PHE F 234 TYR 0.023 0.001 TYR G 182 ARG 0.015 0.000 ARG K 71 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 1150) hydrogen bonds : angle 4.56972 ( 3233) covalent geometry : bond 0.00397 (28066) covalent geometry : angle 0.60841 (38514) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7071 (tpp) REVERT: A 140 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7868 (tp30) REVERT: A 166 ASP cc_start: 0.8122 (t0) cc_final: 0.7679 (t0) REVERT: A 167 ASN cc_start: 0.7951 (m-40) cc_final: 0.7581 (p0) REVERT: B 98 PHE cc_start: 0.4661 (OUTLIER) cc_final: 0.4391 (t80) REVERT: F 77 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8448 (mtm110) REVERT: F 108 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8848 (tt) REVERT: F 166 ASP cc_start: 0.8132 (t0) cc_final: 0.7778 (t0) REVERT: G 77 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.7716 (mtm-85) REVERT: G 137 MET cc_start: 0.8612 (tpp) cc_final: 0.8402 (tpp) REVERT: G 170 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7366 (pt) REVERT: G 302 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8124 (mtt90) REVERT: I 42 LEU cc_start: 0.8942 (mt) cc_final: 0.8695 (tp) REVERT: I 323 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8132 (mmtt) REVERT: I 324 TYR cc_start: 0.8350 (m-80) cc_final: 0.7948 (m-10) REVERT: I 439 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7991 (tp30) REVERT: J 22 MET cc_start: 0.7233 (ppp) cc_final: 0.6845 (ppp) REVERT: J 56 TYR cc_start: 0.8534 (p90) cc_final: 0.8206 (p90) REVERT: J 71 ARG cc_start: 0.8495 (mtt180) cc_final: 0.8167 (mtt-85) REVERT: J 112 ASP cc_start: 0.4409 (OUTLIER) cc_final: 0.3122 (p0) REVERT: K 38 ASP cc_start: 0.8590 (t0) cc_final: 0.8270 (t0) REVERT: L 47 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8648 (tpt-90) outliers start: 56 outliers final: 44 residues processed: 211 average time/residue: 0.4712 time to fit residues: 154.5179 Evaluate side-chains 214 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain G residue 302 ARG Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 90 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 chunk 251 optimal weight: 0.8980 chunk 37 optimal weight: 40.0000 chunk 124 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 101 optimal weight: 0.0870 chunk 253 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 overall best weight: 1.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN B 162 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN E 71 GLN F 30 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** I 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.100116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.072058 restraints weight = 97514.057| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.04 r_work: 0.3286 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28066 Z= 0.134 Angle : 0.582 9.463 38514 Z= 0.311 Chirality : 0.040 0.250 4133 Planarity : 0.004 0.090 4439 Dihedral : 19.070 172.581 5053 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.78 % Favored : 92.74 % Rotamer: Outliers : 2.06 % Allowed : 20.08 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % 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: 0.08 (0.16), residues: 2921 helix: 1.53 (0.16), residues: 1023 sheet: -0.74 (0.21), residues: 593 loop : -0.68 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 73 HIS 0.008 0.001 HIS F 31 PHE 0.017 0.001 PHE F 234 TYR 0.021 0.001 TYR G 182 ARG 0.013 0.000 ARG K 71 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 1150) hydrogen bonds : angle 4.45579 ( 3233) covalent geometry : bond 0.00300 (28066) covalent geometry : angle 0.58245 (38514) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 4.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6888 (tpp) REVERT: A 140 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7730 (tp30) REVERT: A 166 ASP cc_start: 0.8060 (t0) cc_final: 0.7635 (t0) REVERT: A 167 ASN cc_start: 0.7919 (m-40) cc_final: 0.7537 (p0) REVERT: B 98 PHE cc_start: 0.4602 (OUTLIER) cc_final: 0.4295 (t80) REVERT: F 77 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8431 (mtm110) REVERT: F 108 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8784 (tt) REVERT: F 166 ASP cc_start: 0.7921 (t0) cc_final: 0.7585 (t0) REVERT: G 77 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.7798 (mtm-85) REVERT: G 137 MET cc_start: 0.8643 (tpp) cc_final: 0.8437 (tpp) REVERT: G 170 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7278 (pt) REVERT: G 302 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8236 (mtt90) REVERT: H 302 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7015 (mtm180) REVERT: I 42 LEU cc_start: 0.8932 (mt) cc_final: 0.8697 (tp) REVERT: I 310 ILE cc_start: 0.7452 (mm) cc_final: 0.7159 (mt) REVERT: I 323 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8134 (mmtt) REVERT: I 324 TYR cc_start: 0.8336 (m-80) cc_final: 0.7951 (m-10) REVERT: I 439 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7952 (tp30) REVERT: J 22 MET cc_start: 0.7383 (ppp) cc_final: 0.6981 (ppp) REVERT: J 56 TYR cc_start: 0.8462 (p90) cc_final: 0.8174 (p90) REVERT: J 71 ARG cc_start: 0.8399 (mtt180) cc_final: 0.8088 (mtt-85) REVERT: J 74 LEU cc_start: 0.7000 (tp) cc_final: 0.6761 (mt) REVERT: J 112 ASP cc_start: 0.4540 (OUTLIER) cc_final: 0.3317 (p0) REVERT: K 38 ASP cc_start: 0.8562 (t0) cc_final: 0.8247 (t0) REVERT: L 47 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8626 (tpt-90) outliers start: 54 outliers final: 38 residues processed: 212 average time/residue: 0.7359 time to fit residues: 249.2548 Evaluate side-chains 211 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 163 time to evaluate : 4.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain G residue 302 ARG Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 284 GLN Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 212 CYS Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 376 PHE Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain L residue 41 ILE Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 115 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 287 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 217 optimal weight: 40.0000 chunk 212 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.099982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.071922 restraints weight = 98019.835| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.04 r_work: 0.3288 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 28066 Z= 0.165 Angle : 0.728 59.182 38514 Z= 0.417 Chirality : 0.040 0.383 4133 Planarity : 0.004 0.090 4439 Dihedral : 19.071 172.560 5053 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.74 % Favored : 92.81 % Rotamer: Outliers : 1.83 % Allowed : 20.27 % Favored : 77.90 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.93 % 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: 0.08 (0.16), residues: 2921 helix: 1.52 (0.16), residues: 1023 sheet: -0.74 (0.21), residues: 593 loop : -0.68 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 73 HIS 0.007 0.001 HIS F 31 PHE 0.015 0.001 PHE F 234 TYR 0.021 0.001 TYR G 182 ARG 0.011 0.000 ARG K 71 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 1150) hydrogen bonds : angle 4.45616 ( 3233) covalent geometry : bond 0.00340 (28066) covalent geometry : angle 0.72763 (38514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17671.59 seconds wall clock time: 310 minutes 18.28 seconds (18618.28 seconds total)