Starting phenix.real_space_refine on Fri Jun 20 17:08:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dfo_27409/06_2025/8dfo_27409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfo_27409/06_2025/8dfo_27409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dfo_27409/06_2025/8dfo_27409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfo_27409/06_2025/8dfo_27409.map" model { file = "/net/cci-nas-00/data/ceres_data/8dfo_27409/06_2025/8dfo_27409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfo_27409/06_2025/8dfo_27409.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 45 5.49 5 S 135 5.16 5 C 14839 2.51 5 N 4259 2.21 5 O 4583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 209 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23861 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1774 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "B" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2112 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 2 Chain: "C" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "D" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "E" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "F" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "G" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "H" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2238 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "I" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3261 Classifications: {'peptide': 415} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 388} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "K" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain breaks: 1 Chain: "L" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 960 Classifications: {'RNA': 45} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 8, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna2p': 17, 'rna3p': 27} Chain: "M" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 466 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Time building chain proxies: 14.58, per 1000 atoms: 0.61 Number of scatterers: 23861 At special positions: 0 Unit cell: (119.38, 117.5, 202.1, 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 135 16.00 P 45 15.00 O 4583 8.00 N 4259 7.00 C 14839 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: 5.35 Conformation dependent library (CDL) restraints added in 2.7 seconds 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5458 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 36 sheets defined 38.0% alpha, 23.7% beta 0 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 7.38 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.784A pdb=" N LYS A 28 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 Processing helix chain 'A' and resid 88 through 93 removed outlier: 4.167A pdb=" N ASP A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'B' and resid 43 through 60 Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.883A pdb=" N ASN B 112 " --> pdb=" O TRP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 119 Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 193 through 199 removed outlier: 3.561A pdb=" N LYS B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 217 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'C' and resid 43 through 60 removed outlier: 3.545A pdb=" N LEU C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 removed outlier: 3.548A pdb=" N ALA C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 113 Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.567A pdb=" N LYS C 199 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 217 through 221 removed outlier: 4.320A pdb=" N HIS C 220 " --> pdb=" O MET C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'D' and resid 43 through 60 removed outlier: 3.628A pdb=" N LEU D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 86 removed outlier: 3.606A pdb=" N THR D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 113 Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.539A pdb=" N LYS D 199 " --> pdb=" O PRO D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.785A pdb=" N SER D 263 " --> pdb=" O ALA D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'E' and resid 43 through 60 removed outlier: 3.540A pdb=" N LEU E 47 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 98 through 113 Processing helix chain 'E' and resid 113 through 120 Processing helix chain 'E' and resid 193 through 201 removed outlier: 3.930A pdb=" N LYS E 199 " --> pdb=" O PRO E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 247 through 253 Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'F' and resid 43 through 60 removed outlier: 3.551A pdb=" N LEU F 47 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 98 through 113 Processing helix chain 'F' and resid 113 through 120 Processing helix chain 'F' and resid 193 through 201 removed outlier: 3.595A pdb=" N LYS F 199 " --> pdb=" O PRO F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 Processing helix chain 'F' and resid 247 through 253 Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'G' and resid 24 through 28 removed outlier: 3.916A pdb=" N GLY G 28 " --> pdb=" O PRO G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 60 removed outlier: 3.645A pdb=" N LEU G 47 " --> pdb=" O THR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 98 through 113 Processing helix chain 'G' and resid 113 through 120 Processing helix chain 'G' and resid 193 through 201 removed outlier: 3.560A pdb=" N LYS G 199 " --> pdb=" O PRO G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 216 Processing helix chain 'G' and resid 217 through 221 removed outlier: 4.163A pdb=" N HIS G 220 " --> pdb=" O MET G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 255 removed outlier: 3.607A pdb=" N LEU G 254 " --> pdb=" O LYS G 250 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL G 255 " --> pdb=" O LEU G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'H' and resid 24 through 28 removed outlier: 3.787A pdb=" N GLY H 28 " --> pdb=" O PRO H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 removed outlier: 3.763A pdb=" N LEU H 47 " --> pdb=" O THR H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 87 Processing helix chain 'H' and resid 98 through 113 Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'H' and resid 193 through 201 removed outlier: 4.177A pdb=" N LYS H 199 " --> pdb=" O PRO H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 Processing helix chain 'H' and resid 247 through 255 removed outlier: 3.583A pdb=" N ASP H 253 " --> pdb=" O HIS H 249 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL H 255 " --> pdb=" O LEU H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 271 No H-bonds generated for 'chain 'H' and resid 269 through 271' Processing helix chain 'I' and resid 4 through 14 Processing helix chain 'I' and resid 239 through 255 removed outlier: 3.568A pdb=" N VAL I 247 " --> pdb=" O ALA I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 287 removed outlier: 4.343A pdb=" N ALA I 284 " --> pdb=" O GLU I 280 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY I 285 " --> pdb=" O ASP I 281 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE I 287 " --> pdb=" O PHE I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 335 Processing helix chain 'I' and resid 338 through 342 Processing helix chain 'I' and resid 373 through 389 Processing helix chain 'I' and resid 402 through 409 Processing helix chain 'I' and resid 420 through 427 Processing helix chain 'I' and resid 430 through 434 Processing helix chain 'I' and resid 440 through 452 Processing helix chain 'I' and resid 455 through 459 removed outlier: 4.018A pdb=" N ASP I 458 " --> pdb=" O ARG I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 468 through 482 Processing helix chain 'I' and resid 497 through 517 Processing helix chain 'I' and resid 523 through 528 removed outlier: 3.758A pdb=" N ARG I 527 " --> pdb=" O THR I 523 " (cutoff:3.500A) Processing helix chain 'I' and resid 528 through 535 Processing helix chain 'I' and resid 535 through 557 removed outlier: 3.885A pdb=" N VAL I 539 " --> pdb=" O ASN I 535 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N HIS I 541 " --> pdb=" O GLY I 537 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N MET I 542 " --> pdb=" O GLN I 538 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS I 556 " --> pdb=" O ALA I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 564 through 576 removed outlier: 3.825A pdb=" N GLU I 568 " --> pdb=" O ALA I 564 " (cutoff:3.500A) Processing helix chain 'I' and resid 586 through 603 Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 35 through 40 Processing helix chain 'J' and resid 40 through 47 Processing helix chain 'J' and resid 47 through 69 removed outlier: 3.655A pdb=" N VAL J 51 " --> pdb=" O ASN J 47 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N HIS J 53 " --> pdb=" O GLY J 49 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N MET J 54 " --> pdb=" O GLN J 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP J 69 " --> pdb=" O LYS J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.843A pdb=" N ASN J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 118 Processing helix chain 'K' and resid 9 through 29 Processing helix chain 'K' and resid 35 through 47 removed outlier: 3.516A pdb=" N ARG K 39 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA K 42 " --> pdb=" O ASP K 38 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 68 removed outlier: 3.708A pdb=" N VAL K 51 " --> pdb=" O ASN K 47 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS K 53 " --> pdb=" O GLY K 49 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET K 54 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN K 61 " --> pdb=" O LYS K 57 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 73 No H-bonds generated for 'chain 'K' and resid 73 through 73' Processing helix chain 'K' and resid 77 through 90 Processing helix chain 'K' and resid 98 through 118 Processing helix chain 'M' and resid 6 through 8 No H-bonds generated for 'chain 'M' and resid 6 through 8' Processing helix chain 'M' and resid 9 through 18 Processing helix chain 'M' and resid 42 through 56 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.769A pdb=" N ARG A 31 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N LEU A 115 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG A 116 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR A 19 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 78 removed outlier: 3.552A pdb=" N ARG A 75 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP A 119 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL A 64 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 121 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 62 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU A 123 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 196 removed outlier: 5.697A pdb=" N ALA A 208 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR A 190 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE A 206 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU A 192 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU A 204 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP A 194 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THR A 202 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.867A pdb=" N THR B 174 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 136 through 138 removed outlier: 3.506A pdb=" N GLY B 184 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP B 15 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N SER B 231 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLU B 17 " --> pdb=" O MET B 229 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N MET B 229 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 234 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 122 Processing sheet with id=AA8, first strand: chain 'B' and resid 255 through 259 Processing sheet with id=AA9, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 19 removed outlier: 6.921A pdb=" N GLU C 17 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR C 183 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 121 through 124 removed outlier: 4.515A pdb=" N GLY C 130 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 255 through 259 Processing sheet with id=AB5, first strand: chain 'D' and resid 41 through 42 Processing sheet with id=AB6, first strand: chain 'D' and resid 136 through 138 removed outlier: 6.753A pdb=" N TYR D 183 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU D 17 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU D 185 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP D 15 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL D 187 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU D 13 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N HIS D 189 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 11 " --> pdb=" O HIS D 189 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE D 191 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU D 9 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASP D 15 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER D 231 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLU D 17 " --> pdb=" O MET D 229 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N MET D 229 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU D 234 " --> pdb=" O MET D 289 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 121 through 122 Processing sheet with id=AB8, first strand: chain 'D' and resid 255 through 258 Processing sheet with id=AB9, first strand: chain 'E' and resid 41 through 42 Processing sheet with id=AC1, first strand: chain 'E' and resid 136 through 138 removed outlier: 6.880A pdb=" N ASP E 15 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N SER E 231 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU E 234 " --> pdb=" O MET E 289 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 121 through 122 Processing sheet with id=AC3, first strand: chain 'E' and resid 255 through 259 Processing sheet with id=AC4, first strand: chain 'F' and resid 41 through 42 removed outlier: 3.643A pdb=" N THR F 174 " --> pdb=" O ARG F 156 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 136 through 138 removed outlier: 3.832A pdb=" N ARG F 7 " --> pdb=" O HIS F 239 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP F 15 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER F 231 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLU F 17 " --> pdb=" O MET F 229 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N MET F 229 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 121 through 123 removed outlier: 3.557A pdb=" N GLY F 130 " --> pdb=" O MET F 123 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 255 through 259 Processing sheet with id=AC8, first strand: chain 'G' and resid 39 through 42 removed outlier: 5.134A pdb=" N GLY G 40 " --> pdb=" O SER G 143 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU G 185 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR G 183 " --> pdb=" O PRO G 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 136 through 138 removed outlier: 5.939A pdb=" N ASP G 15 " --> pdb=" O SER G 231 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER G 231 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLU G 17 " --> pdb=" O MET G 229 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N MET G 229 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 121 through 124 removed outlier: 3.737A pdb=" N GLY G 130 " --> pdb=" O MET G 123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 41 through 42 Processing sheet with id=AD3, first strand: chain 'H' and resid 136 through 138 removed outlier: 3.585A pdb=" N LYS H 233 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP H 15 " --> pdb=" O SER H 231 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N SER H 231 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLU H 17 " --> pdb=" O MET H 229 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N MET H 229 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 121 through 123 Processing sheet with id=AD5, first strand: chain 'H' and resid 257 through 259 Processing sheet with id=AD6, first strand: chain 'I' and resid 181 through 182 Processing sheet with id=AD7, first strand: chain 'I' and resid 201 through 202 Processing sheet with id=AD8, first strand: chain 'I' and resid 262 through 264 removed outlier: 6.630A pdb=" N VAL I 354 " --> pdb=" O TRP I 369 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP I 369 " --> pdb=" O VAL I 354 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY I 356 " --> pdb=" O ARG I 367 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 22 through 24 1005 hydrogen bonds defined for protein. 2841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 8.18 Time building geometry restraints manager: 6.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.43: 10772 1.43 - 1.82: 13669 1.82 - 2.21: 0 2.21 - 2.61: 0 2.61 - 3.00: 2 Bond restraints: 24443 Sorted by residual: bond pdb=" C LYS J 73 " pdb=" N ALA J 76 " ideal model delta sigma weight residual 1.332 2.998 -1.665 1.40e-02 5.10e+03 1.41e+04 bond pdb=" CB PRO H 92 " pdb=" CG PRO H 92 " ideal model delta sigma weight residual 1.492 2.673 -1.181 5.00e-02 4.00e+02 5.58e+02 bond pdb=" CG PRO H 92 " pdb=" CD PRO H 92 " ideal model delta sigma weight residual 1.503 1.038 0.465 3.40e-02 8.65e+02 1.87e+02 bond pdb=" CE1 HIS C 249 " pdb=" NE2 HIS C 249 " ideal model delta sigma weight residual 1.321 1.231 0.090 1.00e-02 1.00e+04 8.02e+01 bond pdb=" CE1 HIS C 54 " pdb=" NE2 HIS C 54 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.90e+01 ... (remaining 24438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.21: 33265 21.21 - 42.42: 3 42.42 - 63.63: 0 63.63 - 84.84: 0 84.84 - 106.05: 2 Bond angle restraints: 33270 Sorted by residual: angle pdb=" O LYS J 73 " pdb=" C LYS J 73 " pdb=" N ALA J 76 " ideal model delta sigma weight residual 122.59 37.08 85.51 1.33e+00 5.65e-01 4.13e+03 angle pdb=" CB PRO H 92 " pdb=" CG PRO H 92 " pdb=" CD PRO H 92 " ideal model delta sigma weight residual 106.10 0.05 106.05 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA LYS J 73 " pdb=" C LYS J 73 " pdb=" N ALA J 76 " ideal model delta sigma weight residual 116.84 84.80 32.04 1.71e+00 3.42e-01 3.51e+02 angle pdb=" CA PRO H 92 " pdb=" N PRO H 92 " pdb=" CD PRO H 92 " ideal model delta sigma weight residual 112.00 89.53 22.47 1.40e+00 5.10e-01 2.58e+02 angle pdb=" N PRO H 92 " pdb=" CA PRO H 92 " pdb=" CB PRO H 92 " ideal model delta sigma weight residual 103.19 92.31 10.88 1.00e+00 1.00e+00 1.18e+02 ... (remaining 33265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 14362 35.53 - 71.07: 523 71.07 - 106.60: 50 106.60 - 142.14: 7 142.14 - 177.67: 14 Dihedral angle restraints: 14956 sinusoidal: 6527 harmonic: 8429 Sorted by residual: dihedral pdb=" C5' U L 5 " pdb=" C4' U L 5 " pdb=" C3' U L 5 " pdb=" O3' U L 5 " ideal model delta sinusoidal sigma weight residual 147.00 74.29 72.71 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C4' C L 18 " pdb=" C3' C L 18 " pdb=" C2' C L 18 " pdb=" C1' C L 18 " ideal model delta sinusoidal sigma weight residual -35.00 36.08 -71.08 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' G L 31 " pdb=" C3' G L 31 " pdb=" C2' G L 31 " pdb=" C1' G L 31 " ideal model delta sinusoidal sigma weight residual -35.00 35.81 -70.81 1 8.00e+00 1.56e-02 1.01e+02 ... (remaining 14953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 3302 0.148 - 0.296: 73 0.296 - 0.444: 84 0.444 - 0.592: 171 0.592 - 0.740: 64 Chirality restraints: 3694 Sorted by residual: chirality pdb=" CG LEU I 364 " pdb=" CB LEU I 364 " pdb=" CD1 LEU I 364 " pdb=" CD2 LEU I 364 " both_signs ideal model delta sigma weight residual False -2.59 -1.85 -0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CG LEU C 12 " pdb=" CB LEU C 12 " pdb=" CD1 LEU C 12 " pdb=" CD2 LEU C 12 " both_signs ideal model delta sigma weight residual False -2.59 -1.85 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CB VAL C 11 " pdb=" CA VAL C 11 " pdb=" CG1 VAL C 11 " pdb=" CG2 VAL C 11 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.33e+01 ... (remaining 3691 not shown) Planarity restraints: 4206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U L 6 " -0.179 2.00e-02 2.50e+03 8.31e-02 1.55e+02 pdb=" N1 U L 6 " 0.078 2.00e-02 2.50e+03 pdb=" C2 U L 6 " 0.033 2.00e-02 2.50e+03 pdb=" O2 U L 6 " 0.046 2.00e-02 2.50e+03 pdb=" N3 U L 6 " 0.009 2.00e-02 2.50e+03 pdb=" C4 U L 6 " -0.016 2.00e-02 2.50e+03 pdb=" O4 U L 6 " -0.102 2.00e-02 2.50e+03 pdb=" C5 U L 6 " 0.039 2.00e-02 2.50e+03 pdb=" C6 U L 6 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G L 7 " 0.118 2.00e-02 2.50e+03 5.10e-02 7.82e+01 pdb=" N9 G L 7 " -0.015 2.00e-02 2.50e+03 pdb=" C8 G L 7 " -0.064 2.00e-02 2.50e+03 pdb=" N7 G L 7 " -0.050 2.00e-02 2.50e+03 pdb=" C5 G L 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G L 7 " 0.029 2.00e-02 2.50e+03 pdb=" O6 G L 7 " 0.045 2.00e-02 2.50e+03 pdb=" N1 G L 7 " 0.052 2.00e-02 2.50e+03 pdb=" C2 G L 7 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G L 7 " -0.051 2.00e-02 2.50e+03 pdb=" N3 G L 7 " -0.044 2.00e-02 2.50e+03 pdb=" C4 G L 7 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 8 " -0.077 2.00e-02 2.50e+03 3.95e-02 3.13e+01 pdb=" CG TYR C 8 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR C 8 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR C 8 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR C 8 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR C 8 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 8 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 8 " -0.049 2.00e-02 2.50e+03 ... (remaining 4203 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 75 2.36 - 2.99: 13234 2.99 - 3.63: 34940 3.63 - 4.26: 55886 4.26 - 4.90: 95992 Nonbonded interactions: 200127 Sorted by model distance: nonbonded pdb=" O2' G L 12 " pdb=" O5' C L 13 " model vdw 1.724 3.040 nonbonded pdb=" O2' A L 15 " pdb=" O5' U L 16 " model vdw 1.742 3.040 nonbonded pdb=" O2' U L 42 " pdb=" O5' C L 43 " model vdw 1.797 3.040 nonbonded pdb=" O2' G L 33 " pdb=" O5' C L 34 " model vdw 1.802 3.040 nonbonded pdb=" O2' C L 34 " pdb=" OP1 G L 35 " model vdw 1.839 3.040 ... (remaining 200122 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'D' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'E' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'F' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'G' and (resid 1 through 84 or resid 101 through 290)) selection = (chain 'H' and (resid 1 through 84 or resid 101 through 290)) } ncs_group { reference = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.230 Set scattering table: 0.210 Process input model: 56.210 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0735 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 : 0.022 1.665 24443 Z= 1.194 Angle : 1.638 106.046 33270 Z= 0.977 Chirality : 0.163 0.740 3694 Planarity : 0.006 0.100 4206 Dihedral : 18.530 177.673 9498 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.76 % Favored : 95.21 % Rotamer: Outliers : 0.57 % Allowed : 11.72 % Favored : 87.71 % Cbeta Deviations : 3.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 2860 helix: 0.78 (0.17), residues: 916 sheet: -0.09 (0.22), residues: 559 loop : -1.10 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 211 HIS 0.017 0.001 HIS I 198 PHE 0.054 0.003 PHE I 225 TYR 0.077 0.003 TYR C 8 ARG 0.008 0.000 ARG I 363 Details of bonding type rmsd hydrogen bonds : bond 0.18960 ( 1001) hydrogen bonds : angle 8.21135 ( 2841) covalent geometry : bond 0.02152 (24443) covalent geometry : angle 1.63834 (33270) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5720 Ramachandran restraints generated. 2860 Oldfield, 0 Emsley, 2860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 335 time to evaluate : 2.279 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: C 175 MET cc_start: 0.2011 (tpp) cc_final: 0.1500 (ptt) REVERT: D 183 TYR cc_start: 0.1513 (t80) cc_final: 0.0787 (t80) REVERT: E 138 MET cc_start: 0.2902 (mtt) cc_final: 0.0628 (mpp) REVERT: G 175 MET cc_start: 0.5701 (tmm) cc_final: 0.5314 (tmm) REVERT: H 251 LEU cc_start: -0.0135 (mt) cc_final: -0.0390 (mt) REVERT: I 343 MET cc_start: -0.2998 (mtp) cc_final: -0.4121 (tpt) REVERT: I 526 ASP cc_start: 0.2245 (m-30) cc_final: 0.2024 (m-30) REVERT: K 78 HIS cc_start: 0.4984 (t70) cc_final: 0.4741 (t-170) REVERT: M 1 MET cc_start: 0.3480 (mtt) cc_final: 0.2897 (ttp) outliers start: 14 outliers final: 2 residues processed: 347 average time/residue: 0.4156 time to fit residues: 216.9853 Evaluate side-chains 221 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain I residue 364 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 226 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 157 GLN C 70 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN ** D 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 HIS H 216 ASN I 198 HIS ** I 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 535 ASN I 538 GLN J 33 ASN J 111 HIS J 112 GLN ** M 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5253 r_free = 0.5253 target = 0.302667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.289038 restraints weight = 43782.030| |-----------------------------------------------------------------------------| r_work (start): 0.5148 rms_B_bonded: 2.45 r_work: 0.5085 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.5085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2145 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 24443 Z= 0.240 Angle : 0.927 15.242 33270 Z= 0.480 Chirality : 0.054 0.486 3694 Planarity : 0.007 0.079 4206 Dihedral : 15.520 158.076 3894 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 3.44 % Allowed : 12.99 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 2862 helix: 0.48 (0.16), residues: 946 sheet: 0.09 (0.23), residues: 489 loop : -0.97 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP M 40 HIS 0.018 0.002 HIS E 39 PHE 0.036 0.003 PHE J 105 TYR 0.024 0.003 TYR J 12 ARG 0.012 0.001 ARG A 220 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 1001) hydrogen bonds : angle 6.14624 ( 2841) covalent geometry : bond 0.00517 (24443) covalent geometry : angle 0.92725 (33270) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 264 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.6919 (ttt) cc_final: 0.6710 (ttt) REVERT: A 197 PHE cc_start: 0.6825 (m-80) cc_final: 0.6389 (m-80) REVERT: B 1 MET cc_start: -0.0696 (OUTLIER) cc_final: -0.1062 (ppp) REVERT: B 30 MET cc_start: 0.1493 (ppp) cc_final: 0.1253 (ppp) REVERT: B 123 MET cc_start: 0.3010 (mmt) cc_final: 0.2768 (mtt) REVERT: B 221 ASP cc_start: 0.0699 (OUTLIER) cc_final: 0.0281 (m-30) REVERT: C 30 MET cc_start: 0.2672 (mtp) cc_final: 0.0804 (mtp) REVERT: C 123 MET cc_start: -0.1789 (ptp) cc_final: -0.2825 (mtm) REVERT: C 138 MET cc_start: 0.4216 (ppp) cc_final: 0.0791 (mpp) REVERT: C 175 MET cc_start: 0.2788 (tpp) cc_final: 0.2517 (mtt) REVERT: E 138 MET cc_start: 0.3812 (mtt) cc_final: 0.1920 (mpp) REVERT: F 1 MET cc_start: -0.0729 (ptm) cc_final: -0.2016 (mtp) REVERT: G 138 MET cc_start: -0.1336 (ptp) cc_final: -0.3402 (mtm) REVERT: G 142 ARG cc_start: 0.0126 (OUTLIER) cc_final: -0.0181 (ttt-90) REVERT: G 272 ASP cc_start: 0.5319 (m-30) cc_final: 0.4862 (t0) REVERT: I 343 MET cc_start: -0.2895 (mtp) cc_final: -0.4375 (tpt) REVERT: I 346 MET cc_start: -0.1417 (OUTLIER) cc_final: -0.2248 (mmm) REVERT: I 448 ARG cc_start: 0.3231 (OUTLIER) cc_final: 0.1727 (tpp-160) REVERT: I 514 GLU cc_start: 0.1605 (pt0) cc_final: 0.0910 (tt0) REVERT: J 50 GLN cc_start: 0.3617 (OUTLIER) cc_final: 0.1905 (mp10) REVERT: J 82 MET cc_start: 0.1031 (mtm) cc_final: 0.0257 (tmm) REVERT: K 97 MET cc_start: -0.0313 (mmp) cc_final: -0.1929 (mtm) outliers start: 84 outliers final: 28 residues processed: 322 average time/residue: 0.3767 time to fit residues: 190.5227 Evaluate side-chains 251 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 268 THR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 448 ARG Chi-restraints excluded: chain I residue 578 ILE Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 77 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 39 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 258 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 188 optimal weight: 0.0570 chunk 13 optimal weight: 0.7980 chunk 280 optimal weight: 4.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN C 76 ASN D 150 GLN D 189 HIS D 239 HIS E 216 ASN E 245 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 HIS ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 ASN I 327 HIS ** M 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.303344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.5159 r_free = 0.5159 target = 0.289829 restraints weight = 43598.110| |-----------------------------------------------------------------------------| r_work (start): 0.5154 rms_B_bonded: 2.50 r_work: 0.5089 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.5089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2225 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24443 Z= 0.130 Angle : 0.647 11.135 33270 Z= 0.335 Chirality : 0.046 0.267 3694 Planarity : 0.005 0.055 4206 Dihedral : 14.614 172.137 3891 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 2.17 % Allowed : 14.95 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 2862 helix: 1.21 (0.16), residues: 962 sheet: 0.22 (0.22), residues: 550 loop : -0.74 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 40 HIS 0.005 0.001 HIS F 179 PHE 0.029 0.002 PHE B 113 TYR 0.016 0.002 TYR F 68 ARG 0.009 0.001 ARG G 232 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 1001) hydrogen bonds : angle 5.50153 ( 2841) covalent geometry : bond 0.00270 (24443) covalent geometry : angle 0.64678 (33270) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 234 time to evaluate : 5.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.5938 (mmm) cc_final: 0.5666 (tpp) REVERT: A 201 MET cc_start: 0.6936 (mtm) cc_final: 0.6660 (mtt) REVERT: B 1 MET cc_start: -0.0193 (ttm) cc_final: -0.0787 (ppp) REVERT: B 109 MET cc_start: 0.5721 (mpp) cc_final: 0.4975 (mpp) REVERT: B 123 MET cc_start: 0.3341 (mmt) cc_final: 0.2903 (mtm) REVERT: C 30 MET cc_start: 0.2575 (mtp) cc_final: 0.0312 (mtp) REVERT: C 123 MET cc_start: -0.1932 (ptp) cc_final: -0.2829 (mtm) REVERT: C 138 MET cc_start: 0.4560 (ppp) cc_final: 0.2410 (ppp) REVERT: C 175 MET cc_start: 0.2643 (tpp) cc_final: 0.2365 (mtt) REVERT: D 229 MET cc_start: 0.5925 (mtm) cc_final: 0.5694 (mtp) REVERT: D 239 HIS cc_start: 0.2008 (OUTLIER) cc_final: 0.1343 (m170) REVERT: E 138 MET cc_start: 0.3402 (mtt) cc_final: 0.1615 (mpp) REVERT: E 157 MET cc_start: -0.0095 (ptp) cc_final: -0.0307 (ptp) REVERT: G 138 MET cc_start: -0.1285 (ptp) cc_final: -0.3397 (mtm) REVERT: G 272 ASP cc_start: 0.5194 (m-30) cc_final: 0.4862 (t0) REVERT: I 343 MET cc_start: -0.2675 (mtp) cc_final: -0.4241 (tpt) REVERT: I 346 MET cc_start: -0.1097 (OUTLIER) cc_final: -0.2074 (mmm) REVERT: J 50 GLN cc_start: 0.3354 (OUTLIER) cc_final: 0.2216 (mp10) REVERT: J 82 MET cc_start: 0.1207 (mtm) cc_final: 0.0328 (tmm) REVERT: K 83 MET cc_start: 0.3553 (tpt) cc_final: 0.3046 (tpt) REVERT: K 97 MET cc_start: -0.0191 (mmp) cc_final: -0.2993 (mmm) REVERT: M 36 MET cc_start: 0.1486 (mmm) cc_final: 0.1122 (mmp) REVERT: M 51 GLU cc_start: 0.3394 (OUTLIER) cc_final: 0.2064 (mp0) outliers start: 53 outliers final: 25 residues processed: 276 average time/residue: 0.4974 time to fit residues: 222.1899 Evaluate side-chains 240 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 268 THR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 517 VAL Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 179 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN D 240 GLN E 70 GLN ** E 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 HIS H 70 GLN H 112 ASN I 221 ASN ** I 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 546 ASN ** M 18 ASN ** 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 = 0.5241 r_free = 0.5241 target = 0.301285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.5143 r_free = 0.5143 target = 0.286962 restraints weight = 43218.552| |-----------------------------------------------------------------------------| r_work (start): 0.5135 rms_B_bonded: 2.47 r_work: 0.5071 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.5071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2787 moved from start: 0.6930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24443 Z= 0.157 Angle : 0.691 11.496 33270 Z= 0.358 Chirality : 0.047 0.269 3694 Planarity : 0.005 0.060 4206 Dihedral : 14.459 174.894 3891 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.70 % Rotamer: Outliers : 2.95 % Allowed : 16.02 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2862 helix: 1.13 (0.16), residues: 962 sheet: 0.23 (0.23), residues: 493 loop : -0.72 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 40 HIS 0.056 0.002 HIS D 239 PHE 0.026 0.002 PHE B 113 TYR 0.017 0.002 TYR E 68 ARG 0.013 0.001 ARG B 142 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 1001) hydrogen bonds : angle 5.48795 ( 2841) covalent geometry : bond 0.00330 (24443) covalent geometry : angle 0.69120 (33270) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 237 time to evaluate : 2.603 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: A 13 LEU cc_start: 0.8051 (tp) cc_final: 0.7801 (tp) REVERT: A 190 TYR cc_start: 0.3757 (m-10) cc_final: 0.3408 (m-80) REVERT: A 201 MET cc_start: 0.7477 (mtm) cc_final: 0.7251 (mtt) REVERT: B 68 TYR cc_start: 0.4864 (OUTLIER) cc_final: 0.4144 (m-80) REVERT: B 109 MET cc_start: 0.6059 (mpp) cc_final: 0.5489 (mpp) REVERT: B 112 ASN cc_start: 0.5900 (m-40) cc_final: 0.5606 (m-40) REVERT: B 217 MET cc_start: 0.4526 (mmp) cc_final: 0.4296 (mmp) REVERT: C 30 MET cc_start: 0.3002 (mtp) cc_final: 0.0413 (mtp) REVERT: C 138 MET cc_start: 0.5096 (OUTLIER) cc_final: 0.3491 (ppp) REVERT: C 175 MET cc_start: 0.2740 (tpp) cc_final: 0.2443 (mtm) REVERT: D 109 MET cc_start: -0.0134 (mmt) cc_final: -0.2237 (mtt) REVERT: E 109 MET cc_start: -0.0771 (mmm) cc_final: -0.1242 (mtm) REVERT: E 138 MET cc_start: 0.3573 (mtt) cc_final: 0.1941 (mpp) REVERT: F 175 MET cc_start: 0.4452 (tmm) cc_final: 0.3612 (ttp) REVERT: G 272 ASP cc_start: 0.4880 (m-30) cc_final: 0.4623 (t0) REVERT: H 52 ARG cc_start: 0.2879 (ptt180) cc_final: 0.2553 (ptt90) REVERT: H 157 MET cc_start: 0.3332 (OUTLIER) cc_final: 0.2356 (mmt) REVERT: I 192 LYS cc_start: 0.5603 (mttp) cc_final: 0.5227 (mmtm) REVERT: I 343 MET cc_start: -0.2758 (mtp) cc_final: -0.4167 (tpt) REVERT: I 346 MET cc_start: -0.1232 (OUTLIER) cc_final: -0.2259 (mmm) REVERT: I 514 GLU cc_start: 0.0832 (pt0) cc_final: 0.0384 (tt0) REVERT: I 571 MET cc_start: 0.1687 (mmp) cc_final: 0.1448 (tpp) REVERT: I 594 MET cc_start: 0.1523 (tpp) cc_final: 0.0429 (mmp) REVERT: J 50 GLN cc_start: 0.4191 (OUTLIER) cc_final: 0.2770 (mp10) REVERT: M 36 MET cc_start: 0.1792 (OUTLIER) cc_final: 0.1534 (mmp) outliers start: 72 outliers final: 41 residues processed: 293 average time/residue: 0.3374 time to fit residues: 159.1786 Evaluate side-chains 257 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 189 HIS Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 157 MET Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 268 THR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain M residue 36 MET Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 286 optimal weight: 0.0030 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 276 optimal weight: 0.0170 chunk 246 optimal weight: 3.9990 chunk 195 optimal weight: 0.0980 chunk 56 optimal weight: 0.2980 chunk 135 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 overall best weight: 0.2628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN C 70 GLN E 245 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 ASN H 112 ASN I 258 ASN I 360 ASN M 18 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5252 r_free = 0.5252 target = 0.302610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.288726 restraints weight = 43254.651| |-----------------------------------------------------------------------------| r_work (start): 0.5137 rms_B_bonded: 2.44 r_work: 0.5074 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.5074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2689 moved from start: 0.7126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 24443 Z= 0.108 Angle : 0.604 11.121 33270 Z= 0.308 Chirality : 0.044 0.238 3694 Planarity : 0.004 0.054 4206 Dihedral : 14.234 178.243 3891 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 2.29 % Allowed : 17.53 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2862 helix: 1.41 (0.17), residues: 966 sheet: 0.41 (0.23), residues: 496 loop : -0.64 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 108 HIS 0.005 0.001 HIS H 39 PHE 0.032 0.001 PHE H 113 TYR 0.024 0.001 TYR K 110 ARG 0.007 0.000 ARG C 259 Details of bonding type rmsd hydrogen bonds : bond 0.03015 ( 1001) hydrogen bonds : angle 5.11068 ( 2841) covalent geometry : bond 0.00225 (24443) covalent geometry : angle 0.60369 (33270) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 232 time to evaluate : 2.380 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 13 LEU cc_start: 0.8185 (tp) cc_final: 0.7943 (tp) REVERT: A 185 LYS cc_start: 0.6698 (tmmt) cc_final: 0.6265 (tppt) REVERT: A 190 TYR cc_start: 0.4121 (m-10) cc_final: 0.3865 (m-80) REVERT: B 30 MET cc_start: 0.3011 (mpp) cc_final: 0.1767 (mtp) REVERT: B 68 TYR cc_start: 0.4923 (OUTLIER) cc_final: 0.4122 (m-80) REVERT: B 112 ASN cc_start: 0.6024 (m-40) cc_final: 0.5817 (m110) REVERT: C 30 MET cc_start: 0.2824 (mtp) cc_final: 0.0182 (mtp) REVERT: C 138 MET cc_start: 0.4625 (OUTLIER) cc_final: 0.2270 (ptt) REVERT: C 175 MET cc_start: 0.2562 (tpp) cc_final: 0.1762 (mtm) REVERT: C 229 MET cc_start: 0.0171 (mmt) cc_final: -0.0175 (ptt) REVERT: D 67 ILE cc_start: 0.4169 (OUTLIER) cc_final: 0.3906 (tt) REVERT: D 109 MET cc_start: -0.0361 (mmt) cc_final: -0.1960 (mtt) REVERT: E 109 MET cc_start: -0.0937 (mmm) cc_final: -0.1301 (mtm) REVERT: E 128 ASN cc_start: 0.4051 (t0) cc_final: 0.3781 (m-40) REVERT: E 138 MET cc_start: 0.3380 (mtt) cc_final: 0.1765 (mpp) REVERT: E 229 MET cc_start: 0.4438 (mmm) cc_final: 0.3806 (mmt) REVERT: G 51 ILE cc_start: 0.2378 (OUTLIER) cc_final: 0.1232 (mt) REVERT: G 136 VAL cc_start: 0.5780 (OUTLIER) cc_final: 0.5214 (p) REVERT: G 138 MET cc_start: -0.1765 (ptp) cc_final: -0.2424 (mpp) REVERT: G 175 MET cc_start: 0.6689 (tmm) cc_final: 0.6470 (tmm) REVERT: G 217 MET cc_start: 0.2290 (ptm) cc_final: 0.1472 (ppp) REVERT: H 138 MET cc_start: 0.3845 (tmm) cc_final: 0.3244 (tmm) REVERT: H 157 MET cc_start: 0.3308 (ttp) cc_final: 0.2277 (mmp) REVERT: I 343 MET cc_start: -0.3011 (mtp) cc_final: -0.3916 (tpt) REVERT: I 346 MET cc_start: -0.1369 (mmt) cc_final: -0.2545 (tpt) REVERT: I 571 MET cc_start: 0.1628 (mmp) cc_final: 0.1198 (tpp) REVERT: I 594 MET cc_start: 0.1348 (tpp) cc_final: 0.0224 (mmp) REVERT: J 82 MET cc_start: 0.1127 (mtm) cc_final: 0.0117 (tmm) REVERT: K 83 MET cc_start: 0.4149 (tpt) cc_final: 0.3841 (tpt) REVERT: M 51 GLU cc_start: 0.3408 (OUTLIER) cc_final: 0.2207 (mp0) outliers start: 56 outliers final: 32 residues processed: 271 average time/residue: 0.3345 time to fit residues: 147.0904 Evaluate side-chains 252 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 273 TYR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 268 THR Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 219 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 288 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 HIS ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 566 HIS ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5205 r_free = 0.5205 target = 0.297753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.281820 restraints weight = 41742.270| |-----------------------------------------------------------------------------| r_work (start): 0.5095 rms_B_bonded: 2.47 r_work: 0.5030 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.5030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3223 moved from start: 0.8517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24443 Z= 0.156 Angle : 0.692 12.394 33270 Z= 0.357 Chirality : 0.047 0.265 3694 Planarity : 0.005 0.062 4206 Dihedral : 14.294 171.708 3891 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 3.24 % Allowed : 17.37 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 2862 helix: 0.98 (0.16), residues: 968 sheet: 0.07 (0.22), residues: 535 loop : -0.82 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 40 HIS 0.007 0.001 HIS B 54 PHE 0.026 0.002 PHE K 105 TYR 0.022 0.002 TYR I 246 ARG 0.006 0.001 ARG H 232 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 1001) hydrogen bonds : angle 5.58291 ( 2841) covalent geometry : bond 0.00335 (24443) covalent geometry : angle 0.69221 (33270) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 240 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.3872 (tp-100) cc_final: 0.3471 (tp-100) REVERT: B 68 TYR cc_start: 0.5412 (OUTLIER) cc_final: 0.4613 (m-80) REVERT: B 157 MET cc_start: 0.2587 (mtp) cc_final: 0.2081 (mtp) REVERT: C 138 MET cc_start: 0.5018 (OUTLIER) cc_final: 0.3224 (ptt) REVERT: C 175 MET cc_start: 0.2704 (tpp) cc_final: 0.1839 (mtm) REVERT: D 109 MET cc_start: -0.0436 (mmt) cc_final: -0.2258 (mtp) REVERT: E 109 MET cc_start: -0.1290 (mmm) cc_final: -0.1709 (mtm) REVERT: E 138 MET cc_start: 0.3614 (mtt) cc_final: 0.1983 (mpp) REVERT: E 229 MET cc_start: 0.4858 (mmm) cc_final: 0.4238 (mmt) REVERT: F 191 PHE cc_start: 0.3384 (OUTLIER) cc_final: 0.2513 (m-80) REVERT: F 229 MET cc_start: 0.0571 (ttm) cc_final: -0.0079 (ttm) REVERT: G 123 MET cc_start: 0.1776 (ptm) cc_final: 0.1134 (ptp) REVERT: H 157 MET cc_start: 0.3355 (ttp) cc_final: 0.2299 (mmp) REVERT: I 326 MET cc_start: 0.1509 (tpt) cc_final: -0.0478 (ptp) REVERT: I 343 MET cc_start: -0.3160 (mtp) cc_final: -0.3958 (tpt) REVERT: I 346 MET cc_start: -0.1596 (OUTLIER) cc_final: -0.2408 (mmm) REVERT: I 571 MET cc_start: 0.0990 (mmp) cc_final: 0.0607 (tpp) REVERT: I 578 ILE cc_start: -0.1654 (OUTLIER) cc_final: -0.2101 (pt) REVERT: I 594 MET cc_start: 0.1785 (tpp) cc_final: 0.0678 (mmp) REVERT: J 50 GLN cc_start: 0.4228 (OUTLIER) cc_final: 0.2340 (mp-120) REVERT: M 51 GLU cc_start: 0.4308 (OUTLIER) cc_final: 0.3186 (mp0) outliers start: 79 outliers final: 51 residues processed: 298 average time/residue: 0.3350 time to fit residues: 162.3455 Evaluate side-chains 276 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 273 TYR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 189 HIS Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain H residue 39 HIS Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 227 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 268 THR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 578 ILE Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 260 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 242 optimal weight: 0.3980 chunk 215 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 112 ASN B 131 GLN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 HIS G 239 HIS H 216 ASN ** H 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5163 r_free = 0.5163 target = 0.290461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.271780 restraints weight = 41596.285| |-----------------------------------------------------------------------------| r_work (start): 0.5007 rms_B_bonded: 2.42 r_work: 0.4943 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3851 moved from start: 1.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24443 Z= 0.251 Angle : 0.930 17.432 33270 Z= 0.490 Chirality : 0.055 0.314 3694 Planarity : 0.007 0.108 4206 Dihedral : 14.970 172.513 3891 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.97 % Favored : 93.96 % Rotamer: Outliers : 3.32 % Allowed : 17.86 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.15), residues: 2862 helix: -0.08 (0.16), residues: 942 sheet: -0.39 (0.23), residues: 496 loop : -1.53 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP C 211 HIS 0.033 0.003 HIS H 39 PHE 0.035 0.003 PHE E 14 TYR 0.033 0.003 TYR I 528 ARG 0.017 0.001 ARG G 52 Details of bonding type rmsd hydrogen bonds : bond 0.05839 ( 1001) hydrogen bonds : angle 6.92998 ( 2841) covalent geometry : bond 0.00543 (24443) covalent geometry : angle 0.93024 (33270) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 261 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.5692 (OUTLIER) cc_final: 0.4548 (m-80) REVERT: C 7 ARG cc_start: 0.6573 (ttp-170) cc_final: 0.5889 (ttp-170) REVERT: C 138 MET cc_start: 0.4390 (OUTLIER) cc_final: 0.3216 (mmm) REVERT: C 175 MET cc_start: 0.2831 (tpp) cc_final: 0.1896 (mtm) REVERT: C 289 MET cc_start: 0.4688 (ppp) cc_final: 0.3801 (ppp) REVERT: D 41 LEU cc_start: 0.6145 (mt) cc_final: 0.5830 (mp) REVERT: D 109 MET cc_start: -0.0047 (mmt) cc_final: -0.1866 (mmm) REVERT: D 157 MET cc_start: 0.1983 (pmm) cc_final: 0.1646 (pmm) REVERT: E 109 MET cc_start: -0.1231 (mmm) cc_final: -0.2761 (mtt) REVERT: E 229 MET cc_start: 0.5026 (mmm) cc_final: 0.4347 (mmt) REVERT: E 288 GLU cc_start: 0.2835 (OUTLIER) cc_final: 0.2094 (mp0) REVERT: F 9 GLU cc_start: 0.0146 (OUTLIER) cc_final: -0.2345 (mm-30) REVERT: G 119 PHE cc_start: 0.5880 (m-80) cc_final: 0.5559 (m-80) REVERT: G 123 MET cc_start: 0.2039 (ptm) cc_final: 0.1828 (ptp) REVERT: G 219 GLU cc_start: 0.3080 (OUTLIER) cc_final: 0.2407 (tp30) REVERT: H 157 MET cc_start: 0.3226 (ttp) cc_final: 0.2111 (mmp) REVERT: H 205 GLU cc_start: 0.5331 (mp0) cc_final: 0.4600 (pt0) REVERT: I 343 MET cc_start: -0.3545 (mtp) cc_final: -0.4172 (tpt) REVERT: I 346 MET cc_start: -0.0651 (OUTLIER) cc_final: -0.1482 (mmm) REVERT: I 483 ARG cc_start: 0.5473 (mmp-170) cc_final: 0.5194 (mmt180) REVERT: I 571 MET cc_start: 0.0788 (mmp) cc_final: 0.0564 (tpp) REVERT: J 50 GLN cc_start: 0.4638 (OUTLIER) cc_final: 0.1824 (mp10) REVERT: J 52 PHE cc_start: -0.0747 (OUTLIER) cc_final: -0.1071 (m-80) REVERT: K 106 MET cc_start: 0.2549 (tmm) cc_final: 0.1761 (mpp) REVERT: M 51 GLU cc_start: 0.5316 (OUTLIER) cc_final: 0.4745 (mp0) outliers start: 81 outliers final: 40 residues processed: 326 average time/residue: 0.3943 time to fit residues: 208.5369 Evaluate side-chains 270 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 273 TYR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 39 HIS Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 227 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 413 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 597 TYR Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 52 PHE Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 31 TRP Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 0.0570 chunk 26 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 240 optimal weight: 0.0070 chunk 165 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 131 GLN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS C 179 HIS D 76 ASN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 ASN ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 ASN ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS J 84 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5188 r_free = 0.5188 target = 0.293847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5060 r_free = 0.5060 target = 0.276477 restraints weight = 41335.776| |-----------------------------------------------------------------------------| r_work (start): 0.5045 rms_B_bonded: 2.62 r_work: 0.4965 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3699 moved from start: 1.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24443 Z= 0.137 Angle : 0.676 15.323 33270 Z= 0.347 Chirality : 0.046 0.239 3694 Planarity : 0.005 0.060 4206 Dihedral : 14.383 171.825 3891 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.88 % Favored : 96.09 % Rotamer: Outliers : 2.17 % Allowed : 18.80 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 2862 helix: 0.50 (0.16), residues: 955 sheet: -0.22 (0.23), residues: 489 loop : -1.23 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 108 HIS 0.010 0.001 HIS E 39 PHE 0.024 0.002 PHE D 270 TYR 0.019 0.002 TYR A 34 ARG 0.011 0.001 ARG H 142 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 1001) hydrogen bonds : angle 5.92695 ( 2841) covalent geometry : bond 0.00293 (24443) covalent geometry : angle 0.67583 (33270) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 249 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.7286 (m-80) cc_final: 0.7076 (m-80) REVERT: B 68 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.4568 (m-80) REVERT: C 7 ARG cc_start: 0.6133 (ttp-170) cc_final: 0.5361 (ttp-170) REVERT: C 175 MET cc_start: 0.2775 (tpp) cc_final: 0.1895 (mtm) REVERT: D 41 LEU cc_start: 0.5950 (mt) cc_final: 0.5707 (mp) REVERT: D 157 MET cc_start: 0.2188 (pmm) cc_final: 0.1905 (pmm) REVERT: E 109 MET cc_start: -0.1523 (mmm) cc_final: -0.2625 (mtt) REVERT: E 138 MET cc_start: 0.4331 (mpp) cc_final: 0.3802 (mtm) REVERT: E 288 GLU cc_start: 0.2339 (OUTLIER) cc_final: 0.1972 (mp0) REVERT: G 51 ILE cc_start: 0.2664 (OUTLIER) cc_final: 0.1518 (mt) REVERT: G 119 PHE cc_start: 0.5854 (m-80) cc_final: 0.5591 (m-80) REVERT: G 123 MET cc_start: 0.1588 (ptm) cc_final: 0.1000 (ptp) REVERT: H 157 MET cc_start: 0.3020 (ttp) cc_final: 0.2054 (mmt) REVERT: H 205 GLU cc_start: 0.5318 (mp0) cc_final: 0.4770 (pt0) REVERT: I 326 MET cc_start: 0.2346 (tpt) cc_final: -0.1243 (ptt) REVERT: I 343 MET cc_start: -0.3750 (mtp) cc_final: -0.4136 (tpt) REVERT: I 346 MET cc_start: -0.1469 (OUTLIER) cc_final: -0.2224 (mmm) REVERT: I 571 MET cc_start: 0.0867 (mmp) cc_final: 0.0612 (tpp) REVERT: M 36 MET cc_start: 0.1246 (mmm) cc_final: 0.0688 (mmm) REVERT: M 51 GLU cc_start: 0.5482 (OUTLIER) cc_final: 0.5154 (mp0) outliers start: 53 outliers final: 33 residues processed: 290 average time/residue: 0.3373 time to fit residues: 157.7898 Evaluate side-chains 258 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 273 TYR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 189 HIS Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 227 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain K residue 47 ASN Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 241 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 222 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 ASN ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5186 r_free = 0.5186 target = 0.293337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.274826 restraints weight = 41123.874| |-----------------------------------------------------------------------------| r_work (start): 0.5030 rms_B_bonded: 2.42 r_work: 0.4966 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3762 moved from start: 1.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24443 Z= 0.139 Angle : 0.680 14.536 33270 Z= 0.347 Chirality : 0.046 0.222 3694 Planarity : 0.005 0.056 4206 Dihedral : 14.266 172.726 3891 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 2.01 % Allowed : 19.30 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 2862 helix: 0.61 (0.16), residues: 956 sheet: -0.07 (0.23), residues: 483 loop : -1.18 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 211 HIS 0.012 0.001 HIS H 54 PHE 0.024 0.002 PHE D 270 TYR 0.029 0.002 TYR K 79 ARG 0.005 0.001 ARG G 32 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 1001) hydrogen bonds : angle 5.82690 ( 2841) covalent geometry : bond 0.00303 (24443) covalent geometry : angle 0.68000 (33270) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.5264 (OUTLIER) cc_final: 0.3861 (m-80) REVERT: C 17 GLU cc_start: 0.2586 (tm-30) cc_final: 0.2237 (mp0) REVERT: C 175 MET cc_start: 0.2966 (tpp) cc_final: 0.2111 (mtm) REVERT: D 22 ASN cc_start: 0.3126 (OUTLIER) cc_final: 0.2918 (t0) REVERT: D 41 LEU cc_start: 0.5948 (mt) cc_final: 0.5519 (mp) REVERT: D 109 MET cc_start: -0.0425 (mmt) cc_final: -0.2146 (mtp) REVERT: D 157 MET cc_start: 0.2197 (pmm) cc_final: 0.1914 (pmm) REVERT: D 217 MET cc_start: 0.1862 (tpt) cc_final: 0.1612 (tpt) REVERT: E 109 MET cc_start: -0.1643 (mmm) cc_final: -0.2719 (mtt) REVERT: E 229 MET cc_start: 0.4750 (mmm) cc_final: 0.4009 (mmt) REVERT: E 242 ARG cc_start: 0.3448 (ttp80) cc_final: 0.2691 (ttt-90) REVERT: E 288 GLU cc_start: 0.2276 (OUTLIER) cc_final: 0.2050 (mp0) REVERT: F 9 GLU cc_start: -0.0392 (OUTLIER) cc_final: -0.2730 (tp30) REVERT: G 123 MET cc_start: 0.1342 (ptm) cc_final: 0.0852 (ptp) REVERT: H 157 MET cc_start: 0.3105 (ttp) cc_final: 0.2127 (mmp) REVERT: H 205 GLU cc_start: 0.5471 (mp0) cc_final: 0.4888 (pt0) REVERT: I 244 PHE cc_start: 0.6230 (t80) cc_final: 0.5983 (t80) REVERT: I 326 MET cc_start: 0.1837 (tpt) cc_final: -0.1564 (ptt) REVERT: I 343 MET cc_start: -0.3630 (mtp) cc_final: -0.4105 (tpt) REVERT: I 346 MET cc_start: -0.1409 (OUTLIER) cc_final: -0.2151 (mmm) REVERT: I 542 MET cc_start: 0.2075 (ppp) cc_final: 0.1431 (ptp) REVERT: J 50 GLN cc_start: 0.4034 (OUTLIER) cc_final: 0.1698 (mp10) REVERT: J 110 TYR cc_start: 0.3270 (m-80) cc_final: 0.2708 (m-80) REVERT: J 111 HIS cc_start: 0.1658 (OUTLIER) cc_final: -0.0782 (p90) REVERT: K 86 ILE cc_start: 0.7436 (mm) cc_final: 0.7146 (mt) REVERT: M 51 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5664 (mp0) outliers start: 49 outliers final: 33 residues processed: 283 average time/residue: 0.4086 time to fit residues: 185.3391 Evaluate side-chains 262 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 3.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 273 TYR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 189 HIS Chi-restraints excluded: chain I residue 7 HIS Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 227 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 62 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 282 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 ASN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 ASN ** I 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5151 r_free = 0.5151 target = 0.288360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.268353 restraints weight = 40815.264| |-----------------------------------------------------------------------------| r_work (start): 0.4979 rms_B_bonded: 2.41 r_work: 0.4913 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4032 moved from start: 1.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24443 Z= 0.203 Angle : 0.804 16.449 33270 Z= 0.414 Chirality : 0.050 0.258 3694 Planarity : 0.006 0.091 4206 Dihedral : 14.454 170.139 3891 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.94 % Favored : 94.03 % Rotamer: Outliers : 2.05 % Allowed : 19.25 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 2862 helix: 0.11 (0.16), residues: 951 sheet: -0.50 (0.23), residues: 522 loop : -1.41 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 40 HIS 0.012 0.002 HIS C 239 PHE 0.035 0.003 PHE C 14 TYR 0.026 0.002 TYR E 68 ARG 0.010 0.001 ARG C 7 Details of bonding type rmsd hydrogen bonds : bond 0.04805 ( 1001) hydrogen bonds : angle 6.47277 ( 2841) covalent geometry : bond 0.00441 (24443) covalent geometry : angle 0.80416 (33270) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 232 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.4809 (p90) cc_final: 0.4465 (p90) REVERT: B 68 TYR cc_start: 0.5876 (OUTLIER) cc_final: 0.4868 (m-80) REVERT: B 123 MET cc_start: 0.6175 (mmt) cc_final: 0.5328 (mmt) REVERT: B 157 MET cc_start: 0.2227 (mtp) cc_final: 0.1758 (mtp) REVERT: C 138 MET cc_start: 0.4416 (OUTLIER) cc_final: 0.3911 (mmm) REVERT: C 175 MET cc_start: 0.3080 (tpp) cc_final: 0.2392 (mtp) REVERT: D 41 LEU cc_start: 0.6084 (mt) cc_final: 0.5844 (mp) REVERT: D 109 MET cc_start: -0.0239 (mmt) cc_final: -0.1933 (mmm) REVERT: D 157 MET cc_start: 0.2873 (pmm) cc_final: 0.2543 (pmm) REVERT: D 217 MET cc_start: 0.1808 (tpt) cc_final: 0.1314 (tpt) REVERT: D 229 MET cc_start: 0.6450 (ptp) cc_final: 0.6060 (ptp) REVERT: E 109 MET cc_start: -0.1547 (mmm) cc_final: -0.2826 (mtt) REVERT: E 288 GLU cc_start: 0.2511 (OUTLIER) cc_final: 0.1968 (mp0) REVERT: F 9 GLU cc_start: -0.0046 (OUTLIER) cc_final: -0.2661 (tp30) REVERT: F 191 PHE cc_start: 0.3648 (OUTLIER) cc_final: 0.2559 (m-80) REVERT: G 123 MET cc_start: 0.1305 (ptm) cc_final: 0.1027 (ptp) REVERT: H 2 THR cc_start: -0.1320 (OUTLIER) cc_final: -0.1675 (m) REVERT: H 157 MET cc_start: 0.3100 (ttp) cc_final: 0.2119 (mmp) REVERT: H 205 GLU cc_start: 0.5586 (mp0) cc_final: 0.5056 (pt0) REVERT: H 217 MET cc_start: 0.4642 (ptm) cc_final: 0.3591 (ptm) REVERT: I 13 MET cc_start: 0.3181 (ppp) cc_final: 0.2960 (ppp) REVERT: I 343 MET cc_start: -0.3432 (mtp) cc_final: -0.3964 (tpt) REVERT: I 346 MET cc_start: -0.1327 (OUTLIER) cc_final: -0.2204 (mmm) REVERT: I 483 ARG cc_start: 0.5666 (mmp-170) cc_final: 0.5401 (mmt180) REVERT: I 542 MET cc_start: 0.2295 (ppp) cc_final: 0.1927 (ptp) REVERT: I 570 MET cc_start: 0.3110 (mtt) cc_final: 0.2033 (ptt) REVERT: M 51 GLU cc_start: 0.6079 (OUTLIER) cc_final: 0.5743 (mp0) outliers start: 50 outliers final: 36 residues processed: 272 average time/residue: 0.3431 time to fit residues: 151.4168 Evaluate side-chains 259 residues out of total 2443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 14 PHE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 273 TYR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 191 PHE Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 191 PHE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 191 PHE Chi-restraints excluded: chain I residue 227 SER Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 287 PHE Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 524 ILE Chi-restraints excluded: chain I residue 598 TYR Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 111 HIS Chi-restraints excluded: chain M residue 51 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 250 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 277 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 chunk 192 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 39 HIS ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 ASN ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 232 GLN I 418 ASN ** I 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 550 HIS ** K 47 ASN ** 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 = 0.5142 r_free = 0.5142 target = 0.286498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.266041 restraints weight = 39746.615| |-----------------------------------------------------------------------------| r_work (start): 0.4962 rms_B_bonded: 2.36 r_work: 0.4895 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4156 moved from start: 1.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24443 Z= 0.205 Angle : 0.814 16.257 33270 Z= 0.421 Chirality : 0.051 0.308 3694 Planarity : 0.006 0.065 4206 Dihedral : 14.521 170.080 3891 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.43 % Favored : 93.54 % Rotamer: Outliers : 2.34 % Allowed : 19.30 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 2862 helix: -0.16 (0.16), residues: 951 sheet: -0.55 (0.23), residues: 505 loop : -1.53 (0.15), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP M 40 HIS 0.019 0.002 HIS H 54 PHE 0.038 0.003 PHE E 14 TYR 0.029 0.003 TYR D 114 ARG 0.022 0.001 ARG C 7 Details of bonding type rmsd hydrogen bonds : bond 0.05029 ( 1001) hydrogen bonds : angle 6.57662 ( 2841) covalent geometry : bond 0.00448 (24443) covalent geometry : angle 0.81403 (33270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15051.81 seconds wall clock time: 266 minutes 3.81 seconds (15963.81 seconds total)