Starting phenix.real_space_refine on Wed Jun 26 23:19:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fef_50340/06_2024/9fef_50340.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fef_50340/06_2024/9fef_50340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fef_50340/06_2024/9fef_50340.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fef_50340/06_2024/9fef_50340.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fef_50340/06_2024/9fef_50340.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fef_50340/06_2024/9fef_50340.pdb" } resolution = 2.98 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= 0.044 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 7106 2.51 5 N 1959 2.21 5 O 2065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 24": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "E GLU 364": "OE1" <-> "OE2" Residue "E GLU 407": "OE1" <-> "OE2" Residue "E GLU 563": "OE1" <-> "OE2" Residue "E GLU 566": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 11192 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2320 Classifications: {'peptide': 314} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 291} Chain breaks: 1 Chain: "B" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2304 Classifications: {'peptide': 312} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 289} Chain breaks: 1 Chain: "C" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2326 Classifications: {'peptide': 315} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 292} Chain breaks: 1 Chain: "D" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2320 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 22, 'TRANS': 291} Chain breaks: 1 Chain: "E" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1922 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain breaks: 2 Time building chain proxies: 7.23, per 1000 atoms: 0.65 Number of scatterers: 11192 At special positions: 0 Unit cell: (88.2, 102.48, 138.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2065 8.00 N 1959 7.00 C 7106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 2.1 seconds 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2748 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 55.1% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 11 through 25 removed outlier: 4.041A pdb=" N SER A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.510A pdb=" N ASP A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 156 through 171 removed outlier: 4.193A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 removed outlier: 3.524A pdb=" N ILE A 197 " --> pdb=" O TYR A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.607A pdb=" N GLU A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 Processing helix chain 'A' and resid 294 through 319 removed outlier: 3.684A pdb=" N LYS A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 25 removed outlier: 3.969A pdb=" N SER B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.675A pdb=" N VAL B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 100 through 118 removed outlier: 3.688A pdb=" N SER B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 145 removed outlier: 3.651A pdb=" N THR B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Proline residue: B 135 - end of helix removed outlier: 3.602A pdb=" N ILE B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 156 through 170 removed outlier: 4.227A pdb=" N GLY B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 197 removed outlier: 3.916A pdb=" N ILE B 197 " --> pdb=" O TYR B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.882A pdb=" N GLU B 220 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.807A pdb=" N MET B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 318 removed outlier: 3.919A pdb=" N GLY B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 23 removed outlier: 4.202A pdb=" N SER C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 47 removed outlier: 3.767A pdb=" N ASP C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 97 through 116 removed outlier: 3.871A pdb=" N ASN C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 157 through 171 Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.867A pdb=" N GLU C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 222 " --> pdb=" O GLY C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 251 Processing helix chain 'C' and resid 294 through 320 removed outlier: 3.822A pdb=" N GLU C 299 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 25 removed outlier: 3.817A pdb=" N GLN D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 removed outlier: 4.453A pdb=" N ASP D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 76 removed outlier: 3.513A pdb=" N GLU D 74 " --> pdb=" O PRO D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 4.364A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 145 Proline residue: D 135 - end of helix Processing helix chain 'D' and resid 156 through 171 removed outlier: 4.250A pdb=" N GLY D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 removed outlier: 3.755A pdb=" N ILE D 197 " --> pdb=" O TYR D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 194 through 197' Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 216 through 225 removed outlier: 3.523A pdb=" N GLU D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 221 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 222 " --> pdb=" O GLY D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 251 removed outlier: 3.578A pdb=" N MET D 251 " --> pdb=" O VAL D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 319 removed outlier: 3.734A pdb=" N GLY D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 371 removed outlier: 3.726A pdb=" N GLN E 371 " --> pdb=" O ILE E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 382 Processing helix chain 'E' and resid 395 through 404 Processing helix chain 'E' and resid 408 through 423 Processing helix chain 'E' and resid 426 through 440 removed outlier: 3.652A pdb=" N HIS E 430 " --> pdb=" O ASP E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 457 removed outlier: 3.815A pdb=" N GLN E 457 " --> pdb=" O TRP E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 507 Processing helix chain 'E' and resid 510 through 523 removed outlier: 3.515A pdb=" N LEU E 523 " --> pdb=" O VAL E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 541 Processing helix chain 'E' and resid 544 through 558 removed outlier: 3.602A pdb=" N TRP E 548 " --> pdb=" O ASP E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 575 Processing helix chain 'E' and resid 578 through 592 removed outlier: 3.791A pdb=" N MET E 582 " --> pdb=" O TYR E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 611 removed outlier: 3.518A pdb=" N ALA E 598 " --> pdb=" O GLN E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 638 removed outlier: 3.893A pdb=" N GLY E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU E 627 " --> pdb=" O ALA E 623 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 637 " --> pdb=" O MET E 633 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET E 638 " --> pdb=" O THR E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 648 removed outlier: 3.680A pdb=" N TRP E 648 " --> pdb=" O VAL E 644 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 59 removed outlier: 6.290A pdb=" N LEU A 31 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ALA A 59 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A 33 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 4 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N TYR A 34 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL A 6 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN A 3 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL A 83 " --> pdb=" O ASN A 3 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA A 5 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 261 removed outlier: 3.699A pdb=" N ALA A 260 " --> pdb=" O MET A 275 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 275 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ARG A 287 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 278 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.081A pdb=" N LEU B 31 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA B 59 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 33 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN B 3 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL B 83 " --> pdb=" O ASN B 3 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA B 5 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'B' and resid 257 through 261 removed outlier: 3.614A pdb=" N ALA B 260 " --> pdb=" O MET B 275 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ARG B 287 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 278 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 55 through 60 removed outlier: 6.084A pdb=" N LEU C 31 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ALA C 59 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 33 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 4 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR C 34 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C 6 " --> pdb=" O TYR C 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN C 3 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL C 83 " --> pdb=" O ASN C 3 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA C 5 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE C 82 " --> pdb=" O CYS C 124 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'C' and resid 257 through 261 removed outlier: 3.764A pdb=" N ALA C 260 " --> pdb=" O MET C 275 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET C 275 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ARG C 287 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C 278 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 55 through 60 removed outlier: 3.961A pdb=" N ASP D 35 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL D 4 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N TYR D 34 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL D 6 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB3, first strand: chain 'D' and resid 257 through 259 removed outlier: 5.160A pdb=" N ARG D 287 " --> pdb=" O PRO D 276 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL D 278 " --> pdb=" O GLU D 285 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.09: 1 1.09 - 1.31: 1881 1.31 - 1.53: 7788 1.53 - 1.75: 1611 1.75 - 1.97: 106 Bond restraints: 11387 Sorted by residual: bond pdb=" CG PRO D 173 " pdb=" CD PRO D 173 " ideal model delta sigma weight residual 1.503 0.865 0.638 3.40e-02 8.65e+02 3.53e+02 bond pdb=" CB PRO D 173 " pdb=" CG PRO D 173 " ideal model delta sigma weight residual 1.492 1.968 -0.476 5.00e-02 4.00e+02 9.05e+01 bond pdb=" N PRO D 173 " pdb=" CD PRO D 173 " ideal model delta sigma weight residual 1.473 1.562 -0.089 1.40e-02 5.10e+03 4.07e+01 bond pdb=" CA PRO D 173 " pdb=" CB PRO D 173 " ideal model delta sigma weight residual 1.534 1.441 0.093 1.79e-02 3.12e+03 2.70e+01 bond pdb=" C HIS D 172 " pdb=" N PRO D 173 " ideal model delta sigma weight residual 1.337 1.379 -0.043 1.06e-02 8.90e+03 1.65e+01 ... (remaining 11382 not shown) Histogram of bond angle deviations from ideal: 70.01 - 82.82: 3 82.82 - 95.63: 1 95.63 - 108.43: 673 108.43 - 121.24: 11974 121.24 - 134.05: 2850 Bond angle restraints: 15501 Sorted by residual: angle pdb=" N PRO D 173 " pdb=" CD PRO D 173 " pdb=" CG PRO D 173 " ideal model delta sigma weight residual 103.20 70.01 33.19 1.50e+00 4.44e-01 4.90e+02 angle pdb=" CA PRO D 173 " pdb=" CB PRO D 173 " pdb=" CG PRO D 173 " ideal model delta sigma weight residual 104.50 72.67 31.83 1.90e+00 2.77e-01 2.81e+02 angle pdb=" N PRO D 173 " pdb=" CA PRO D 173 " pdb=" CB PRO D 173 " ideal model delta sigma weight residual 103.20 88.39 14.81 9.50e-01 1.11e+00 2.43e+02 angle pdb=" CB PRO D 173 " pdb=" CG PRO D 173 " pdb=" CD PRO D 173 " ideal model delta sigma weight residual 106.10 74.71 31.39 3.20e+00 9.77e-02 9.62e+01 angle pdb=" CA PRO D 173 " pdb=" N PRO D 173 " pdb=" CD PRO D 173 " ideal model delta sigma weight residual 112.00 102.42 9.58 1.40e+00 5.10e-01 4.69e+01 ... (remaining 15496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5980 17.93 - 35.87: 723 35.87 - 53.80: 189 53.80 - 71.74: 32 71.74 - 89.67: 11 Dihedral angle restraints: 6935 sinusoidal: 2666 harmonic: 4269 Sorted by residual: dihedral pdb=" CA HIS D 172 " pdb=" C HIS D 172 " pdb=" N PRO D 173 " pdb=" CA PRO D 173 " ideal model delta harmonic sigma weight residual 180.00 126.91 53.09 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA ALA E 564 " pdb=" C ALA E 564 " pdb=" N LEU E 565 " pdb=" CA LEU E 565 " ideal model delta harmonic sigma weight residual 180.00 135.67 44.33 0 5.00e+00 4.00e-02 7.86e+01 dihedral pdb=" N PRO D 173 " pdb=" C PRO D 173 " pdb=" CA PRO D 173 " pdb=" CB PRO D 173 " ideal model delta harmonic sigma weight residual 115.10 96.71 18.39 0 2.50e+00 1.60e-01 5.41e+01 ... (remaining 6932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1651 0.071 - 0.142: 218 0.142 - 0.213: 3 0.213 - 0.284: 1 0.284 - 0.355: 2 Chirality restraints: 1875 Sorted by residual: chirality pdb=" CA ASN C 128 " pdb=" N ASN C 128 " pdb=" C ASN C 128 " pdb=" CB ASN C 128 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA ASN B 128 " pdb=" N ASN B 128 " pdb=" C ASN B 128 " pdb=" CB ASN B 128 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ASN A 128 " pdb=" N ASN A 128 " pdb=" C ASN A 128 " pdb=" CB ASN A 128 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1872 not shown) Planarity restraints: 2004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 172 " -0.101 5.00e-02 4.00e+02 1.46e-01 3.39e+01 pdb=" N PRO D 173 " 0.251 5.00e-02 4.00e+02 pdb=" CA PRO D 173 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO D 173 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 127 " 0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C THR C 127 " -0.075 2.00e-02 2.50e+03 pdb=" O THR C 127 " 0.029 2.00e-02 2.50e+03 pdb=" N ASN C 128 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 128 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C ASN C 128 " 0.058 2.00e-02 2.50e+03 pdb=" O ASN C 128 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO C 129 " -0.021 2.00e-02 2.50e+03 ... (remaining 2001 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 383 2.72 - 3.26: 10977 3.26 - 3.81: 17850 3.81 - 4.35: 21756 4.35 - 4.90: 37846 Nonbonded interactions: 88812 Sorted by model distance: nonbonded pdb=" O LEU C 25 " pdb=" NH2 ARG C 51 " model vdw 2.173 2.520 nonbonded pdb=" O LEU A 25 " pdb=" NH2 ARG A 51 " model vdw 2.206 2.520 nonbonded pdb=" OG1 THR A 264 " pdb=" O CYS A 270 " model vdw 2.216 2.440 nonbonded pdb=" O LEU B 25 " pdb=" NH2 ARG B 51 " model vdw 2.247 2.520 nonbonded pdb=" O ASN C 128 " pdb=" N VAL C 130 " model vdw 2.288 2.520 ... (remaining 88807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 318) selection = chain 'B' selection = (chain 'C' and resid 1 through 318) selection = (chain 'D' and resid 1 through 318) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.970 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.250 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 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:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.008 0.638 11387 Z= 0.727 Angle : 0.830 33.187 15501 Z= 0.479 Chirality : 0.046 0.355 1875 Planarity : 0.006 0.146 2004 Dihedral : 16.727 89.670 4187 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.74 % Favored : 93.99 % Rotamer: Outliers : 0.58 % Allowed : 23.74 % Favored : 75.68 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.14 % 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 (0.22), residues: 1480 helix: 1.47 (0.19), residues: 764 sheet: -1.44 (0.38), residues: 158 loop : -1.49 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 548 HIS 0.004 0.001 HIS C 268 PHE 0.011 0.001 PHE A 27 TYR 0.013 0.001 TYR E 568 ARG 0.004 0.000 ARG E 570 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 108 average time/residue: 1.3605 time to fit residues: 158.5681 Evaluate side-chains 96 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain C residue 132 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 40.0000 chunk 112 optimal weight: 0.0470 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN ** E 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11387 Z= 0.190 Angle : 0.570 11.676 15501 Z= 0.287 Chirality : 0.044 0.270 1875 Planarity : 0.005 0.070 2004 Dihedral : 5.032 51.061 1602 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.39 % Allowed : 23.24 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1480 helix: 1.70 (0.19), residues: 778 sheet: -1.35 (0.38), residues: 158 loop : -1.46 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 548 HIS 0.005 0.001 HIS D 172 PHE 0.011 0.001 PHE B 27 TYR 0.007 0.001 TYR B 261 ARG 0.003 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 103 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8027 (mttp) REVERT: B 235 MET cc_start: 0.8245 (tpt) cc_final: 0.7907 (mtp) REVERT: D 47 SER cc_start: 0.8522 (p) cc_final: 0.8275 (m) outliers start: 41 outliers final: 14 residues processed: 132 average time/residue: 1.1887 time to fit residues: 169.9565 Evaluate side-chains 110 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 216 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 134 optimal weight: 50.0000 chunk 145 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 172 HIS E 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11387 Z= 0.346 Angle : 0.645 8.622 15501 Z= 0.323 Chirality : 0.048 0.241 1875 Planarity : 0.006 0.097 2004 Dihedral : 5.175 55.213 1597 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.30 % Allowed : 22.17 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1480 helix: 1.48 (0.19), residues: 785 sheet: -1.35 (0.37), residues: 158 loop : -1.77 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 548 HIS 0.007 0.001 HIS D 172 PHE 0.018 0.002 PHE A 27 TYR 0.017 0.002 TYR E 578 ARG 0.004 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 107 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.5915 (OUTLIER) cc_final: 0.5631 (m-30) REVERT: A 248 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8136 (mttp) REVERT: B 1 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6294 (pmm) REVERT: B 235 MET cc_start: 0.8345 (tpt) cc_final: 0.8019 (mtp) REVERT: C 223 LYS cc_start: 0.7637 (ttpp) cc_final: 0.7250 (mptm) REVERT: C 293 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.7900 (pt) REVERT: C 302 GLU cc_start: 0.7056 (tt0) cc_final: 0.6835 (tt0) outliers start: 52 outliers final: 18 residues processed: 143 average time/residue: 1.2479 time to fit residues: 192.5264 Evaluate side-chains 115 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain E residue 565 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.0020 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 64 optimal weight: 0.0670 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.0930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN B 172 HIS E 559 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11387 Z= 0.208 Angle : 0.565 7.325 15501 Z= 0.280 Chirality : 0.044 0.280 1875 Planarity : 0.005 0.099 2004 Dihedral : 4.904 52.422 1597 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.98 % Allowed : 23.74 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % 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: 0.24 (0.22), residues: 1480 helix: 1.66 (0.19), residues: 787 sheet: -1.31 (0.37), residues: 158 loop : -1.69 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 548 HIS 0.004 0.001 HIS D 172 PHE 0.017 0.002 PHE B 318 TYR 0.008 0.001 TYR A 261 ARG 0.002 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 97 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7266 (tp30) REVERT: B 1 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6481 (pmm) REVERT: B 223 LYS cc_start: 0.7884 (ttmt) cc_final: 0.7542 (tttp) REVERT: B 235 MET cc_start: 0.8281 (tpt) cc_final: 0.7958 (mtp) REVERT: C 223 LYS cc_start: 0.7584 (ttpp) cc_final: 0.7222 (mptm) REVERT: D 303 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6822 (tp30) outliers start: 36 outliers final: 16 residues processed: 123 average time/residue: 1.2610 time to fit residues: 167.3146 Evaluate side-chains 111 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 4.9990 chunk 81 optimal weight: 0.3980 chunk 2 optimal weight: 0.0570 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 chunk 128 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 559 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11387 Z= 0.154 Angle : 0.530 7.416 15501 Z= 0.262 Chirality : 0.043 0.262 1875 Planarity : 0.005 0.103 2004 Dihedral : 4.617 49.245 1597 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.47 % Allowed : 23.24 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1480 helix: 1.94 (0.19), residues: 785 sheet: -1.23 (0.38), residues: 158 loop : -1.57 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 548 HIS 0.002 0.001 HIS B 268 PHE 0.014 0.001 PHE B 318 TYR 0.010 0.001 TYR E 568 ARG 0.001 0.000 ARG E 570 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 98 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7207 (tp30) REVERT: A 267 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6943 (mm-30) REVERT: B 1 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6501 (pmm) REVERT: B 223 LYS cc_start: 0.7835 (ttmt) cc_final: 0.7513 (tttp) REVERT: B 235 MET cc_start: 0.8246 (tpt) cc_final: 0.7909 (mtp) REVERT: C 122 CYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7770 (m) REVERT: C 223 LYS cc_start: 0.7574 (ttpp) cc_final: 0.7220 (mptm) REVERT: C 293 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7736 (pt) REVERT: D 47 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8248 (m) REVERT: D 303 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6827 (tp30) outliers start: 42 outliers final: 19 residues processed: 127 average time/residue: 1.2483 time to fit residues: 171.7371 Evaluate side-chains 122 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS E 559 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11387 Z= 0.217 Angle : 0.579 9.401 15501 Z= 0.283 Chirality : 0.044 0.260 1875 Planarity : 0.005 0.105 2004 Dihedral : 4.762 49.757 1597 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.05 % Allowed : 22.83 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.22), residues: 1480 helix: 1.88 (0.19), residues: 787 sheet: -1.23 (0.38), residues: 158 loop : -1.61 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 548 HIS 0.005 0.001 HIS D 172 PHE 0.013 0.002 PHE A 27 TYR 0.008 0.001 TYR E 568 ARG 0.002 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 98 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.5698 (OUTLIER) cc_final: 0.5309 (m-30) REVERT: A 237 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7301 (tp30) REVERT: A 267 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.7033 (mm-30) REVERT: B 1 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6576 (pmm) REVERT: B 223 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7540 (tttp) REVERT: B 235 MET cc_start: 0.8303 (tpt) cc_final: 0.7962 (mtp) REVERT: C 122 CYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7758 (m) REVERT: C 223 LYS cc_start: 0.7569 (ttpp) cc_final: 0.7247 (mptm) REVERT: C 293 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7843 (pt) REVERT: D 303 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6798 (tp30) outliers start: 49 outliers final: 25 residues processed: 134 average time/residue: 1.1325 time to fit residues: 165.5166 Evaluate side-chains 129 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 97 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 504 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 30.0000 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 0.0570 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 79 optimal weight: 0.3980 chunk 142 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS B 268 HIS C 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11387 Z= 0.151 Angle : 0.538 9.929 15501 Z= 0.261 Chirality : 0.043 0.223 1875 Planarity : 0.005 0.108 2004 Dihedral : 4.535 46.392 1597 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.06 % Allowed : 23.41 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % 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: 0.73 (0.23), residues: 1480 helix: 2.09 (0.19), residues: 785 sheet: -1.12 (0.35), residues: 178 loop : -1.50 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 548 HIS 0.002 0.001 HIS B 268 PHE 0.011 0.001 PHE B 318 TYR 0.008 0.001 TYR E 568 ARG 0.001 0.000 ARG E 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 94 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7226 (tp30) REVERT: B 223 LYS cc_start: 0.7779 (ttmt) cc_final: 0.7466 (tttp) REVERT: B 235 MET cc_start: 0.8256 (tpt) cc_final: 0.7912 (mtp) REVERT: C 122 CYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7776 (m) REVERT: C 223 LYS cc_start: 0.7549 (ttpp) cc_final: 0.7214 (mptm) REVERT: C 286 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7166 (ttp-170) REVERT: C 293 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7680 (pt) REVERT: D 1 MET cc_start: 0.6767 (ptp) cc_final: 0.5711 (ttm) REVERT: D 47 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8231 (m) REVERT: D 303 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6793 (tp30) REVERT: E 580 ARG cc_start: 0.3954 (mmt180) cc_final: 0.3404 (tpt-90) outliers start: 37 outliers final: 20 residues processed: 119 average time/residue: 1.2220 time to fit residues: 158.1214 Evaluate side-chains 122 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 286 ARG Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 27 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS C 131 ASN E 439 ASN E 514 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11387 Z= 0.264 Angle : 0.593 7.931 15501 Z= 0.291 Chirality : 0.045 0.205 1875 Planarity : 0.005 0.104 2004 Dihedral : 4.782 47.320 1597 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.56 % Allowed : 22.99 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % 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: 0.45 (0.22), residues: 1480 helix: 1.87 (0.19), residues: 787 sheet: -1.19 (0.35), residues: 178 loop : -1.67 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 548 HIS 0.006 0.001 HIS D 172 PHE 0.015 0.002 PHE A 27 TYR 0.014 0.001 TYR E 568 ARG 0.003 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 94 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.5769 (OUTLIER) cc_final: 0.5320 (m-30) REVERT: A 237 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7328 (tp30) REVERT: A 248 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8058 (mttp) REVERT: A 267 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7168 (mm-30) REVERT: B 223 LYS cc_start: 0.7859 (ttmt) cc_final: 0.7534 (tttp) REVERT: B 235 MET cc_start: 0.8329 (tpt) cc_final: 0.7992 (mtp) REVERT: C 122 CYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7797 (m) REVERT: C 157 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8595 (tt) REVERT: C 286 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7156 (ttp-170) REVERT: C 293 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7853 (pt) REVERT: D 303 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6773 (tp30) outliers start: 43 outliers final: 20 residues processed: 128 average time/residue: 1.2835 time to fit residues: 177.9160 Evaluate side-chains 118 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 89 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 286 ARG Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 504 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 140 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS C 311 ASN D 311 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11387 Z= 0.313 Angle : 0.628 8.398 15501 Z= 0.310 Chirality : 0.047 0.200 1875 Planarity : 0.005 0.117 2004 Dihedral : 5.003 49.711 1597 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.14 % Allowed : 23.66 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % 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: 0.18 (0.22), residues: 1480 helix: 1.64 (0.19), residues: 787 sheet: -1.35 (0.33), residues: 186 loop : -1.77 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 548 HIS 0.007 0.001 HIS D 172 PHE 0.016 0.002 PHE A 27 TYR 0.011 0.001 TYR E 568 ARG 0.003 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 93 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: A 248 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8056 (mttp) REVERT: B 1 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6479 (pmm) REVERT: B 223 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7554 (tttp) REVERT: B 235 MET cc_start: 0.8348 (tpt) cc_final: 0.8021 (mtp) REVERT: C 157 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8630 (tt) REVERT: C 286 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7141 (ttp-170) REVERT: C 293 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7946 (pt) REVERT: D 303 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6818 (tp30) REVERT: E 582 MET cc_start: 0.5125 (OUTLIER) cc_final: 0.4901 (mmm) outliers start: 38 outliers final: 23 residues processed: 120 average time/residue: 1.2946 time to fit residues: 168.1817 Evaluate side-chains 124 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 286 ARG Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 568 TYR Chi-restraints excluded: chain E residue 582 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 117 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS C 311 ASN E 521 HIS E 533 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11387 Z= 0.183 Angle : 0.564 9.034 15501 Z= 0.275 Chirality : 0.043 0.187 1875 Planarity : 0.005 0.115 2004 Dihedral : 4.696 45.749 1597 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.65 % Allowed : 24.15 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % 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: 0.46 (0.22), residues: 1480 helix: 1.86 (0.19), residues: 787 sheet: -1.14 (0.35), residues: 173 loop : -1.67 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 548 HIS 0.003 0.001 HIS D 172 PHE 0.010 0.001 PHE B 318 TYR 0.011 0.001 TYR E 568 ARG 0.002 0.000 ARG C 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 95 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7292 (tp30) REVERT: B 223 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7514 (tttm) REVERT: B 235 MET cc_start: 0.8274 (tpt) cc_final: 0.7946 (mtp) REVERT: C 122 CYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7745 (m) REVERT: C 286 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7185 (ttp-170) REVERT: C 293 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7854 (pt) REVERT: D 1 MET cc_start: 0.6737 (ptp) cc_final: 0.5778 (ttm) REVERT: D 47 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8285 (m) REVERT: D 303 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6827 (tp30) REVERT: E 582 MET cc_start: 0.5240 (mmt) cc_final: 0.4996 (mmm) outliers start: 32 outliers final: 20 residues processed: 116 average time/residue: 1.3109 time to fit residues: 164.3678 Evaluate side-chains 121 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 286 ARG Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain E residue 568 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.1980 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS C 131 ASN E 457 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.158375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.107513 restraints weight = 11765.046| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.07 r_work: 0.2978 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11387 Z= 0.185 Angle : 0.565 9.432 15501 Z= 0.275 Chirality : 0.043 0.190 1875 Planarity : 0.005 0.106 2004 Dihedral : 4.623 44.774 1597 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.48 % Allowed : 24.40 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.22 % 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: 0.57 (0.22), residues: 1480 helix: 1.95 (0.19), residues: 789 sheet: -1.09 (0.36), residues: 173 loop : -1.63 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 548 HIS 0.004 0.001 HIS C 245 PHE 0.010 0.001 PHE A 27 TYR 0.012 0.001 TYR E 568 ARG 0.001 0.000 ARG C 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3622.40 seconds wall clock time: 64 minutes 18.07 seconds (3858.07 seconds total)