Starting phenix.real_space_refine on Tue Jun 17 00:19:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t38_25651/06_2025/7t38_25651.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t38_25651/06_2025/7t38_25651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t38_25651/06_2025/7t38_25651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t38_25651/06_2025/7t38_25651.map" model { file = "/net/cci-nas-00/data/ceres_data/7t38_25651/06_2025/7t38_25651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t38_25651/06_2025/7t38_25651.cif" } resolution = 3.8 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= 0.016 sd= 0.056 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 112 5.16 5 C 12736 2.51 5 N 3256 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 19404 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4851 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 586} Chain breaks: 4 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'GLU:plan': 14, 'ARG:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 90 Restraints were copied for chains: C, B, D Time building chain proxies: 11.38, per 1000 atoms: 0.59 Number of scatterers: 19404 At special positions: 0 Unit cell: (144.45, 144.45, 115.56, 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 112 16.00 O 3300 8.00 N 3256 7.00 C 12736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.53 Conformation dependent library (CDL) restraints added in 2.7 seconds 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4592 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 8 sheets defined 62.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.505A pdb=" N GLY A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.706A pdb=" N THR A 93 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.643A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.565A pdb=" N GLY A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.532A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.738A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.782A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 removed outlier: 3.567A pdb=" N GLY A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.762A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 370 through 375 removed outlier: 4.018A pdb=" N VAL A 374 " --> pdb=" O HIS A 370 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 375' Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.346A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 470 through 492 Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.953A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.573A pdb=" N THR A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 517' Processing helix chain 'A' and resid 521 through 534 removed outlier: 3.991A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 558 removed outlier: 4.258A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 618 through 649 removed outlier: 3.978A pdb=" N LEU A 638 " --> pdb=" O TYR A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 673 removed outlier: 3.945A pdb=" N SER A 656 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.505A pdb=" N GLY B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.707A pdb=" N THR B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.642A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.565A pdb=" N GLY B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.532A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 185 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.738A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.782A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 removed outlier: 3.567A pdb=" N GLY B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.762A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 370 through 375 removed outlier: 4.018A pdb=" N VAL B 374 " --> pdb=" O HIS B 370 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 375' Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.346A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 470 through 492 Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.953A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.573A pdb=" N THR B 516 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 517' Processing helix chain 'B' and resid 521 through 534 removed outlier: 3.991A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 558 removed outlier: 4.259A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 618 through 649 removed outlier: 3.979A pdb=" N LEU B 638 " --> pdb=" O TYR B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 673 removed outlier: 3.944A pdb=" N SER B 656 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.504A pdb=" N GLY C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.707A pdb=" N THR C 93 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.642A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.566A pdb=" N GLY C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.532A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.738A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.782A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 removed outlier: 3.567A pdb=" N GLY C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.763A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 370 through 375 removed outlier: 4.018A pdb=" N VAL C 374 " --> pdb=" O HIS C 370 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU C 375 " --> pdb=" O ARG C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 370 through 375' Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.346A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 467 through 469 No H-bonds generated for 'chain 'C' and resid 467 through 469' Processing helix chain 'C' and resid 470 through 492 Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.954A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 517 removed outlier: 3.573A pdb=" N THR C 516 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 517' Processing helix chain 'C' and resid 521 through 534 removed outlier: 3.991A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 529 " --> pdb=" O TYR C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 558 removed outlier: 4.259A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY C 550 " --> pdb=" O VAL C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 618 through 649 removed outlier: 3.979A pdb=" N LEU C 638 " --> pdb=" O TYR C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 673 removed outlier: 3.944A pdb=" N SER C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.505A pdb=" N GLY D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.707A pdb=" N THR D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.643A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.565A pdb=" N GLY D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.532A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 185 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.738A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.783A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 removed outlier: 3.567A pdb=" N GLY D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.762A pdb=" N HIS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 370 through 375 removed outlier: 4.018A pdb=" N VAL D 374 " --> pdb=" O HIS D 370 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 375' Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.346A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 467 through 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'D' and resid 470 through 492 Processing helix chain 'D' and resid 496 through 512 removed outlier: 3.953A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 517 removed outlier: 3.573A pdb=" N THR D 516 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 517' Processing helix chain 'D' and resid 521 through 534 removed outlier: 3.991A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 529 " --> pdb=" O TYR D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 558 removed outlier: 4.259A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY D 550 " --> pdb=" O VAL D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 618 through 649 removed outlier: 3.978A pdb=" N LEU D 638 " --> pdb=" O TYR D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 673 removed outlier: 3.944A pdb=" N SER D 656 " --> pdb=" O VAL D 652 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 158 Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 335 removed outlier: 7.533A pdb=" N LYS A 329 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASP A 344 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP A 333 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 338 " --> pdb=" O TYR A 335 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 702 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 689 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AA4, first strand: chain 'B' and resid 329 through 335 removed outlier: 7.534A pdb=" N LYS B 329 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASP B 344 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP B 333 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 338 " --> pdb=" O TYR B 335 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 702 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 689 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 158 Processing sheet with id=AA6, first strand: chain 'C' and resid 329 through 335 removed outlier: 7.533A pdb=" N LYS C 329 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASP C 344 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP C 333 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 338 " --> pdb=" O TYR C 335 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 702 " --> pdb=" O LEU C 689 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 689 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 157 through 158 Processing sheet with id=AA8, first strand: chain 'D' and resid 329 through 335 removed outlier: 7.533A pdb=" N LYS D 329 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASP D 344 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP D 333 " --> pdb=" O VAL D 340 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 338 " --> pdb=" O TYR D 335 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG D 702 " --> pdb=" O LEU D 689 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 689 " --> pdb=" O ARG D 702 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3060 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: 8.78 Time building geometry restraints manager: 7.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5977 1.34 - 1.46: 4821 1.46 - 1.58: 8922 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 19892 Sorted by residual: bond pdb=" C PRO D 325 " pdb=" N LEU D 326 " ideal model delta sigma weight residual 1.330 1.263 0.067 1.20e-02 6.94e+03 3.08e+01 bond pdb=" C PRO C 325 " pdb=" N LEU C 326 " ideal model delta sigma weight residual 1.330 1.263 0.066 1.20e-02 6.94e+03 3.06e+01 bond pdb=" C PRO A 325 " pdb=" N LEU A 326 " ideal model delta sigma weight residual 1.330 1.263 0.066 1.20e-02 6.94e+03 3.06e+01 bond pdb=" C PRO B 325 " pdb=" N LEU B 326 " ideal model delta sigma weight residual 1.330 1.263 0.066 1.20e-02 6.94e+03 3.06e+01 bond pdb=" C ARG B 539 " pdb=" N PHE B 540 " ideal model delta sigma weight residual 1.335 1.393 -0.058 1.31e-02 5.83e+03 1.98e+01 ... (remaining 19887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 26154 1.93 - 3.85: 695 3.85 - 5.78: 95 5.78 - 7.71: 60 7.71 - 9.63: 12 Bond angle restraints: 27016 Sorted by residual: angle pdb=" C GLN B 520 " pdb=" CA GLN B 520 " pdb=" CB GLN B 520 " ideal model delta sigma weight residual 116.54 110.61 5.93 1.15e+00 7.56e-01 2.66e+01 angle pdb=" C GLN C 520 " pdb=" CA GLN C 520 " pdb=" CB GLN C 520 " ideal model delta sigma weight residual 116.54 110.64 5.90 1.15e+00 7.56e-01 2.63e+01 angle pdb=" C GLN A 520 " pdb=" CA GLN A 520 " pdb=" CB GLN A 520 " ideal model delta sigma weight residual 116.54 110.66 5.88 1.15e+00 7.56e-01 2.61e+01 angle pdb=" C GLN D 520 " pdb=" CA GLN D 520 " pdb=" CB GLN D 520 " ideal model delta sigma weight residual 116.54 110.70 5.84 1.15e+00 7.56e-01 2.58e+01 angle pdb=" N LEU A 296 " pdb=" CA LEU A 296 " pdb=" C LEU A 296 " ideal model delta sigma weight residual 110.42 116.83 -6.41 1.55e+00 4.16e-01 1.71e+01 ... (remaining 27011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10576 17.99 - 35.99: 896 35.99 - 53.98: 132 53.98 - 71.98: 24 71.98 - 89.97: 8 Dihedral angle restraints: 11636 sinusoidal: 4532 harmonic: 7104 Sorted by residual: dihedral pdb=" CA VAL D 546 " pdb=" C VAL D 546 " pdb=" N PHE D 547 " pdb=" CA PHE D 547 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA VAL C 546 " pdb=" C VAL C 546 " pdb=" N PHE C 547 " pdb=" CA PHE C 547 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA VAL B 546 " pdb=" C VAL B 546 " pdb=" N PHE B 547 " pdb=" CA PHE B 547 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 11633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2508 0.055 - 0.110: 534 0.110 - 0.164: 42 0.164 - 0.219: 4 0.219 - 0.274: 4 Chirality restraints: 3092 Sorted by residual: chirality pdb=" CB VAL C 546 " pdb=" CA VAL C 546 " pdb=" CG1 VAL C 546 " pdb=" CG2 VAL C 546 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL D 546 " pdb=" CA VAL D 546 " pdb=" CG1 VAL D 546 " pdb=" CG2 VAL D 546 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB VAL B 546 " pdb=" CA VAL B 546 " pdb=" CG1 VAL B 546 " pdb=" CG2 VAL B 546 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 3089 not shown) Planarity restraints: 3316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 556 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C VAL B 556 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL B 556 " 0.017 2.00e-02 2.50e+03 pdb=" N SER B 557 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 556 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C VAL C 556 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL C 556 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 557 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 556 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" C VAL A 556 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL A 556 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A 557 " 0.015 2.00e-02 2.50e+03 ... (remaining 3313 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6038 2.84 - 3.35: 18083 3.35 - 3.87: 31097 3.87 - 4.38: 32953 4.38 - 4.90: 58711 Nonbonded interactions: 146882 Sorted by model distance: nonbonded pdb=" OH TYR B 544 " pdb=" OG1 THR B 604 " model vdw 2.319 3.040 nonbonded pdb=" OH TYR C 544 " pdb=" OG1 THR C 604 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR D 544 " pdb=" OG1 THR D 604 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR A 544 " pdb=" OG1 THR A 604 " model vdw 2.320 3.040 nonbonded pdb=" O PHE A 209 " pdb=" OG SER A 215 " model vdw 2.326 3.040 ... (remaining 146877 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 169.240 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: 1.910 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 48.930 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 224.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 0.004 0.067 19892 Z= 0.203 Angle : 0.777 9.631 27016 Z= 0.403 Chirality : 0.044 0.274 3092 Planarity : 0.005 0.062 3316 Dihedral : 13.601 89.971 7044 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.39 % Allowed : 0.92 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.24 (0.15), residues: 2392 helix: -0.02 (0.13), residues: 1424 sheet: 0.04 (0.44), residues: 64 loop : -2.16 (0.16), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 333 HIS 0.003 0.001 HIS D 251 PHE 0.016 0.001 PHE D 407 TYR 0.034 0.002 TYR D 525 ARG 0.002 0.000 ARG B 617 Details of bonding type rmsd hydrogen bonds : bond 0.17023 ( 1044) hydrogen bonds : angle 5.17740 ( 3060) covalent geometry : bond 0.00355 (19892) covalent geometry : angle 0.77692 (27016) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 211 time to evaluate : 3.112 Fit side-chains REVERT: A 122 MET cc_start: 0.8573 (mtm) cc_final: 0.8113 (mtm) REVERT: A 141 GLN cc_start: 0.8579 (mm-40) cc_final: 0.7949 (tp-100) REVERT: A 162 TYR cc_start: 0.8050 (p90) cc_final: 0.7649 (p90) REVERT: B 122 MET cc_start: 0.8575 (mtm) cc_final: 0.8126 (mtm) REVERT: B 141 GLN cc_start: 0.8542 (mm-40) cc_final: 0.7919 (tp-100) REVERT: B 162 TYR cc_start: 0.8036 (p90) cc_final: 0.7613 (p90) REVERT: C 122 MET cc_start: 0.8573 (mtm) cc_final: 0.8123 (mtm) REVERT: C 141 GLN cc_start: 0.8548 (mm-40) cc_final: 0.7920 (tp-100) REVERT: C 162 TYR cc_start: 0.8040 (p90) cc_final: 0.7616 (p90) REVERT: D 122 MET cc_start: 0.8563 (mtm) cc_final: 0.8122 (mtm) REVERT: D 141 GLN cc_start: 0.8509 (mm-40) cc_final: 0.7886 (tp-100) REVERT: D 162 TYR cc_start: 0.8043 (p90) cc_final: 0.7622 (p90) REVERT: D 243 ASP cc_start: 0.8151 (p0) cc_final: 0.7946 (p0) outliers start: 8 outliers final: 0 residues processed: 211 average time/residue: 0.3569 time to fit residues: 123.8947 Evaluate side-chains 155 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.091220 restraints weight = 34909.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.093538 restraints weight = 23792.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095092 restraints weight = 18607.092| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19892 Z= 0.228 Angle : 0.634 8.978 27016 Z= 0.311 Chirality : 0.040 0.132 3092 Planarity : 0.004 0.047 3316 Dihedral : 3.712 14.818 2632 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.74 % Allowed : 9.53 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.13 (0.16), residues: 2392 helix: 1.00 (0.14), residues: 1432 sheet: 0.47 (0.56), residues: 64 loop : -1.96 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 712 HIS 0.003 0.001 HIS B 313 PHE 0.020 0.002 PHE D 407 TYR 0.012 0.002 TYR C 629 ARG 0.003 0.000 ARG D 617 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 1044) hydrogen bonds : angle 3.62540 ( 3060) covalent geometry : bond 0.00541 (19892) covalent geometry : angle 0.63373 (27016) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 2.288 Fit side-chains REVERT: A 141 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8046 (tp-100) REVERT: B 141 GLN cc_start: 0.8622 (mm-40) cc_final: 0.7985 (tp-100) REVERT: C 141 GLN cc_start: 0.8615 (mm-40) cc_final: 0.7984 (tp-100) REVERT: D 141 GLN cc_start: 0.8614 (mm-40) cc_final: 0.7969 (tp-100) outliers start: 36 outliers final: 25 residues processed: 179 average time/residue: 0.2624 time to fit residues: 78.8248 Evaluate side-chains 173 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 144 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 511 ASN D 511 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.117217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.092237 restraints weight = 34887.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.094592 restraints weight = 23592.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096229 restraints weight = 18352.735| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 19892 Z= 0.157 Angle : 0.520 7.834 27016 Z= 0.258 Chirality : 0.038 0.126 3092 Planarity : 0.003 0.041 3316 Dihedral : 3.474 12.695 2632 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.84 % Allowed : 13.01 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.51 (0.17), residues: 2392 helix: 1.58 (0.14), residues: 1440 sheet: 0.42 (0.56), residues: 64 loop : -1.84 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 223 HIS 0.004 0.001 HIS C 313 PHE 0.014 0.001 PHE B 407 TYR 0.026 0.001 TYR A 162 ARG 0.002 0.000 ARG A 617 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 1044) hydrogen bonds : angle 3.33057 ( 3060) covalent geometry : bond 0.00374 (19892) covalent geometry : angle 0.51977 (27016) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 5.190 Fit side-chains REVERT: A 141 GLN cc_start: 0.8696 (mm-40) cc_final: 0.7970 (tp-100) REVERT: B 141 GLN cc_start: 0.8650 (mm-40) cc_final: 0.7922 (tp-100) REVERT: C 141 GLN cc_start: 0.8647 (mm-40) cc_final: 0.7919 (tp-100) REVERT: C 511 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8723 (t0) REVERT: D 141 GLN cc_start: 0.8641 (mm-40) cc_final: 0.7915 (tp-100) REVERT: D 511 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8717 (t0) outliers start: 38 outliers final: 28 residues processed: 180 average time/residue: 0.3482 time to fit residues: 104.9158 Evaluate side-chains 172 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 511 ASN Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 547 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 511 ASN Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 221 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN B 511 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.093567 restraints weight = 34864.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.096021 restraints weight = 23350.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.097691 restraints weight = 18003.294| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 19892 Z= 0.108 Angle : 0.486 7.141 27016 Z= 0.242 Chirality : 0.036 0.124 3092 Planarity : 0.003 0.041 3316 Dihedral : 3.304 12.280 2632 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.37 % Allowed : 14.31 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.94 (0.17), residues: 2392 helix: 1.96 (0.14), residues: 1440 sheet: 0.62 (0.56), residues: 64 loop : -1.74 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 223 HIS 0.003 0.000 HIS D 313 PHE 0.009 0.001 PHE C 476 TYR 0.023 0.001 TYR A 162 ARG 0.001 0.000 ARG B 617 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 1044) hydrogen bonds : angle 3.15168 ( 3060) covalent geometry : bond 0.00247 (19892) covalent geometry : angle 0.48602 (27016) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 2.664 Fit side-chains REVERT: A 141 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8015 (tp-100) REVERT: A 277 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7592 (mpp) REVERT: A 607 MET cc_start: 0.8779 (tpt) cc_final: 0.8551 (tpt) REVERT: B 141 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8019 (tp-100) REVERT: B 277 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7586 (mpp) REVERT: B 607 MET cc_start: 0.8784 (tpt) cc_final: 0.8540 (tpt) REVERT: C 141 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8017 (tp-100) REVERT: C 277 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7588 (mpp) REVERT: C 372 MET cc_start: 0.8838 (mtp) cc_final: 0.8524 (mtp) REVERT: C 607 MET cc_start: 0.8776 (tpt) cc_final: 0.8538 (tpt) REVERT: D 141 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8006 (tp-100) REVERT: D 277 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7590 (mpp) REVERT: D 607 MET cc_start: 0.8775 (tpt) cc_final: 0.8534 (tpt) outliers start: 49 outliers final: 35 residues processed: 196 average time/residue: 0.3434 time to fit residues: 108.9693 Evaluate side-chains 182 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 683 HIS Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 683 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 40 optimal weight: 0.9980 chunk 236 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 233 optimal weight: 0.0870 chunk 196 optimal weight: 3.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 511 ASN D 511 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.093113 restraints weight = 35140.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.095523 restraints weight = 23651.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097154 restraints weight = 18313.121| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 19892 Z= 0.117 Angle : 0.496 9.087 27016 Z= 0.241 Chirality : 0.036 0.126 3092 Planarity : 0.003 0.042 3316 Dihedral : 3.243 11.971 2632 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.32 % Allowed : 15.76 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.10 (0.17), residues: 2392 helix: 2.12 (0.14), residues: 1440 sheet: 0.09 (0.55), residues: 64 loop : -1.66 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 223 HIS 0.003 0.001 HIS C 313 PHE 0.008 0.001 PHE A 407 TYR 0.019 0.001 TYR A 162 ARG 0.004 0.000 ARG B 392 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 1044) hydrogen bonds : angle 3.05581 ( 3060) covalent geometry : bond 0.00274 (19892) covalent geometry : angle 0.49579 (27016) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 2.204 Fit side-chains REVERT: A 141 GLN cc_start: 0.8732 (mm-40) cc_final: 0.7971 (tp-100) REVERT: A 277 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7582 (mpp) REVERT: A 607 MET cc_start: 0.8774 (tpt) cc_final: 0.8491 (tpt) REVERT: B 141 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8007 (tp-100) REVERT: B 277 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7583 (mpp) REVERT: B 607 MET cc_start: 0.8789 (tpt) cc_final: 0.8513 (tpt) REVERT: C 141 GLN cc_start: 0.8680 (mm-40) cc_final: 0.7972 (tp-100) REVERT: C 277 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7583 (mpp) REVERT: C 607 MET cc_start: 0.8779 (tpt) cc_final: 0.8508 (tpt) REVERT: D 141 GLN cc_start: 0.8688 (mm-40) cc_final: 0.7998 (tp-100) REVERT: D 277 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7582 (mpp) REVERT: D 607 MET cc_start: 0.8783 (tpt) cc_final: 0.8509 (tpt) outliers start: 48 outliers final: 35 residues processed: 183 average time/residue: 0.2611 time to fit residues: 79.2179 Evaluate side-chains 192 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 547 PHE Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 60 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 186 ASN B 186 ASN C 186 ASN D 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.094328 restraints weight = 34531.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096806 restraints weight = 22785.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098508 restraints weight = 17409.713| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 19892 Z= 0.096 Angle : 0.482 9.689 27016 Z= 0.233 Chirality : 0.036 0.121 3092 Planarity : 0.003 0.044 3316 Dihedral : 3.135 11.530 2632 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.37 % Allowed : 16.68 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.33 (0.17), residues: 2392 helix: 2.33 (0.14), residues: 1440 sheet: 0.04 (0.58), residues: 64 loop : -1.63 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 223 HIS 0.002 0.000 HIS D 313 PHE 0.006 0.001 PHE C 476 TYR 0.018 0.001 TYR D 162 ARG 0.003 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.02862 ( 1044) hydrogen bonds : angle 2.89489 ( 3060) covalent geometry : bond 0.00219 (19892) covalent geometry : angle 0.48219 (27016) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 2.445 Fit side-chains REVERT: A 141 GLN cc_start: 0.8634 (mm-40) cc_final: 0.7926 (tp-100) REVERT: A 277 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7450 (mpp) REVERT: B 141 GLN cc_start: 0.8630 (mm-40) cc_final: 0.7935 (tp-100) REVERT: B 277 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7451 (mpp) REVERT: C 141 GLN cc_start: 0.8629 (mm-40) cc_final: 0.7931 (tp-100) REVERT: C 277 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7451 (mpp) REVERT: D 141 GLN cc_start: 0.8624 (mm-40) cc_final: 0.7932 (tp-100) REVERT: D 277 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7448 (mpp) outliers start: 49 outliers final: 29 residues processed: 199 average time/residue: 0.2611 time to fit residues: 86.6670 Evaluate side-chains 189 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.6980 chunk 16 optimal weight: 0.0670 chunk 40 optimal weight: 0.0010 chunk 197 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 overall best weight: 0.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.121314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.096570 restraints weight = 35003.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099064 restraints weight = 23553.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100709 restraints weight = 18171.795| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 19892 Z= 0.082 Angle : 0.494 10.287 27016 Z= 0.230 Chirality : 0.035 0.119 3092 Planarity : 0.003 0.045 3316 Dihedral : 2.996 11.260 2632 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.03 % Allowed : 17.31 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.54 (0.17), residues: 2392 helix: 2.47 (0.14), residues: 1440 sheet: 0.82 (0.58), residues: 56 loop : -1.53 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 223 HIS 0.002 0.000 HIS A 651 PHE 0.006 0.001 PHE B 551 TYR 0.017 0.001 TYR D 162 ARG 0.003 0.000 ARG D 392 Details of bonding type rmsd hydrogen bonds : bond 0.02604 ( 1044) hydrogen bonds : angle 2.72665 ( 3060) covalent geometry : bond 0.00176 (19892) covalent geometry : angle 0.49410 (27016) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 2.310 Fit side-chains REVERT: A 141 GLN cc_start: 0.8677 (mm-40) cc_final: 0.7890 (tp-100) REVERT: A 277 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7624 (mpp) REVERT: A 534 LEU cc_start: 0.4557 (OUTLIER) cc_final: 0.4087 (mt) REVERT: A 645 MET cc_start: 0.7142 (tmm) cc_final: 0.6720 (tmm) REVERT: B 141 GLN cc_start: 0.8721 (mm-40) cc_final: 0.7934 (tp-100) REVERT: B 211 GLU cc_start: 0.7785 (pm20) cc_final: 0.7542 (pm20) REVERT: B 243 ASP cc_start: 0.7759 (p0) cc_final: 0.7305 (p0) REVERT: B 277 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7625 (mpp) REVERT: B 534 LEU cc_start: 0.4552 (OUTLIER) cc_final: 0.4077 (mt) REVERT: C 141 GLN cc_start: 0.8710 (mm-40) cc_final: 0.7912 (tp-100) REVERT: C 277 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7621 (mpp) REVERT: C 534 LEU cc_start: 0.4555 (OUTLIER) cc_final: 0.4090 (mt) REVERT: D 141 GLN cc_start: 0.8726 (mm-40) cc_final: 0.7938 (tp-100) REVERT: D 277 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7621 (mpp) outliers start: 42 outliers final: 15 residues processed: 196 average time/residue: 0.2677 time to fit residues: 86.7500 Evaluate side-chains 182 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 0.2980 chunk 88 optimal weight: 0.0870 chunk 162 optimal weight: 5.9990 chunk 208 optimal weight: 0.0010 chunk 196 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 153 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.6980 chunk 47 optimal weight: 0.0670 overall best weight: 0.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097558 restraints weight = 34751.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.100190 restraints weight = 22533.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101995 restraints weight = 17021.192| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19892 Z= 0.080 Angle : 0.492 9.228 27016 Z= 0.232 Chirality : 0.034 0.120 3092 Planarity : 0.003 0.044 3316 Dihedral : 2.946 11.167 2632 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.79 % Allowed : 17.84 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.60 (0.17), residues: 2392 helix: 2.57 (0.14), residues: 1440 sheet: 0.57 (0.55), residues: 56 loop : -1.59 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 223 HIS 0.002 0.000 HIS B 651 PHE 0.007 0.001 PHE B 551 TYR 0.015 0.001 TYR D 162 ARG 0.003 0.000 ARG D 392 Details of bonding type rmsd hydrogen bonds : bond 0.02401 ( 1044) hydrogen bonds : angle 2.63917 ( 3060) covalent geometry : bond 0.00167 (19892) covalent geometry : angle 0.49208 (27016) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 2.175 Fit side-chains REVERT: A 277 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8010 (mmt) REVERT: A 534 LEU cc_start: 0.4332 (OUTLIER) cc_final: 0.3937 (mt) REVERT: A 645 MET cc_start: 0.7112 (tmm) cc_final: 0.6694 (tmm) REVERT: B 144 LYS cc_start: 0.8310 (mtpp) cc_final: 0.8092 (mtpp) REVERT: B 277 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8016 (mmt) REVERT: B 534 LEU cc_start: 0.4324 (OUTLIER) cc_final: 0.3933 (mt) REVERT: C 277 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8009 (mmt) REVERT: D 144 LYS cc_start: 0.8305 (mtpp) cc_final: 0.8090 (mtpp) REVERT: D 277 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8016 (mmt) REVERT: D 534 LEU cc_start: 0.4419 (OUTLIER) cc_final: 0.4031 (mt) outliers start: 37 outliers final: 25 residues processed: 194 average time/residue: 0.2581 time to fit residues: 83.5152 Evaluate side-chains 180 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 683 HIS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 683 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 158 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 147 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094162 restraints weight = 35109.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.096571 restraints weight = 23717.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.098209 restraints weight = 18372.368| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19892 Z= 0.118 Angle : 0.515 9.378 27016 Z= 0.246 Chirality : 0.036 0.122 3092 Planarity : 0.003 0.044 3316 Dihedral : 3.016 11.867 2632 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.93 % Allowed : 17.12 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.61 (0.17), residues: 2392 helix: 2.57 (0.14), residues: 1436 sheet: 0.37 (0.54), residues: 56 loop : -1.53 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 223 HIS 0.002 0.001 HIS B 313 PHE 0.015 0.001 PHE D 330 TYR 0.015 0.001 TYR B 525 ARG 0.002 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.02850 ( 1044) hydrogen bonds : angle 2.77156 ( 3060) covalent geometry : bond 0.00277 (19892) covalent geometry : angle 0.51549 (27016) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 2.176 Fit side-chains REVERT: A 277 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7750 (mpp) REVERT: A 534 LEU cc_start: 0.4667 (OUTLIER) cc_final: 0.4320 (mt) REVERT: A 645 MET cc_start: 0.7250 (tmm) cc_final: 0.6841 (tmm) REVERT: B 277 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7727 (mpp) REVERT: B 534 LEU cc_start: 0.4662 (OUTLIER) cc_final: 0.4316 (mt) REVERT: C 277 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7780 (mpp) REVERT: C 534 LEU cc_start: 0.4652 (OUTLIER) cc_final: 0.4307 (mt) REVERT: D 277 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7727 (mpp) REVERT: D 534 LEU cc_start: 0.4687 (OUTLIER) cc_final: 0.4345 (mt) outliers start: 40 outliers final: 30 residues processed: 180 average time/residue: 0.2525 time to fit residues: 75.5441 Evaluate side-chains 185 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 683 HIS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 683 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 174 optimal weight: 6.9990 chunk 27 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 192 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 179 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.122144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.097390 restraints weight = 34752.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099850 restraints weight = 23151.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.101560 restraints weight = 17847.145| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19892 Z= 0.085 Angle : 0.501 9.722 27016 Z= 0.241 Chirality : 0.035 0.121 3092 Planarity : 0.003 0.043 3316 Dihedral : 2.942 11.299 2632 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.45 % Allowed : 17.65 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.72 (0.17), residues: 2392 helix: 2.66 (0.14), residues: 1436 sheet: 0.37 (0.53), residues: 56 loop : -1.48 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 223 HIS 0.002 0.000 HIS B 651 PHE 0.014 0.001 PHE D 330 TYR 0.013 0.001 TYR D 162 ARG 0.002 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.02474 ( 1044) hydrogen bonds : angle 2.62906 ( 3060) covalent geometry : bond 0.00181 (19892) covalent geometry : angle 0.50144 (27016) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 2.111 Fit side-chains REVERT: A 277 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7922 (mmt) REVERT: A 645 MET cc_start: 0.7210 (tmm) cc_final: 0.6778 (tmm) REVERT: B 277 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7916 (mmt) REVERT: C 277 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7919 (mmt) REVERT: C 534 LEU cc_start: 0.4286 (OUTLIER) cc_final: 0.3997 (mt) REVERT: D 277 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7916 (mmt) REVERT: D 534 LEU cc_start: 0.4267 (OUTLIER) cc_final: 0.3983 (mt) outliers start: 30 outliers final: 20 residues processed: 182 average time/residue: 0.2439 time to fit residues: 74.0726 Evaluate side-chains 181 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 557 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 22 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.090321 restraints weight = 35460.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.092595 restraints weight = 24178.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094136 restraints weight = 18922.045| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19892 Z= 0.208 Angle : 0.609 8.865 27016 Z= 0.293 Chirality : 0.039 0.138 3092 Planarity : 0.003 0.044 3316 Dihedral : 3.331 13.003 2632 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.13 % Allowed : 17.41 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.32 (0.17), residues: 2392 helix: 2.32 (0.14), residues: 1444 sheet: -0.44 (0.57), residues: 64 loop : -1.61 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 223 HIS 0.002 0.001 HIS C 313 PHE 0.014 0.002 PHE C 330 TYR 0.013 0.002 TYR B 525 ARG 0.004 0.000 ARG D 392 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 1044) hydrogen bonds : angle 3.13494 ( 3060) covalent geometry : bond 0.00502 (19892) covalent geometry : angle 0.60894 (27016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5516.31 seconds wall clock time: 99 minutes 9.89 seconds (5949.89 seconds total)