Starting phenix.real_space_refine on Sat Jun 14 00:09:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ba4_44395/06_2025/9ba4_44395.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ba4_44395/06_2025/9ba4_44395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ba4_44395/06_2025/9ba4_44395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ba4_44395/06_2025/9ba4_44395.map" model { file = "/net/cci-nas-00/data/ceres_data/9ba4_44395/06_2025/9ba4_44395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ba4_44395/06_2025/9ba4_44395.cif" } resolution = 3.54 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= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 224 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 9556 2.51 5 N 2676 2.21 5 O 2918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15204 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7490 Classifications: {'peptide': 970} Link IDs: {'PCIS': 8, 'PTRANS': 66, 'TRANS': 895} Chain: "B" Number of atoms: 7490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7490 Classifications: {'peptide': 970} Link IDs: {'PCIS': 8, 'PTRANS': 66, 'TRANS': 895} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.84, per 1000 atoms: 0.58 Number of scatterers: 15204 At special positions: 0 Unit cell: (197.4, 240.45, 158.55, 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 54 16.00 O 2918 8.00 N 2676 7.00 C 9556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 348 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 440 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 587 " distance=2.02 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 111 " distance=2.02 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 348 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 440 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 587 " distance=2.02 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1101 " - " ASN A 198 " " NAG A1102 " - " ASN A 525 " " NAG B1101 " - " ASN B 198 " " NAG B1102 " - " ASN B 525 " " NAG C 1 " - " ASN A 76 " " NAG E 1 " - " ASN A 461 " " NAG F 1 " - " ASN A 498 " " NAG H 1 " - " ASN B 76 " " NAG J 1 " - " ASN B 461 " " NAG K 1 " - " ASN B 498 " Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.9 seconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3556 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 57 sheets defined 3.0% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.976A pdb=" N ALA A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 4.062A pdb=" N LEU A 202 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.772A pdb=" N GLU A 301 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.797A pdb=" N SER A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.726A pdb=" N GLY A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 740 removed outlier: 3.612A pdb=" N GLN A 739 " --> pdb=" O SER A 735 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN A 740 " --> pdb=" O ARG A 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 735 through 740' Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.819A pdb=" N ALA B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.556A pdb=" N ASP B 201 " --> pdb=" O ASN B 198 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 202 " --> pdb=" O ALA B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 202' Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.637A pdb=" N GLU B 301 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.768A pdb=" N SER B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 582 removed outlier: 3.998A pdb=" N GLY B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 41 removed outlier: 5.812A pdb=" N GLY A 36 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER A 66 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG A 62 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.781A pdb=" N GLY A 107 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.781A pdb=" N GLY A 107 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 59 Processing sheet with id=AA5, first strand: chain 'A' and resid 131 through 132 removed outlier: 3.501A pdb=" N PHE A 131 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 161 " --> pdb=" O PHE A 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 143 through 147 removed outlier: 5.853A pdb=" N VAL A 143 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA A 230 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA A 145 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU A 232 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU A 147 " --> pdb=" O GLU A 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 151 through 153 removed outlier: 4.220A pdb=" N ILE A 194 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 153 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A 192 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 165 through 169 removed outlier: 3.807A pdb=" N ARG A 167 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 169 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 206 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 209 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 220 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 218 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 249 through 251 removed outlier: 6.017A pdb=" N THR A 249 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 257 through 260 removed outlier: 3.559A pdb=" N VAL A 257 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 325 through 331 removed outlier: 5.153A pdb=" N GLN A 326 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS A 353 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA A 349 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 336 through 339 removed outlier: 7.043A pdb=" N THR A 336 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLN A 413 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA A 338 " --> pdb=" O GLN A 413 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.879A pdb=" N LEU A 344 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 427 through 431 removed outlier: 6.443A pdb=" N ILE A 428 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG A 506 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA A 430 " --> pdb=" O ARG A 506 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 497 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 484 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 451 " --> pdb=" O PHE A 489 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 435 through 438 removed outlier: 3.720A pdb=" N ILE A 436 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 475 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 510 through 513 removed outlier: 3.571A pdb=" N THR A 512 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N HIS A 531 " --> pdb=" O THR A 512 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 518 through 519 removed outlier: 6.943A pdb=" N ALA A 518 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.554A pdb=" N LEU A 572 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 615 through 617 removed outlier: 3.619A pdb=" N ILE A 624 " --> pdb=" O VAL A 672 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 626 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 654 through 655 removed outlier: 4.092A pdb=" N ILE A 663 " --> pdb=" O TYR A 641 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.935A pdb=" N LYS A 640 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 646 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 689 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 692 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 718 through 719 removed outlier: 3.558A pdb=" N VAL A 729 " --> pdb=" O PHE A 771 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 771 " --> pdb=" O VAL A 729 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 759 through 760 removed outlier: 3.701A pdb=" N VAL A 763 " --> pdb=" O TYR A 746 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 759 through 760 removed outlier: 3.614A pdb=" N ALA A 803 " --> pdb=" O VAL A 786 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 820 through 823 Processing sheet with id=AC8, first strand: chain 'A' and resid 862 through 865 Processing sheet with id=AC9, first strand: chain 'A' and resid 920 through 923 Processing sheet with id=AD1, first strand: chain 'A' and resid 960 through 964 removed outlier: 3.550A pdb=" N TYR A 947 " --> pdb=" O THR A 964 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 35 through 41 removed outlier: 5.859A pdb=" N GLY B 36 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER B 66 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 38 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG B 62 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.247A pdb=" N PHE B 48 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LEU B 132 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 107 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 78 through 79 removed outlier: 3.678A pdb=" N GLY B 107 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR B 161 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 56 through 59 Processing sheet with id=AD6, first strand: chain 'B' and resid 143 through 147 removed outlier: 5.792A pdb=" N VAL B 143 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA B 230 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA B 145 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLU B 232 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU B 147 " --> pdb=" O GLU B 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.565A pdb=" N LEU B 153 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B 193 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 168 through 169 Processing sheet with id=AD9, first strand: chain 'B' and resid 211 through 212 removed outlier: 3.549A pdb=" N LYS B 218 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 240 through 243 removed outlier: 3.501A pdb=" N SER B 240 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE B 262 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 249 through 251 Processing sheet with id=AE3, first strand: chain 'B' and resid 257 through 260 removed outlier: 3.505A pdb=" N VAL B 257 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 328 through 331 removed outlier: 6.892A pdb=" N ALA B 349 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 336 through 339 removed outlier: 6.934A pdb=" N THR B 336 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLN B 413 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 338 " --> pdb=" O GLN B 413 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 344 through 346 Processing sheet with id=AE7, first strand: chain 'B' and resid 427 through 431 removed outlier: 3.617A pdb=" N ALA B 497 " --> pdb=" O ALA B 490 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 435 through 438 removed outlier: 3.558A pdb=" N ILE B 436 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 475 " --> pdb=" O ILE B 436 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 510 through 513 removed outlier: 6.798A pdb=" N HIS B 531 " --> pdb=" O THR B 512 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 518 through 519 removed outlier: 6.560A pdb=" N ALA B 518 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 598 " --> pdb=" O CYS B 587 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 526 through 528 Processing sheet with id=AF3, first strand: chain 'B' and resid 615 through 617 removed outlier: 3.539A pdb=" N ILE B 624 " --> pdb=" O VAL B 672 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 626 " --> pdb=" O ALA B 670 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 670 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN B 671 " --> pdb=" O ASN B 659 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN B 659 " --> pdb=" O GLN B 671 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.566A pdb=" N LYS B 654 " --> pdb=" O ALA B 645 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 646 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 682 " --> pdb=" O ARG B 646 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN B 689 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY B 692 " --> pdb=" O ASN B 689 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.566A pdb=" N LYS B 654 " --> pdb=" O ALA B 645 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 646 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 682 " --> pdb=" O ARG B 646 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 718 through 719 Processing sheet with id=AF7, first strand: chain 'B' and resid 759 through 760 removed outlier: 3.617A pdb=" N VAL B 763 " --> pdb=" O TYR B 746 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AF9, first strand: chain 'B' and resid 820 through 823 Processing sheet with id=AG1, first strand: chain 'B' and resid 862 through 865 Processing sheet with id=AG2, first strand: chain 'B' and resid 920 through 923 removed outlier: 3.517A pdb=" N ILE B 969 " --> pdb=" O ILE B 930 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 960 through 964 removed outlier: 3.505A pdb=" N TYR B 947 " --> pdb=" O THR B 964 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 981 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: 6.43 Time building geometry restraints manager: 4.00 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: 4870 1.34 - 1.46: 3601 1.46 - 1.58: 7030 1.58 - 1.70: 5 1.70 - 1.82: 84 Bond restraints: 15590 Sorted by residual: bond pdb=" C1 NAG B1101 " pdb=" O5 NAG B1101 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C1 NAG B1102 " pdb=" O5 NAG B1102 " ideal model delta sigma weight residual 1.406 1.539 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.539 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C1 NAG A1101 " pdb=" O5 NAG A1101 " ideal model delta sigma weight residual 1.406 1.539 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C1 NAG A1102 " pdb=" O5 NAG A1102 " ideal model delta sigma weight residual 1.406 1.539 -0.133 2.00e-02 2.50e+03 4.40e+01 ... (remaining 15585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 20894 3.99 - 7.98: 310 7.98 - 11.97: 37 11.97 - 15.96: 6 15.96 - 19.95: 3 Bond angle restraints: 21250 Sorted by residual: angle pdb=" C ASP B 547 " pdb=" N ASP B 548 " pdb=" CA ASP B 548 " ideal model delta sigma weight residual 122.08 132.31 -10.23 1.47e+00 4.63e-01 4.84e+01 angle pdb=" CB LEU B 427 " pdb=" CG LEU B 427 " pdb=" CD2 LEU B 427 " ideal model delta sigma weight residual 110.70 90.75 19.95 3.00e+00 1.11e-01 4.42e+01 angle pdb=" C VAL A 712 " pdb=" N ALA A 713 " pdb=" CA ALA A 713 " ideal model delta sigma weight residual 120.68 130.63 -9.95 1.52e+00 4.33e-01 4.29e+01 angle pdb=" C PRO B 677 " pdb=" N TRP B 678 " pdb=" CA TRP B 678 " ideal model delta sigma weight residual 121.54 133.92 -12.38 1.91e+00 2.74e-01 4.20e+01 angle pdb=" CA ASN A 659 " pdb=" CB ASN A 659 " pdb=" CG ASN A 659 " ideal model delta sigma weight residual 112.60 118.91 -6.31 1.00e+00 1.00e+00 3.98e+01 ... (remaining 21245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 8860 17.34 - 34.68: 615 34.68 - 52.02: 66 52.02 - 69.36: 25 69.36 - 86.70: 16 Dihedral angle restraints: 9582 sinusoidal: 4032 harmonic: 5550 Sorted by residual: dihedral pdb=" CA LEU A 427 " pdb=" C LEU A 427 " pdb=" N ILE A 428 " pdb=" CA ILE A 428 " ideal model delta harmonic sigma weight residual -180.00 -144.12 -35.88 0 5.00e+00 4.00e-02 5.15e+01 dihedral pdb=" CA PRO B 733 " pdb=" C PRO B 733 " pdb=" N MET B 734 " pdb=" CA MET B 734 " ideal model delta harmonic sigma weight residual -180.00 -144.43 -35.57 0 5.00e+00 4.00e-02 5.06e+01 dihedral pdb=" CA THR A 658 " pdb=" C THR A 658 " pdb=" N ASN A 659 " pdb=" CA ASN A 659 " ideal model delta harmonic sigma weight residual 180.00 145.64 34.36 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 9579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 2335 0.202 - 0.404: 32 0.404 - 0.606: 2 0.606 - 0.808: 0 0.808 - 1.011: 1 Chirality restraints: 2370 Sorted by residual: chirality pdb=" CB ILE A 438 " pdb=" CA ILE A 438 " pdb=" CG1 ILE A 438 " pdb=" CG2 ILE A 438 " both_signs ideal model delta sigma weight residual False 2.64 1.63 1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" CB ILE A 624 " pdb=" CA ILE A 624 " pdb=" CG1 ILE A 624 " pdb=" CG2 ILE A 624 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.57 2.00e-01 2.50e+01 8.25e+00 chirality pdb=" CB ILE B 624 " pdb=" CA ILE B 624 " pdb=" CG1 ILE B 624 " pdb=" CG2 ILE B 624 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.40e+00 ... (remaining 2367 not shown) Planarity restraints: 2790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 168 " 0.061 2.00e-02 2.50e+03 4.63e-02 5.37e+01 pdb=" CG TRP B 168 " -0.120 2.00e-02 2.50e+03 pdb=" CD1 TRP B 168 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP B 168 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 168 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 168 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 168 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 168 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 168 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 653 " -0.039 2.00e-02 2.50e+03 4.28e-02 4.59e+01 pdb=" CG TRP A 653 " 0.113 2.00e-02 2.50e+03 pdb=" CD1 TRP A 653 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP A 653 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 653 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 653 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 653 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 653 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 653 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 653 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 653 " 0.026 2.00e-02 2.50e+03 3.19e-02 2.55e+01 pdb=" CG TRP B 653 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP B 653 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP B 653 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 653 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP B 653 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 653 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 653 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 653 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 653 " 0.004 2.00e-02 2.50e+03 ... (remaining 2787 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 5240 2.89 - 3.39: 10670 3.39 - 3.90: 24962 3.90 - 4.40: 24280 4.40 - 4.90: 44299 Nonbonded interactions: 109451 Sorted by model distance: nonbonded pdb=" OG1 THR B 591 " pdb=" OD1 ASP B 594 " model vdw 2.392 3.040 nonbonded pdb=" OG SER B 136 " pdb=" OE1 GLU B 138 " model vdw 2.392 3.040 nonbonded pdb=" OG SER A 136 " pdb=" OE1 GLU A 138 " model vdw 2.393 3.040 nonbonded pdb=" OD1 ASP A 300 " pdb=" OH TYR A 304 " model vdw 2.395 3.040 nonbonded pdb=" OD2 ASP A 535 " pdb=" OG1 THR A 537 " model vdw 2.396 3.040 ... (remaining 109446 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.290 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 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 : 0.010 0.138 15618 Z= 0.465 Angle : 1.295 26.975 21322 Z= 0.680 Chirality : 0.070 1.011 2370 Planarity : 0.011 0.129 2780 Dihedral : 12.634 86.704 5990 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.17), residues: 1936 helix: None (None), residues: 0 sheet: -0.33 (0.18), residues: 792 loop : -1.91 (0.16), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.120 0.005 TRP B 168 HIS 0.018 0.002 HIS B 534 PHE 0.031 0.003 PHE A 35 TYR 0.035 0.003 TYR A 71 ARG 0.028 0.001 ARG B 580 Details of bonding type rmsd link_NAG-ASN : bond 0.00719 ( 10) link_NAG-ASN : angle 9.02827 ( 30) link_BETA1-4 : bond 0.00790 ( 6) link_BETA1-4 : angle 4.76822 ( 18) hydrogen bonds : bond 0.27236 ( 398) hydrogen bonds : angle 9.24483 ( 981) SS BOND : bond 0.00534 ( 12) SS BOND : angle 0.96445 ( 24) covalent geometry : bond 0.01021 (15590) covalent geometry : angle 1.24425 (21250) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 TRP cc_start: 0.6220 (m100) cc_final: 0.5750 (m100) REVERT: A 506 ARG cc_start: 0.7456 (mmt180) cc_final: 0.5498 (mmt-90) REVERT: A 949 MET cc_start: 0.1596 (ttp) cc_final: 0.1389 (ttp) REVERT: B 46 VAL cc_start: 0.7952 (m) cc_final: 0.7549 (p) REVERT: B 161 TYR cc_start: 0.7451 (t80) cc_final: 0.6731 (t80) REVERT: B 213 MET cc_start: 0.4323 (mtt) cc_final: 0.4059 (mtt) REVERT: B 244 ARG cc_start: 0.7590 (ttt-90) cc_final: 0.7068 (tpt-90) REVERT: B 245 PHE cc_start: 0.7549 (p90) cc_final: 0.6494 (p90) REVERT: B 336 THR cc_start: 0.8040 (m) cc_final: 0.7810 (p) REVERT: B 420 ARG cc_start: 0.6783 (mpp80) cc_final: 0.6501 (mpp80) REVERT: B 454 LYS cc_start: 0.8171 (tttp) cc_final: 0.7946 (ttmm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3738 time to fit residues: 83.0981 Evaluate side-chains 148 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.6980 chunk 147 optimal weight: 0.0670 chunk 81 optimal weight: 7.9990 chunk 50 optimal weight: 0.0370 chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 644 GLN B 326 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.256048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.216600 restraints weight = 26700.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.216693 restraints weight = 36668.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.219154 restraints weight = 21439.884| |-----------------------------------------------------------------------------| r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15618 Z= 0.148 Angle : 0.670 20.063 21322 Z= 0.329 Chirality : 0.044 0.230 2370 Planarity : 0.006 0.053 2780 Dihedral : 6.059 37.098 2454 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.37 % Allowed : 4.96 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.95 (0.18), residues: 1936 helix: None (None), residues: 0 sheet: 0.19 (0.17), residues: 860 loop : -1.36 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 168 HIS 0.003 0.001 HIS A 885 PHE 0.015 0.001 PHE B 245 TYR 0.015 0.001 TYR B 109 ARG 0.004 0.001 ARG A 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 10) link_NAG-ASN : angle 6.52375 ( 30) link_BETA1-4 : bond 0.00248 ( 6) link_BETA1-4 : angle 1.90226 ( 18) hydrogen bonds : bond 0.03525 ( 398) hydrogen bonds : angle 6.41063 ( 981) SS BOND : bond 0.00444 ( 12) SS BOND : angle 0.70735 ( 24) covalent geometry : bond 0.00345 (15590) covalent geometry : angle 0.62138 (21250) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 506 ARG cc_start: 0.7666 (mmt180) cc_final: 0.5903 (mmt-90) REVERT: A 628 TRP cc_start: 0.5556 (p90) cc_final: 0.5145 (p90) REVERT: B 46 VAL cc_start: 0.7929 (m) cc_final: 0.7632 (p) REVERT: B 98 MET cc_start: 0.6356 (mpp) cc_final: 0.6146 (mpp) REVERT: B 454 LYS cc_start: 0.8222 (tttp) cc_final: 0.7597 (tttm) REVERT: B 506 ARG cc_start: 0.7839 (mtt-85) cc_final: 0.6005 (mmt180) REVERT: B 675 LEU cc_start: 0.6609 (mp) cc_final: 0.5770 (tt) outliers start: 6 outliers final: 4 residues processed: 158 average time/residue: 0.3765 time to fit residues: 81.7238 Evaluate side-chains 156 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 949 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 23 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 187 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.248152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.205130 restraints weight = 26220.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.199711 restraints weight = 27252.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.200981 restraints weight = 20987.003| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15618 Z= 0.164 Angle : 0.620 16.798 21322 Z= 0.301 Chirality : 0.043 0.252 2370 Planarity : 0.005 0.042 2780 Dihedral : 5.485 37.707 2454 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.74 % Allowed : 6.51 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.80 (0.19), residues: 1936 helix: -3.82 (1.15), residues: 12 sheet: 0.19 (0.17), residues: 906 loop : -1.16 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 168 HIS 0.004 0.001 HIS B 635 PHE 0.012 0.001 PHE A 245 TYR 0.016 0.001 TYR B 560 ARG 0.007 0.000 ARG A 426 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 10) link_NAG-ASN : angle 5.60360 ( 30) link_BETA1-4 : bond 0.00289 ( 6) link_BETA1-4 : angle 1.74061 ( 18) hydrogen bonds : bond 0.03051 ( 398) hydrogen bonds : angle 5.72497 ( 981) SS BOND : bond 0.00555 ( 12) SS BOND : angle 0.63106 ( 24) covalent geometry : bond 0.00388 (15590) covalent geometry : angle 0.58153 (21250) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 ARG cc_start: 0.7886 (mmt180) cc_final: 0.5607 (mpt180) REVERT: A 593 VAL cc_start: 0.6777 (OUTLIER) cc_final: 0.6473 (m) REVERT: A 628 TRP cc_start: 0.5785 (p90) cc_final: 0.5302 (p90) REVERT: A 675 LEU cc_start: 0.6860 (mp) cc_final: 0.6224 (tp) REVERT: B 244 ARG cc_start: 0.7243 (tpt-90) cc_final: 0.6926 (tpt-90) REVERT: B 454 LYS cc_start: 0.8176 (tttp) cc_final: 0.7658 (tttm) REVERT: B 475 ILE cc_start: 0.6585 (mt) cc_final: 0.5911 (mm) REVERT: B 476 ARG cc_start: 0.6919 (mtm110) cc_final: 0.6528 (mtm110) REVERT: B 506 ARG cc_start: 0.7824 (mtt-85) cc_final: 0.5774 (mtt-85) REVERT: B 640 LYS cc_start: 0.4855 (pttt) cc_final: 0.4608 (pttt) outliers start: 12 outliers final: 8 residues processed: 162 average time/residue: 0.3880 time to fit residues: 88.0357 Evaluate side-chains 165 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 840 MET Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 949 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 139 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 40.0000 chunk 100 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 67 optimal weight: 0.0070 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 GLN B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.249204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.204994 restraints weight = 26526.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.198235 restraints weight = 20731.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.200147 restraints weight = 19368.812| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15618 Z= 0.170 Angle : 0.599 15.238 21322 Z= 0.291 Chirality : 0.043 0.253 2370 Planarity : 0.004 0.038 2780 Dihedral : 5.269 39.906 2454 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.12 % Allowed : 7.51 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 1936 helix: -3.50 (1.40), residues: 12 sheet: 0.37 (0.17), residues: 874 loop : -0.98 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 168 HIS 0.004 0.001 HIS A 559 PHE 0.014 0.001 PHE B 744 TYR 0.016 0.001 TYR B 560 ARG 0.006 0.000 ARG A 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 10) link_NAG-ASN : angle 5.16114 ( 30) link_BETA1-4 : bond 0.00278 ( 6) link_BETA1-4 : angle 1.54871 ( 18) hydrogen bonds : bond 0.02594 ( 398) hydrogen bonds : angle 5.34777 ( 981) SS BOND : bond 0.00623 ( 12) SS BOND : angle 0.62072 ( 24) covalent geometry : bond 0.00401 (15590) covalent geometry : angle 0.56602 (21250) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 ARG cc_start: 0.6968 (mtm180) cc_final: 0.6660 (mtm180) REVERT: A 506 ARG cc_start: 0.7960 (mmt180) cc_final: 0.5692 (mmt-90) REVERT: A 525 ASN cc_start: 0.6886 (OUTLIER) cc_final: 0.3846 (p0) REVERT: A 593 VAL cc_start: 0.6785 (OUTLIER) cc_final: 0.5712 (t) REVERT: A 628 TRP cc_start: 0.5902 (p90) cc_final: 0.5485 (p90) REVERT: B 71 TYR cc_start: 0.7202 (m-80) cc_final: 0.6948 (m-10) REVERT: B 365 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6819 (mm-30) REVERT: B 475 ILE cc_start: 0.6741 (mt) cc_final: 0.6477 (mm) REVERT: B 476 ARG cc_start: 0.7096 (mtm110) cc_final: 0.6739 (mtm110) REVERT: B 506 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.6302 (mtt-85) REVERT: B 525 ASN cc_start: 0.6529 (OUTLIER) cc_final: 0.3465 (p0) REVERT: B 640 LYS cc_start: 0.4638 (pttt) cc_final: 0.4408 (pttt) outliers start: 18 outliers final: 12 residues processed: 175 average time/residue: 0.3583 time to fit residues: 85.6042 Evaluate side-chains 173 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 840 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 908 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 191 optimal weight: 50.0000 chunk 145 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 177 optimal weight: 0.6980 chunk 85 optimal weight: 40.0000 chunk 67 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 659 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.247004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.203173 restraints weight = 26796.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.196698 restraints weight = 23374.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.198894 restraints weight = 18575.779| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15618 Z= 0.158 Angle : 0.585 14.464 21322 Z= 0.283 Chirality : 0.043 0.258 2370 Planarity : 0.004 0.040 2780 Dihedral : 5.143 40.725 2454 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.24 % Allowed : 7.88 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.52 (0.19), residues: 1936 helix: -3.52 (1.40), residues: 12 sheet: 0.32 (0.17), residues: 884 loop : -0.88 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 168 HIS 0.004 0.001 HIS A 559 PHE 0.014 0.001 PHE B 245 TYR 0.014 0.001 TYR B 560 ARG 0.007 0.000 ARG A 426 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 10) link_NAG-ASN : angle 4.93547 ( 30) link_BETA1-4 : bond 0.00180 ( 6) link_BETA1-4 : angle 1.50486 ( 18) hydrogen bonds : bond 0.02448 ( 398) hydrogen bonds : angle 5.17109 ( 981) SS BOND : bond 0.00552 ( 12) SS BOND : angle 0.54747 ( 24) covalent geometry : bond 0.00373 (15590) covalent geometry : angle 0.55371 (21250) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6657 (mt) REVERT: A 420 ARG cc_start: 0.7052 (mtm180) cc_final: 0.6758 (mtm180) REVERT: A 506 ARG cc_start: 0.7994 (mmt180) cc_final: 0.6259 (mmt180) REVERT: A 525 ASN cc_start: 0.6941 (OUTLIER) cc_final: 0.3952 (p0) REVERT: A 593 VAL cc_start: 0.6772 (OUTLIER) cc_final: 0.5668 (t) REVERT: A 628 TRP cc_start: 0.5936 (p90) cc_final: 0.5579 (p90) REVERT: A 675 LEU cc_start: 0.6891 (mp) cc_final: 0.6197 (tp) REVERT: B 244 ARG cc_start: 0.7482 (tpt170) cc_final: 0.7141 (tpt-90) REVERT: B 331 LYS cc_start: 0.8697 (mtpp) cc_final: 0.8208 (mtmm) REVERT: B 475 ILE cc_start: 0.6804 (mt) cc_final: 0.6567 (mm) REVERT: B 476 ARG cc_start: 0.7070 (mtm110) cc_final: 0.6808 (mtm110) REVERT: B 506 ARG cc_start: 0.7800 (mtt-85) cc_final: 0.6231 (mmt180) REVERT: B 525 ASN cc_start: 0.6510 (OUTLIER) cc_final: 0.3485 (p0) outliers start: 20 outliers final: 14 residues processed: 175 average time/residue: 0.4637 time to fit residues: 112.6110 Evaluate side-chains 179 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 840 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 908 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 151 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.249124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.205831 restraints weight = 25927.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.196958 restraints weight = 20606.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.198471 restraints weight = 18579.337| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15618 Z= 0.172 Angle : 0.587 14.092 21322 Z= 0.284 Chirality : 0.043 0.264 2370 Planarity : 0.004 0.040 2780 Dihedral : 5.100 41.383 2454 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.30 % Allowed : 8.19 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.19), residues: 1936 helix: -3.78 (1.29), residues: 12 sheet: 0.30 (0.17), residues: 884 loop : -0.80 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 168 HIS 0.004 0.001 HIS A 559 PHE 0.014 0.001 PHE A 35 TYR 0.021 0.001 TYR B 71 ARG 0.007 0.000 ARG A 425 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 10) link_NAG-ASN : angle 4.86540 ( 30) link_BETA1-4 : bond 0.00144 ( 6) link_BETA1-4 : angle 1.44709 ( 18) hydrogen bonds : bond 0.02452 ( 398) hydrogen bonds : angle 5.10158 ( 981) SS BOND : bond 0.00600 ( 12) SS BOND : angle 0.57021 ( 24) covalent geometry : bond 0.00406 (15590) covalent geometry : angle 0.55713 (21250) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6421 (mt) REVERT: A 420 ARG cc_start: 0.7048 (mtm180) cc_final: 0.6771 (mtm180) REVERT: A 506 ARG cc_start: 0.8016 (mmt180) cc_final: 0.6309 (mmt180) REVERT: A 525 ASN cc_start: 0.6947 (OUTLIER) cc_final: 0.4018 (p0) REVERT: A 628 TRP cc_start: 0.5912 (p90) cc_final: 0.5612 (p90) REVERT: B 46 VAL cc_start: 0.8481 (m) cc_final: 0.8177 (p) REVERT: B 71 TYR cc_start: 0.7234 (m-10) cc_final: 0.6990 (m-80) REVERT: B 244 ARG cc_start: 0.7460 (tpt170) cc_final: 0.7113 (tpt-90) REVERT: B 365 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7174 (mm-30) REVERT: B 475 ILE cc_start: 0.6789 (mt) cc_final: 0.6536 (mm) REVERT: B 476 ARG cc_start: 0.7104 (mtm110) cc_final: 0.6820 (mtm110) REVERT: B 506 ARG cc_start: 0.7819 (mtt-85) cc_final: 0.6218 (mtt-85) REVERT: B 525 ASN cc_start: 0.6615 (OUTLIER) cc_final: 0.3625 (p0) outliers start: 21 outliers final: 14 residues processed: 185 average time/residue: 0.3790 time to fit residues: 96.8658 Evaluate side-chains 181 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 908 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 32 optimal weight: 0.6980 chunk 89 optimal weight: 50.0000 chunk 101 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 181 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 94 optimal weight: 40.0000 chunk 102 optimal weight: 0.0470 chunk 66 optimal weight: 0.7980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.246827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.204215 restraints weight = 26451.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.203716 restraints weight = 27100.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.204754 restraints weight = 21040.905| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15618 Z= 0.132 Angle : 0.578 13.415 21322 Z= 0.279 Chirality : 0.043 0.250 2370 Planarity : 0.004 0.041 2780 Dihedral : 4.969 41.310 2454 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.49 % Allowed : 8.75 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.39 (0.19), residues: 1936 helix: -3.74 (1.33), residues: 12 sheet: 0.36 (0.17), residues: 884 loop : -0.74 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 168 HIS 0.002 0.000 HIS B 160 PHE 0.016 0.001 PHE A 35 TYR 0.016 0.001 TYR B 71 ARG 0.007 0.000 ARG A 425 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 10) link_NAG-ASN : angle 4.60679 ( 30) link_BETA1-4 : bond 0.00197 ( 6) link_BETA1-4 : angle 1.41585 ( 18) hydrogen bonds : bond 0.02297 ( 398) hydrogen bonds : angle 4.95780 ( 981) SS BOND : bond 0.00414 ( 12) SS BOND : angle 0.49874 ( 24) covalent geometry : bond 0.00314 (15590) covalent geometry : angle 0.55111 (21250) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6593 (mt) REVERT: A 420 ARG cc_start: 0.7095 (mtm180) cc_final: 0.6797 (mtm180) REVERT: A 506 ARG cc_start: 0.7969 (mmt180) cc_final: 0.5575 (mmt180) REVERT: A 525 ASN cc_start: 0.6959 (OUTLIER) cc_final: 0.4052 (p0) REVERT: A 593 VAL cc_start: 0.6728 (OUTLIER) cc_final: 0.5692 (t) REVERT: A 628 TRP cc_start: 0.5955 (p90) cc_final: 0.5588 (p90) REVERT: B 46 VAL cc_start: 0.8508 (m) cc_final: 0.8232 (p) REVERT: B 244 ARG cc_start: 0.7480 (tpt170) cc_final: 0.7208 (tpt-90) REVERT: B 475 ILE cc_start: 0.6847 (mt) cc_final: 0.6216 (mm) REVERT: B 476 ARG cc_start: 0.7059 (mtm110) cc_final: 0.6777 (mtm110) REVERT: B 506 ARG cc_start: 0.7790 (mtt-85) cc_final: 0.6171 (mtt-85) REVERT: B 525 ASN cc_start: 0.6528 (OUTLIER) cc_final: 0.3528 (p0) REVERT: B 628 TRP cc_start: 0.6006 (p90) cc_final: 0.5608 (p90) REVERT: B 734 MET cc_start: 0.3561 (ppp) cc_final: 0.2812 (tpp) outliers start: 24 outliers final: 12 residues processed: 186 average time/residue: 0.3808 time to fit residues: 97.3248 Evaluate side-chains 185 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 908 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 170 optimal weight: 0.0970 chunk 116 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 95 optimal weight: 40.0000 chunk 161 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 154 optimal weight: 0.0570 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.247542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.205216 restraints weight = 26062.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.201407 restraints weight = 26807.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.202755 restraints weight = 22998.293| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15618 Z= 0.142 Angle : 0.586 13.174 21322 Z= 0.282 Chirality : 0.043 0.253 2370 Planarity : 0.004 0.054 2780 Dihedral : 4.905 40.969 2454 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.18 % Allowed : 9.18 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 1936 helix: -3.82 (1.28), residues: 12 sheet: 0.37 (0.17), residues: 894 loop : -0.71 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 168 HIS 0.003 0.000 HIS A 559 PHE 0.014 0.001 PHE A 35 TYR 0.017 0.001 TYR B 71 ARG 0.010 0.000 ARG B 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 10) link_NAG-ASN : angle 4.56418 ( 30) link_BETA1-4 : bond 0.00213 ( 6) link_BETA1-4 : angle 1.38185 ( 18) hydrogen bonds : bond 0.02274 ( 398) hydrogen bonds : angle 4.94517 ( 981) SS BOND : bond 0.00467 ( 12) SS BOND : angle 0.50193 ( 24) covalent geometry : bond 0.00338 (15590) covalent geometry : angle 0.55951 (21250) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6682 (mt) REVERT: A 420 ARG cc_start: 0.7018 (mtm180) cc_final: 0.6745 (mtm180) REVERT: A 506 ARG cc_start: 0.8020 (mmt180) cc_final: 0.5618 (mmt180) REVERT: A 525 ASN cc_start: 0.6929 (OUTLIER) cc_final: 0.3950 (p0) REVERT: A 628 TRP cc_start: 0.5968 (p90) cc_final: 0.5604 (p90) REVERT: B 46 VAL cc_start: 0.8532 (m) cc_final: 0.8241 (p) REVERT: B 244 ARG cc_start: 0.7463 (tpt170) cc_final: 0.7176 (tpt-90) REVERT: B 273 TRP cc_start: 0.6881 (m100) cc_final: 0.6255 (m100) REVERT: B 435 GLU cc_start: 0.6769 (tp30) cc_final: 0.6550 (tp30) REVERT: B 475 ILE cc_start: 0.6875 (mt) cc_final: 0.6283 (mm) REVERT: B 476 ARG cc_start: 0.7081 (mtm110) cc_final: 0.6754 (mtm110) REVERT: B 480 ARG cc_start: 0.7970 (ttm110) cc_final: 0.7638 (ttm-80) REVERT: B 506 ARG cc_start: 0.7824 (mtt-85) cc_final: 0.5703 (mtt-85) REVERT: B 525 ASN cc_start: 0.6553 (OUTLIER) cc_final: 0.3513 (p0) REVERT: B 628 TRP cc_start: 0.6034 (p90) cc_final: 0.5551 (p90) REVERT: B 734 MET cc_start: 0.3719 (ppp) cc_final: 0.3154 (pmm) outliers start: 19 outliers final: 11 residues processed: 184 average time/residue: 0.3589 time to fit residues: 91.3890 Evaluate side-chains 182 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 908 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 9 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 126 optimal weight: 0.3980 chunk 100 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.246523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.204279 restraints weight = 25680.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.200352 restraints weight = 30915.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.202174 restraints weight = 22771.325| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15618 Z= 0.171 Angle : 0.605 13.334 21322 Z= 0.292 Chirality : 0.043 0.265 2370 Planarity : 0.004 0.047 2780 Dihedral : 4.946 41.629 2454 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.24 % Allowed : 9.49 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.33 (0.19), residues: 1936 helix: -3.86 (1.27), residues: 12 sheet: 0.36 (0.17), residues: 884 loop : -0.65 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP B 168 HIS 0.004 0.001 HIS A 559 PHE 0.016 0.001 PHE A 129 TYR 0.020 0.001 TYR B 71 ARG 0.011 0.000 ARG B 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 10) link_NAG-ASN : angle 4.64771 ( 30) link_BETA1-4 : bond 0.00245 ( 6) link_BETA1-4 : angle 1.37066 ( 18) hydrogen bonds : bond 0.02421 ( 398) hydrogen bonds : angle 4.96441 ( 981) SS BOND : bond 0.00561 ( 12) SS BOND : angle 0.55656 ( 24) covalent geometry : bond 0.00404 (15590) covalent geometry : angle 0.57882 (21250) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6651 (mt) REVERT: A 420 ARG cc_start: 0.7063 (mtm180) cc_final: 0.6779 (mtm180) REVERT: A 506 ARG cc_start: 0.7988 (mmt180) cc_final: 0.6199 (mmt180) REVERT: A 525 ASN cc_start: 0.6983 (OUTLIER) cc_final: 0.4049 (p0) REVERT: A 628 TRP cc_start: 0.5878 (p90) cc_final: 0.5560 (p90) REVERT: B 46 VAL cc_start: 0.8586 (m) cc_final: 0.8306 (p) REVERT: B 71 TYR cc_start: 0.7166 (m-10) cc_final: 0.6858 (m-80) REVERT: B 244 ARG cc_start: 0.7495 (tpt170) cc_final: 0.7223 (tpt-90) REVERT: B 273 TRP cc_start: 0.6886 (m100) cc_final: 0.6290 (m100) REVERT: B 476 ARG cc_start: 0.7084 (mtm110) cc_final: 0.6819 (mtm110) REVERT: B 506 ARG cc_start: 0.7779 (mtt-85) cc_final: 0.6076 (mtt-85) REVERT: B 525 ASN cc_start: 0.6663 (OUTLIER) cc_final: 0.3748 (p0) REVERT: B 628 TRP cc_start: 0.6132 (p90) cc_final: 0.5614 (p90) REVERT: B 734 MET cc_start: 0.3344 (ppp) cc_final: 0.2314 (tpt) outliers start: 20 outliers final: 13 residues processed: 178 average time/residue: 0.4078 time to fit residues: 100.6874 Evaluate side-chains 181 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 614 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 82 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 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 42 GLN ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.245514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.203599 restraints weight = 25773.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.200481 restraints weight = 32548.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.203309 restraints weight = 24479.357| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15618 Z= 0.202 Angle : 0.628 13.881 21322 Z= 0.305 Chirality : 0.045 0.278 2370 Planarity : 0.004 0.046 2780 Dihedral : 5.057 43.005 2454 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.99 % Allowed : 9.86 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.45 (0.19), residues: 1936 helix: -3.93 (1.18), residues: 12 sheet: 0.15 (0.17), residues: 904 loop : -0.61 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 168 HIS 0.005 0.001 HIS A 559 PHE 0.018 0.001 PHE A 129 TYR 0.020 0.001 TYR B 71 ARG 0.009 0.000 ARG A 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 10) link_NAG-ASN : angle 4.81530 ( 30) link_BETA1-4 : bond 0.00147 ( 6) link_BETA1-4 : angle 1.35017 ( 18) hydrogen bonds : bond 0.02581 ( 398) hydrogen bonds : angle 5.07087 ( 981) SS BOND : bond 0.00686 ( 12) SS BOND : angle 0.62984 ( 24) covalent geometry : bond 0.00479 (15590) covalent geometry : angle 0.60071 (21250) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6668 (mt) REVERT: A 420 ARG cc_start: 0.7096 (mtm180) cc_final: 0.6848 (mtm180) REVERT: A 506 ARG cc_start: 0.7950 (mmt180) cc_final: 0.6206 (mmt180) REVERT: A 525 ASN cc_start: 0.7108 (OUTLIER) cc_final: 0.4119 (p0) REVERT: A 628 TRP cc_start: 0.5893 (p90) cc_final: 0.5620 (p90) REVERT: B 46 VAL cc_start: 0.8670 (m) cc_final: 0.8400 (p) REVERT: B 71 TYR cc_start: 0.7206 (m-10) cc_final: 0.6916 (m-80) REVERT: B 79 GLU cc_start: 0.7283 (tt0) cc_final: 0.5668 (mt-10) REVERT: B 244 ARG cc_start: 0.7556 (tpt170) cc_final: 0.7247 (tpt-90) REVERT: B 273 TRP cc_start: 0.6918 (m100) cc_final: 0.6343 (m100) REVERT: B 365 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6793 (mm-30) REVERT: B 506 ARG cc_start: 0.7794 (mtt-85) cc_final: 0.5855 (mtt-85) REVERT: B 525 ASN cc_start: 0.6707 (OUTLIER) cc_final: 0.3892 (p0) REVERT: B 628 TRP cc_start: 0.6192 (p90) cc_final: 0.5600 (p90) REVERT: B 734 MET cc_start: 0.3281 (ppp) cc_final: 0.2651 (tpt) outliers start: 16 outliers final: 13 residues processed: 175 average time/residue: 0.4027 time to fit residues: 98.6886 Evaluate side-chains 180 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 614 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 122 optimal weight: 0.0670 chunk 125 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 41 optimal weight: 0.1980 chunk 102 optimal weight: 0.6980 chunk 171 optimal weight: 0.0570 chunk 21 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 overall best weight: 0.1836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN B 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.248701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.205816 restraints weight = 27849.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.201622 restraints weight = 17048.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.203484 restraints weight = 17889.322| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15618 Z= 0.096 Angle : 0.574 12.555 21322 Z= 0.277 Chirality : 0.042 0.232 2370 Planarity : 0.004 0.042 2780 Dihedral : 4.730 41.071 2454 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.81 % Allowed : 10.24 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -0.33 (0.20), residues: 1936 helix: -3.70 (1.33), residues: 12 sheet: 0.19 (0.17), residues: 930 loop : -0.50 (0.21), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP B 168 HIS 0.002 0.000 HIS B 160 PHE 0.017 0.001 PHE A 35 TYR 0.014 0.001 TYR B 791 ARG 0.009 0.000 ARG B 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 10) link_NAG-ASN : angle 4.24021 ( 30) link_BETA1-4 : bond 0.00176 ( 6) link_BETA1-4 : angle 1.31448 ( 18) hydrogen bonds : bond 0.02294 ( 398) hydrogen bonds : angle 4.72418 ( 981) SS BOND : bond 0.00202 ( 12) SS BOND : angle 0.56423 ( 24) covalent geometry : bond 0.00228 (15590) covalent geometry : angle 0.55036 (21250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8714.46 seconds wall clock time: 153 minutes 29.53 seconds (9209.53 seconds total)