Starting phenix.real_space_refine on Thu Sep 18 09:05:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ba4_44395/09_2025/9ba4_44395.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ba4_44395/09_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_44395/09_2025/9ba4_44395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ba4_44395/09_2025/9ba4_44395.map" model { file = "/net/cci-nas-00/data/ceres_data/9ba4_44395/09_2025/9ba4_44395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ba4_44395/09_2025/9ba4_44395.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.50, per 1000 atoms: 0.23 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: 0.83 Conformation dependent library (CDL) restraints added in 644.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.57 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: 3.07 Time building geometry restraints manager: 1.13 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: 0.03 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.900 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.130 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.028 0.001 ARG B 580 TYR 0.035 0.003 TYR A 71 PHE 0.031 0.003 PHE A 35 TRP 0.120 0.005 TRP B 168 HIS 0.018 0.002 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.01021 (15590) covalent geometry : angle 1.24425 (21250) SS BOND : bond 0.00534 ( 12) SS BOND : angle 0.96445 ( 24) hydrogen bonds : bond 0.27236 ( 398) hydrogen bonds : angle 9.24483 ( 981) link_BETA1-4 : bond 0.00790 ( 6) link_BETA1-4 : angle 4.76822 ( 18) link_NAG-ASN : bond 0.00719 ( 10) link_NAG-ASN : angle 9.02827 ( 30) *********************** 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 : 0.343 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: 0.5751 (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: 0.1688 time to fit residues: 37.0173 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 : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.4980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.4865 r_free = 0.4865 target = 0.257056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.215639 restraints weight = 25094.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.218723 restraints weight = 32514.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.218490 restraints weight = 16659.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.218386 restraints weight = 13053.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.218891 restraints weight = 11791.473| |-----------------------------------------------------------------------------| r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15618 Z= 0.145 Angle : 0.666 19.811 21322 Z= 0.325 Chirality : 0.044 0.230 2370 Planarity : 0.006 0.053 2780 Dihedral : 6.035 37.331 2454 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.31 % Allowed : 5.09 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.19), residues: 1936 helix: -4.71 (0.55), residues: 12 sheet: 0.21 (0.17), residues: 860 loop : -1.35 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 580 TYR 0.015 0.001 TYR B 109 PHE 0.014 0.001 PHE B 245 TRP 0.031 0.002 TRP B 168 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00342 (15590) covalent geometry : angle 0.61794 (21250) SS BOND : bond 0.00428 ( 12) SS BOND : angle 0.72015 ( 24) hydrogen bonds : bond 0.03422 ( 398) hydrogen bonds : angle 6.35832 ( 981) link_BETA1-4 : bond 0.00262 ( 6) link_BETA1-4 : angle 1.90906 ( 18) link_NAG-ASN : bond 0.00402 ( 10) link_NAG-ASN : angle 6.49732 ( 30) *********************** 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 159 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 506 ARG cc_start: 0.7688 (mmt180) cc_final: 0.5881 (mmt-90) REVERT: A 628 TRP cc_start: 0.5513 (p90) cc_final: 0.5097 (p90) REVERT: B 46 VAL cc_start: 0.7863 (m) cc_final: 0.7582 (p) REVERT: B 454 LYS cc_start: 0.8252 (tttp) cc_final: 0.7612 (tttm) REVERT: B 675 LEU cc_start: 0.6437 (mp) cc_final: 0.5704 (tt) outliers start: 5 outliers final: 4 residues processed: 155 average time/residue: 0.1725 time to fit residues: 36.3461 Evaluate side-chains 153 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 149 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 187 optimal weight: 1.9990 chunk 79 optimal weight: 50.0000 chunk 160 optimal weight: 0.0670 chunk 111 optimal weight: 5.9990 chunk 144 optimal weight: 0.0270 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 73 optimal weight: 0.0270 chunk 59 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 0.1634 ------------------------------------------------------------------------------- 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 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.252973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.213787 restraints weight = 28830.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.217080 restraints weight = 28077.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.217589 restraints weight = 17277.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.218386 restraints weight = 11419.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.219069 restraints weight = 10344.903| |-----------------------------------------------------------------------------| r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5807 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15618 Z= 0.093 Angle : 0.576 15.777 21322 Z= 0.280 Chirality : 0.042 0.208 2370 Planarity : 0.005 0.046 2780 Dihedral : 5.239 35.859 2454 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.68 % Allowed : 6.39 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.19), residues: 1936 helix: -3.82 (1.14), residues: 12 sheet: 0.29 (0.17), residues: 894 loop : -1.14 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 426 TYR 0.012 0.001 TYR B 71 PHE 0.013 0.001 PHE A 245 TRP 0.021 0.001 TRP B 168 HIS 0.002 0.000 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00218 (15590) covalent geometry : angle 0.54086 (21250) SS BOND : bond 0.00182 ( 12) SS BOND : angle 0.53976 ( 24) hydrogen bonds : bond 0.02726 ( 398) hydrogen bonds : angle 5.51661 ( 981) link_BETA1-4 : bond 0.00315 ( 6) link_BETA1-4 : angle 1.71607 ( 18) link_NAG-ASN : bond 0.00518 ( 10) link_NAG-ASN : angle 5.18278 ( 30) *********************** 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 166 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 506 ARG cc_start: 0.7741 (mmt180) cc_final: 0.5873 (mmt180) REVERT: A 628 TRP cc_start: 0.5556 (p90) cc_final: 0.5131 (p90) REVERT: B 454 LYS cc_start: 0.8262 (tttp) cc_final: 0.7633 (tttm) REVERT: B 476 ARG cc_start: 0.6867 (mtm110) cc_final: 0.6556 (mtm110) outliers start: 11 outliers final: 7 residues processed: 157 average time/residue: 0.1591 time to fit residues: 34.4402 Evaluate side-chains 157 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 545 THR 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 53 optimal weight: 0.8980 chunk 162 optimal weight: 0.3980 chunk 165 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 78 optimal weight: 40.0000 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 181 optimal weight: 30.0000 chunk 176 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 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 = 0.4685 r_free = 0.4685 target = 0.238445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.186311 restraints weight = 23983.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.186216 restraints weight = 21043.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.186438 restraints weight = 15520.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.186981 restraints weight = 12287.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.187669 restraints weight = 10532.741| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.141 15618 Z= 0.617 Angle : 0.961 18.801 21322 Z= 0.477 Chirality : 0.057 0.433 2370 Planarity : 0.006 0.070 2780 Dihedral : 6.553 44.926 2454 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.92 % Allowed : 7.38 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.19), residues: 1936 helix: -4.31 (1.10), residues: 12 sheet: 0.15 (0.18), residues: 830 loop : -1.33 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 704 TYR 0.045 0.003 TYR B 560 PHE 0.032 0.003 PHE A 382 TRP 0.040 0.003 TRP B 168 HIS 0.018 0.002 HIS B 635 Details of bonding type rmsd covalent geometry : bond 0.01463 (15590) covalent geometry : angle 0.92706 (21250) SS BOND : bond 0.01767 ( 12) SS BOND : angle 1.03072 ( 24) hydrogen bonds : bond 0.04271 ( 398) hydrogen bonds : angle 6.44519 ( 981) link_BETA1-4 : bond 0.00716 ( 6) link_BETA1-4 : angle 1.99242 ( 18) link_NAG-ASN : bond 0.00800 ( 10) link_NAG-ASN : angle 6.64704 ( 30) *********************** 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 210 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6860 (mt) REVERT: A 420 ARG cc_start: 0.7108 (mtm180) cc_final: 0.6829 (mtm180) REVERT: A 476 ARG cc_start: 0.7229 (mpp-170) cc_final: 0.6635 (mtm110) REVERT: A 506 ARG cc_start: 0.8046 (mmt180) cc_final: 0.5863 (mmt180) REVERT: A 525 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.6792 (m110) REVERT: B 46 VAL cc_start: 0.8772 (m) cc_final: 0.8486 (p) REVERT: B 454 LYS cc_start: 0.8356 (tttp) cc_final: 0.7925 (tttm) REVERT: B 475 ILE cc_start: 0.6615 (mt) cc_final: 0.6180 (mm) REVERT: B 506 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.6212 (mtt-85) REVERT: B 525 ASN cc_start: 0.7005 (OUTLIER) cc_final: 0.4566 (p0) REVERT: B 734 MET cc_start: 0.3837 (pmm) cc_final: 0.3249 (tpt) outliers start: 31 outliers final: 13 residues processed: 196 average time/residue: 0.1653 time to fit residues: 44.2902 Evaluate side-chains 182 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 346 TRP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 494 MET 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 152 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 669 THR 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 67 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 50.0000 chunk 44 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 B 531 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.249214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.194987 restraints weight = 22913.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.192271 restraints weight = 17878.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.192140 restraints weight = 13090.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.192534 restraints weight = 10170.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.192874 restraints weight = 8809.381| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15618 Z= 0.212 Angle : 0.660 16.758 21322 Z= 0.323 Chirality : 0.045 0.314 2370 Planarity : 0.005 0.043 2780 Dihedral : 5.876 47.198 2454 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.49 % Allowed : 9.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.19), residues: 1936 helix: -4.15 (1.22), residues: 12 sheet: 0.23 (0.18), residues: 824 loop : -1.22 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 123 TYR 0.026 0.001 TYR B 71 PHE 0.015 0.001 PHE A 129 TRP 0.048 0.002 TRP A 168 HIS 0.004 0.001 HIS B 581 Details of bonding type rmsd covalent geometry : bond 0.00498 (15590) covalent geometry : angle 0.62292 (21250) SS BOND : bond 0.00813 ( 12) SS BOND : angle 0.75858 ( 24) hydrogen bonds : bond 0.02794 ( 398) hydrogen bonds : angle 5.73863 ( 981) link_BETA1-4 : bond 0.00074 ( 6) link_BETA1-4 : angle 1.63896 ( 18) link_NAG-ASN : bond 0.00529 ( 10) link_NAG-ASN : angle 5.70628 ( 30) *********************** 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 197 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.575 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: 0.7092 (mtm180) cc_final: 0.6814 (mtm180) REVERT: A 476 ARG cc_start: 0.7243 (mpp-170) cc_final: 0.6857 (mtm110) REVERT: A 493 PHE cc_start: 0.6587 (p90) cc_final: 0.6000 (p90) REVERT: A 506 ARG cc_start: 0.7983 (mmt180) cc_final: 0.5556 (mmt180) REVERT: B 46 VAL cc_start: 0.8757 (m) cc_final: 0.8476 (p) REVERT: B 71 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6902 (m-80) REVERT: B 244 ARG cc_start: 0.7466 (tpt-90) cc_final: 0.6960 (tpt-90) REVERT: B 273 TRP cc_start: 0.6863 (m100) cc_final: 0.6361 (m100) REVERT: B 454 LYS cc_start: 0.8316 (tttp) cc_final: 0.7870 (tttm) REVERT: B 475 ILE cc_start: 0.6513 (mt) cc_final: 0.5862 (mm) REVERT: B 506 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.6318 (mtt-85) REVERT: B 525 ASN cc_start: 0.6598 (OUTLIER) cc_final: 0.3959 (p0) REVERT: B 734 MET cc_start: 0.3493 (pmm) cc_final: 0.3238 (tpt) outliers start: 24 outliers final: 12 residues processed: 183 average time/residue: 0.1748 time to fit residues: 43.1346 Evaluate side-chains 190 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 840 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 152 MET 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 662 ASN Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 949 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 150 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 175 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 531 HIS ** 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 = 0.4729 r_free = 0.4729 target = 0.244602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.195683 restraints weight = 24204.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.192653 restraints weight = 18985.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.193218 restraints weight = 19106.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.193387 restraints weight = 11135.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.194126 restraints weight = 9655.021| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 15618 Z= 0.257 Angle : 0.685 16.681 21322 Z= 0.331 Chirality : 0.048 0.764 2370 Planarity : 0.005 0.045 2780 Dihedral : 5.741 44.854 2454 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.74 % Allowed : 9.68 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.19), residues: 1936 helix: -4.18 (1.22), residues: 12 sheet: 0.15 (0.18), residues: 840 loop : -1.14 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 244 TYR 0.023 0.001 TYR B 71 PHE 0.016 0.002 PHE A 382 TRP 0.036 0.002 TRP B 168 HIS 0.006 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00607 (15590) covalent geometry : angle 0.64632 (21250) SS BOND : bond 0.00920 ( 12) SS BOND : angle 0.80068 ( 24) hydrogen bonds : bond 0.02840 ( 398) hydrogen bonds : angle 5.67838 ( 981) link_BETA1-4 : bond 0.00197 ( 6) link_BETA1-4 : angle 1.52283 ( 18) link_NAG-ASN : bond 0.00750 ( 10) link_NAG-ASN : angle 5.97296 ( 30) *********************** 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 200 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.4963 (mt-10) REVERT: A 385 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6768 (mt) REVERT: A 420 ARG cc_start: 0.7059 (mtm180) cc_final: 0.6802 (mtm180) REVERT: A 476 ARG cc_start: 0.7226 (mpp-170) cc_final: 0.6894 (mtm110) REVERT: A 506 ARG cc_start: 0.8020 (mmt180) cc_final: 0.5926 (mmt180) REVERT: A 626 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.6013 (mp) REVERT: B 46 VAL cc_start: 0.8787 (m) cc_final: 0.8506 (p) REVERT: B 71 TYR cc_start: 0.7224 (m-10) cc_final: 0.6915 (m-10) REVERT: B 273 TRP cc_start: 0.6872 (m100) cc_final: 0.6400 (m100) REVERT: B 454 LYS cc_start: 0.8363 (tttp) cc_final: 0.7876 (tttm) REVERT: B 475 ILE cc_start: 0.6534 (mt) cc_final: 0.6280 (mt) REVERT: B 485 LYS cc_start: 0.8279 (mmmm) cc_final: 0.7989 (mttm) REVERT: B 496 LYS cc_start: 0.7060 (ptpp) cc_final: 0.6847 (mtmm) REVERT: B 506 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.6042 (mtt-85) REVERT: B 525 ASN cc_start: 0.6664 (OUTLIER) cc_final: 0.3996 (p0) outliers start: 28 outliers final: 15 residues processed: 187 average time/residue: 0.1647 time to fit residues: 41.9578 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 : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 79 GLU 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 483 GLU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 653 TRP Chi-restraints excluded: chain A residue 840 MET Chi-restraints excluded: chain B residue 70 THR 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 572 LEU Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 840 MET 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 98 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 91 optimal weight: 40.0000 chunk 122 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 167 optimal weight: 0.0670 chunk 43 optimal weight: 0.5980 overall best weight: 0.5720 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.247571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.204312 restraints weight = 25639.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.201343 restraints weight = 25483.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.202962 restraints weight = 21208.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.202872 restraints weight = 12296.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.206287 restraints weight = 10541.778| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15618 Z= 0.147 Angle : 0.619 15.555 21322 Z= 0.300 Chirality : 0.045 0.494 2370 Planarity : 0.004 0.046 2780 Dihedral : 5.471 48.579 2454 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.43 % Allowed : 10.48 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.19), residues: 1936 helix: -4.22 (1.17), residues: 12 sheet: 0.17 (0.18), residues: 838 loop : -1.02 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 736 TYR 0.017 0.001 TYR B 71 PHE 0.015 0.001 PHE A 129 TRP 0.052 0.002 TRP B 168 HIS 0.002 0.000 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00345 (15590) covalent geometry : angle 0.58501 (21250) SS BOND : bond 0.00497 ( 12) SS BOND : angle 0.61151 ( 24) hydrogen bonds : bond 0.02525 ( 398) hydrogen bonds : angle 5.35427 ( 981) link_BETA1-4 : bond 0.00166 ( 6) link_BETA1-4 : angle 1.49767 ( 18) link_NAG-ASN : bond 0.00661 ( 10) link_NAG-ASN : angle 5.30472 ( 30) *********************** 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 204 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.507 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: 0.7007 (mtm180) cc_final: 0.6773 (mtm180) REVERT: A 476 ARG cc_start: 0.7272 (mpp-170) cc_final: 0.6935 (mtm110) REVERT: A 506 ARG cc_start: 0.7960 (mmt180) cc_final: 0.6378 (mmt180) REVERT: A 525 ASN cc_start: 0.6083 (OUTLIER) cc_final: 0.3315 (p0) REVERT: B 46 VAL cc_start: 0.8696 (m) cc_final: 0.8395 (p) REVERT: B 71 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6933 (m-80) REVERT: B 273 TRP cc_start: 0.6861 (m100) cc_final: 0.6389 (m100) REVERT: B 454 LYS cc_start: 0.8357 (tttp) cc_final: 0.7853 (tttm) REVERT: B 496 LYS cc_start: 0.6981 (ptpp) cc_final: 0.6777 (mtmm) REVERT: B 506 ARG cc_start: 0.7858 (mtt-85) cc_final: 0.6288 (mtt-85) REVERT: B 525 ASN cc_start: 0.6486 (OUTLIER) cc_final: 0.3760 (p0) REVERT: B 640 LYS cc_start: 0.4468 (pttt) cc_final: 0.4202 (pttt) REVERT: B 704 ARG cc_start: 0.7154 (mmm160) cc_final: 0.6892 (mmm160) outliers start: 23 outliers final: 14 residues processed: 190 average time/residue: 0.1712 time to fit residues: 44.2151 Evaluate side-chains 191 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ILE 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 653 TRP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 292 GLN 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 662 ASN Chi-restraints excluded: chain B residue 840 MET 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 161 optimal weight: 0.3980 chunk 188 optimal weight: 50.0000 chunk 153 optimal weight: 1.9990 chunk 4 optimal weight: 0.0170 chunk 45 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 B 292 GLN B 326 GLN B 644 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.245482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.201727 restraints weight = 26002.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.199313 restraints weight = 26963.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.200829 restraints weight = 21271.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.200800 restraints weight = 12319.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.202233 restraints weight = 10822.713| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15618 Z= 0.135 Angle : 0.609 15.051 21322 Z= 0.296 Chirality : 0.044 0.456 2370 Planarity : 0.004 0.047 2780 Dihedral : 5.299 48.134 2454 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.49 % Allowed : 10.98 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.19), residues: 1936 helix: -4.24 (1.15), residues: 12 sheet: 0.21 (0.18), residues: 844 loop : -0.92 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 244 TYR 0.015 0.001 TYR B 71 PHE 0.014 0.001 PHE A 129 TRP 0.052 0.002 TRP B 168 HIS 0.002 0.000 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00320 (15590) covalent geometry : angle 0.57730 (21250) SS BOND : bond 0.00468 ( 12) SS BOND : angle 0.59493 ( 24) hydrogen bonds : bond 0.02495 ( 398) hydrogen bonds : angle 5.20763 ( 981) link_BETA1-4 : bond 0.00166 ( 6) link_BETA1-4 : angle 1.42009 ( 18) link_NAG-ASN : bond 0.00628 ( 10) link_NAG-ASN : angle 5.13430 ( 30) *********************** 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 201 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.5139 (mt-10) REVERT: A 336 THR cc_start: 0.8045 (p) cc_final: 0.7800 (p) REVERT: A 420 ARG cc_start: 0.7040 (mtm180) cc_final: 0.6781 (mtm180) REVERT: A 476 ARG cc_start: 0.7274 (mpp-170) cc_final: 0.6975 (mtm110) REVERT: A 506 ARG cc_start: 0.7984 (mmt180) cc_final: 0.6247 (mmt180) REVERT: A 525 ASN cc_start: 0.6023 (OUTLIER) cc_final: 0.2666 (p0) REVERT: B 46 VAL cc_start: 0.8715 (m) cc_final: 0.8394 (p) REVERT: B 71 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6879 (m-80) REVERT: B 79 GLU cc_start: 0.7198 (tt0) cc_final: 0.5589 (mt-10) REVERT: B 273 TRP cc_start: 0.6841 (m100) cc_final: 0.6368 (m100) REVERT: B 365 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6854 (mm-30) REVERT: B 454 LYS cc_start: 0.8338 (tttp) cc_final: 0.7847 (tttm) REVERT: B 506 ARG cc_start: 0.7869 (mtt-85) cc_final: 0.6518 (mtt-85) REVERT: B 525 ASN cc_start: 0.6494 (OUTLIER) cc_final: 0.3721 (p0) REVERT: B 640 LYS cc_start: 0.4526 (pttt) cc_final: 0.4254 (pttt) outliers start: 24 outliers final: 16 residues processed: 190 average time/residue: 0.1795 time to fit residues: 45.9284 Evaluate side-chains 194 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 340 ILE 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 572 LEU Chi-restraints excluded: chain A residue 653 TRP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain B residue 71 TYR 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 Chi-restraints excluded: chain B residue 662 ASN 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 62 optimal weight: 0.0000 chunk 113 optimal weight: 0.6980 chunk 154 optimal weight: 0.6980 chunk 175 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 chunk 83 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 168 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4738 r_free = 0.4738 target = 0.245681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.203470 restraints weight = 26369.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.200846 restraints weight = 30972.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.203277 restraints weight = 22107.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.202981 restraints weight = 13433.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.204557 restraints weight = 11329.778| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15618 Z= 0.139 Angle : 0.608 14.545 21322 Z= 0.295 Chirality : 0.045 0.426 2370 Planarity : 0.004 0.047 2780 Dihedral : 5.149 46.902 2454 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.49 % Allowed : 10.86 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.19), residues: 1936 helix: -4.21 (1.17), residues: 12 sheet: 0.31 (0.18), residues: 844 loop : -0.84 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 244 TYR 0.025 0.001 TYR A 71 PHE 0.013 0.001 PHE A 129 TRP 0.047 0.002 TRP B 168 HIS 0.002 0.000 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00327 (15590) covalent geometry : angle 0.57845 (21250) SS BOND : bond 0.00498 ( 12) SS BOND : angle 0.59026 ( 24) hydrogen bonds : bond 0.02428 ( 398) hydrogen bonds : angle 5.14040 ( 981) link_BETA1-4 : bond 0.00183 ( 6) link_BETA1-4 : angle 1.41908 ( 18) link_NAG-ASN : bond 0.00618 ( 10) link_NAG-ASN : angle 4.96657 ( 30) *********************** 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 194 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.5149 (mt-10) REVERT: A 336 THR cc_start: 0.7984 (p) cc_final: 0.7754 (p) REVERT: A 420 ARG cc_start: 0.7029 (mtm180) cc_final: 0.6788 (mtm180) REVERT: A 476 ARG cc_start: 0.7278 (mpp-170) cc_final: 0.6975 (mtm110) REVERT: A 506 ARG cc_start: 0.8001 (mmt180) cc_final: 0.6217 (mmt180) REVERT: B 46 VAL cc_start: 0.8725 (m) cc_final: 0.8419 (p) REVERT: B 71 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.6900 (m-80) REVERT: B 79 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.5922 (mm-30) REVERT: B 273 TRP cc_start: 0.6911 (m100) cc_final: 0.6435 (m100) REVERT: B 331 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8243 (mtmm) REVERT: B 365 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7034 (mm-30) REVERT: B 506 ARG cc_start: 0.7821 (mtt-85) cc_final: 0.6202 (mtt-85) REVERT: B 525 ASN cc_start: 0.6477 (OUTLIER) cc_final: 0.3680 (p0) outliers start: 24 outliers final: 17 residues processed: 183 average time/residue: 0.1730 time to fit residues: 43.1838 Evaluate side-chains 190 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 653 TRP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 79 GLU 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 Chi-restraints excluded: chain B residue 908 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 154 optimal weight: 0.0270 chunk 21 optimal weight: 0.6980 chunk 145 optimal weight: 0.0870 chunk 115 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 193 optimal weight: 30.0000 chunk 14 optimal weight: 0.0030 overall best weight: 0.3026 ------------------------------------------------------------------------------- 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 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.247673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.203652 restraints weight = 26773.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.198340 restraints weight = 19779.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.200255 restraints weight = 16912.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.201690 restraints weight = 10899.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.201952 restraints weight = 9761.178| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15618 Z= 0.106 Angle : 0.591 13.829 21322 Z= 0.285 Chirality : 0.043 0.377 2370 Planarity : 0.004 0.047 2780 Dihedral : 4.950 46.425 2454 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.18 % Allowed : 11.60 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.20), residues: 1936 helix: -4.21 (1.14), residues: 12 sheet: 0.13 (0.17), residues: 924 loop : -0.61 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 244 TYR 0.015 0.001 TYR B 791 PHE 0.012 0.001 PHE A 35 TRP 0.041 0.001 TRP A 628 HIS 0.002 0.000 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00250 (15590) covalent geometry : angle 0.56375 (21250) SS BOND : bond 0.00300 ( 12) SS BOND : angle 0.53531 ( 24) hydrogen bonds : bond 0.02370 ( 398) hydrogen bonds : angle 4.92762 ( 981) link_BETA1-4 : bond 0.00167 ( 6) link_BETA1-4 : angle 1.38348 ( 18) link_NAG-ASN : bond 0.00613 ( 10) link_NAG-ASN : angle 4.66679 ( 30) ********************** 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 187 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.4651 (mt-10) REVERT: A 420 ARG cc_start: 0.7004 (mtm180) cc_final: 0.6770 (mtm180) REVERT: A 476 ARG cc_start: 0.7297 (mpp-170) cc_final: 0.7017 (mtm110) REVERT: A 506 ARG cc_start: 0.8005 (mmt180) cc_final: 0.5815 (mmt180) REVERT: B 46 VAL cc_start: 0.8619 (m) cc_final: 0.8301 (p) REVERT: B 79 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.5786 (mm-30) REVERT: B 245 PHE cc_start: 0.8191 (p90) cc_final: 0.7765 (p90) REVERT: B 273 TRP cc_start: 0.6906 (m100) cc_final: 0.6347 (m100) REVERT: B 331 LYS cc_start: 0.8759 (mtpp) cc_final: 0.8286 (mtmm) REVERT: B 506 ARG cc_start: 0.8018 (mtt-85) cc_final: 0.6231 (mtt-85) REVERT: B 525 ASN cc_start: 0.6223 (OUTLIER) cc_final: 0.3074 (p0) outliers start: 19 outliers final: 13 residues processed: 178 average time/residue: 0.1812 time to fit residues: 43.5727 Evaluate side-chains 182 residues out of total 1612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 653 TRP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 79 GLU 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 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 72 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 191 optimal weight: 9.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4739 r_free = 0.4739 target = 0.245438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.203403 restraints weight = 25676.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.198531 restraints weight = 28794.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.201553 restraints weight = 23085.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.201139 restraints weight = 13810.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.204594 restraints weight = 11953.013| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15618 Z= 0.181 Angle : 0.620 14.415 21322 Z= 0.300 Chirality : 0.045 0.426 2370 Planarity : 0.004 0.047 2780 Dihedral : 5.034 45.398 2454 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.24 % Allowed : 11.79 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.19), residues: 1936 helix: -4.11 (1.26), residues: 12 sheet: 0.20 (0.17), residues: 900 loop : -0.65 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 704 TYR 0.018 0.001 TYR A 71 PHE 0.013 0.001 PHE A 129 TRP 0.048 0.002 TRP A 628 HIS 0.003 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00426 (15590) covalent geometry : angle 0.59146 (21250) SS BOND : bond 0.00634 ( 12) SS BOND : angle 0.61614 ( 24) hydrogen bonds : bond 0.02477 ( 398) hydrogen bonds : angle 5.03590 ( 981) link_BETA1-4 : bond 0.00147 ( 6) link_BETA1-4 : angle 1.37120 ( 18) link_NAG-ASN : bond 0.00590 ( 10) link_NAG-ASN : angle 4.94099 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3809.94 seconds wall clock time: 65 minutes 57.88 seconds (3957.88 seconds total)