Starting phenix.real_space_refine on Tue Aug 6 06:27:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ba4_44395/08_2024/9ba4_44395.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ba4_44395/08_2024/9ba4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ba4_44395/08_2024/9ba4_44395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ba4_44395/08_2024/9ba4_44395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ba4_44395/08_2024/9ba4_44395.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ba4_44395/08_2024/9ba4_44395.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 224 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 9556 2.51 5 N 2676 2.21 5 O 2918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 695": "OE1" <-> "OE2" Residue "A PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 398": "OE1" <-> "OE2" Residue "B PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 524": "OD1" <-> "OD2" Residue "B PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 695": "OE1" <-> "OE2" Residue "B PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15204 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7490 Classifications: {'peptide': 970} Link IDs: {'PCIS': 8, 'PTRANS': 66, 'TRANS': 895} Chain: "B" Number of atoms: 7490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7490 Classifications: {'peptide': 970} Link IDs: {'PCIS': 8, 'PTRANS': 66, 'TRANS': 895} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.43, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 5.33 Conformation dependent library (CDL) restraints added in 2.6 seconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3556 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 57 sheets defined 3.0% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.976A pdb=" N ALA A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 4.062A pdb=" N LEU A 202 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.772A pdb=" N GLU A 301 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.797A pdb=" N SER A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.726A pdb=" N GLY A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 740 removed outlier: 3.612A pdb=" N GLN A 739 " --> pdb=" O SER A 735 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN A 740 " --> pdb=" O ARG A 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 735 through 740' Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.819A pdb=" N ALA B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.556A pdb=" N ASP B 201 " --> pdb=" O ASN B 198 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 202 " --> pdb=" O ALA B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 202' Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.637A pdb=" N GLU B 301 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.768A pdb=" N SER B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 582 removed outlier: 3.998A pdb=" N GLY B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 41 removed outlier: 5.812A pdb=" N GLY A 36 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER A 66 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG A 62 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.781A pdb=" N GLY A 107 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.781A pdb=" N GLY A 107 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 59 Processing sheet with id=AA5, first strand: chain 'A' and resid 131 through 132 removed outlier: 3.501A pdb=" N PHE A 131 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 161 " --> pdb=" O PHE A 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 143 through 147 removed outlier: 5.853A pdb=" N VAL A 143 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA A 230 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA A 145 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLU A 232 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU A 147 " --> pdb=" O GLU A 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 151 through 153 removed outlier: 4.220A pdb=" N ILE A 194 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 153 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A 192 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 165 through 169 removed outlier: 3.807A pdb=" N ARG A 167 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 169 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 206 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 209 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 220 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 218 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 249 through 251 removed outlier: 6.017A pdb=" N THR A 249 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 257 through 260 removed outlier: 3.559A pdb=" N VAL A 257 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 325 through 331 removed outlier: 5.153A pdb=" N GLN A 326 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS A 353 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA A 349 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 336 through 339 removed outlier: 7.043A pdb=" N THR A 336 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLN A 413 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA A 338 " --> pdb=" O GLN A 413 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.879A pdb=" N LEU A 344 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 427 through 431 removed outlier: 6.443A pdb=" N ILE A 428 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG A 506 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA A 430 " --> pdb=" O ARG A 506 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 497 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 484 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 451 " --> pdb=" O PHE A 489 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 435 through 438 removed outlier: 3.720A pdb=" N ILE A 436 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 475 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 510 through 513 removed outlier: 3.571A pdb=" N THR A 512 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N HIS A 531 " --> pdb=" O THR A 512 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 518 through 519 removed outlier: 6.943A pdb=" N ALA A 518 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.554A pdb=" N LEU A 572 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 615 through 617 removed outlier: 3.619A pdb=" N ILE A 624 " --> pdb=" O VAL A 672 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 626 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 654 through 655 removed outlier: 4.092A pdb=" N ILE A 663 " --> pdb=" O TYR A 641 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.935A pdb=" N LYS A 640 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 646 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 689 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 692 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 718 through 719 removed outlier: 3.558A pdb=" N VAL A 729 " --> pdb=" O PHE A 771 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 771 " --> pdb=" O VAL A 729 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 759 through 760 removed outlier: 3.701A pdb=" N VAL A 763 " --> pdb=" O TYR A 746 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 759 through 760 removed outlier: 3.614A pdb=" N ALA A 803 " --> pdb=" O VAL A 786 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 820 through 823 Processing sheet with id=AC8, first strand: chain 'A' and resid 862 through 865 Processing sheet with id=AC9, first strand: chain 'A' and resid 920 through 923 Processing sheet with id=AD1, first strand: chain 'A' and resid 960 through 964 removed outlier: 3.550A pdb=" N TYR A 947 " --> pdb=" O THR A 964 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 35 through 41 removed outlier: 5.859A pdb=" N GLY B 36 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER B 66 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 38 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG B 62 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.247A pdb=" N PHE B 48 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LEU B 132 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 107 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 78 through 79 removed outlier: 3.678A pdb=" N GLY B 107 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR B 161 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 56 through 59 Processing sheet with id=AD6, first strand: chain 'B' and resid 143 through 147 removed outlier: 5.792A pdb=" N VAL B 143 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA B 230 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA B 145 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLU B 232 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU B 147 " --> pdb=" O GLU B 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.565A pdb=" N LEU B 153 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B 193 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 168 through 169 Processing sheet with id=AD9, first strand: chain 'B' and resid 211 through 212 removed outlier: 3.549A pdb=" N LYS B 218 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 240 through 243 removed outlier: 3.501A pdb=" N SER B 240 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE B 262 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 249 through 251 Processing sheet with id=AE3, first strand: chain 'B' and resid 257 through 260 removed outlier: 3.505A pdb=" N VAL B 257 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 328 through 331 removed outlier: 6.892A pdb=" N ALA B 349 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 336 through 339 removed outlier: 6.934A pdb=" N THR B 336 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLN B 413 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 338 " --> pdb=" O GLN B 413 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 344 through 346 Processing sheet with id=AE7, first strand: chain 'B' and resid 427 through 431 removed outlier: 3.617A pdb=" N ALA B 497 " --> pdb=" O ALA B 490 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 435 through 438 removed outlier: 3.558A pdb=" N ILE B 436 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 475 " --> pdb=" O ILE B 436 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 510 through 513 removed outlier: 6.798A pdb=" N HIS B 531 " --> pdb=" O THR B 512 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 518 through 519 removed outlier: 6.560A pdb=" N ALA B 518 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 598 " --> pdb=" O CYS B 587 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 526 through 528 Processing sheet with id=AF3, first strand: chain 'B' and resid 615 through 617 removed outlier: 3.539A pdb=" N ILE B 624 " --> pdb=" O VAL B 672 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 626 " --> pdb=" O ALA B 670 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 670 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN B 671 " --> pdb=" O ASN B 659 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN B 659 " --> pdb=" O GLN B 671 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.566A pdb=" N LYS B 654 " --> pdb=" O ALA B 645 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 646 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 682 " --> pdb=" O ARG B 646 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN B 689 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY B 692 " --> pdb=" O ASN B 689 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.566A pdb=" N LYS B 654 " --> pdb=" O ALA B 645 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 646 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 682 " --> pdb=" O ARG B 646 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 718 through 719 Processing sheet with id=AF7, first strand: chain 'B' and resid 759 through 760 removed outlier: 3.617A pdb=" N VAL B 763 " --> pdb=" O TYR B 746 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AF9, first strand: chain 'B' and resid 820 through 823 Processing sheet with id=AG1, first strand: chain 'B' and resid 862 through 865 Processing sheet with id=AG2, first strand: chain 'B' and resid 920 through 923 removed outlier: 3.517A pdb=" N ILE B 969 " --> pdb=" O ILE B 930 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 960 through 964 removed outlier: 3.505A pdb=" N TYR B 947 " --> pdb=" O THR B 964 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 981 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.66 Time building geometry restraints manager: 5.93 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: 90.75 - 99.58: 4 99.58 - 108.42: 1297 108.42 - 117.25: 10369 117.25 - 126.09: 9181 126.09 - 134.92: 399 Bond angle restraints: 21250 Sorted by residual: angle pdb=" C ASP B 547 " pdb=" N ASP B 548 " pdb=" CA ASP B 548 " ideal model delta sigma weight residual 122.08 132.31 -10.23 1.47e+00 4.63e-01 4.84e+01 angle pdb=" CB LEU B 427 " pdb=" CG LEU B 427 " pdb=" CD2 LEU B 427 " ideal model delta sigma weight residual 110.70 90.75 19.95 3.00e+00 1.11e-01 4.42e+01 angle pdb=" C VAL A 712 " pdb=" N ALA A 713 " pdb=" CA ALA A 713 " ideal model delta sigma weight residual 120.68 130.63 -9.95 1.52e+00 4.33e-01 4.29e+01 angle pdb=" C PRO B 677 " pdb=" N TRP B 678 " pdb=" CA TRP B 678 " ideal model delta sigma weight residual 121.54 133.92 -12.38 1.91e+00 2.74e-01 4.20e+01 angle pdb=" CA ASN A 659 " pdb=" CB ASN A 659 " pdb=" CG ASN A 659 " ideal model delta sigma weight residual 112.60 118.91 -6.31 1.00e+00 1.00e+00 3.98e+01 ... (remaining 21245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 8860 17.34 - 34.68: 615 34.68 - 52.02: 66 52.02 - 69.36: 25 69.36 - 86.70: 16 Dihedral angle restraints: 9582 sinusoidal: 4032 harmonic: 5550 Sorted by residual: dihedral pdb=" CA LEU A 427 " pdb=" C LEU A 427 " pdb=" N ILE A 428 " pdb=" CA ILE A 428 " ideal model delta harmonic sigma weight residual -180.00 -144.12 -35.88 0 5.00e+00 4.00e-02 5.15e+01 dihedral pdb=" CA PRO B 733 " pdb=" C PRO B 733 " pdb=" N MET B 734 " pdb=" CA MET B 734 " ideal model delta harmonic sigma weight residual -180.00 -144.43 -35.57 0 5.00e+00 4.00e-02 5.06e+01 dihedral pdb=" CA THR A 658 " pdb=" C THR A 658 " pdb=" N ASN A 659 " pdb=" CA ASN A 659 " ideal model delta harmonic sigma weight residual 180.00 145.64 34.36 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 9579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 2335 0.202 - 0.404: 32 0.404 - 0.606: 2 0.606 - 0.808: 0 0.808 - 1.011: 1 Chirality restraints: 2370 Sorted by residual: chirality pdb=" CB ILE A 438 " pdb=" CA ILE A 438 " pdb=" CG1 ILE A 438 " pdb=" CG2 ILE A 438 " both_signs ideal model delta sigma weight residual False 2.64 1.63 1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" CB ILE A 624 " pdb=" CA ILE A 624 " pdb=" CG1 ILE A 624 " pdb=" CG2 ILE A 624 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.57 2.00e-01 2.50e+01 8.25e+00 chirality pdb=" CB ILE B 624 " pdb=" CA ILE B 624 " pdb=" CG1 ILE B 624 " pdb=" CG2 ILE B 624 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.40e+00 ... (remaining 2367 not shown) Planarity restraints: 2790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 168 " 0.061 2.00e-02 2.50e+03 4.63e-02 5.37e+01 pdb=" CG TRP B 168 " -0.120 2.00e-02 2.50e+03 pdb=" CD1 TRP B 168 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP B 168 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 168 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 168 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 168 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 168 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 168 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 653 " -0.039 2.00e-02 2.50e+03 4.28e-02 4.59e+01 pdb=" CG TRP A 653 " 0.113 2.00e-02 2.50e+03 pdb=" CD1 TRP A 653 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP A 653 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 653 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 653 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 653 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 653 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 653 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 653 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 653 " 0.026 2.00e-02 2.50e+03 3.19e-02 2.55e+01 pdb=" CG TRP B 653 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP B 653 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP B 653 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 653 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP B 653 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 653 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 653 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 653 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 653 " 0.004 2.00e-02 2.50e+03 ... (remaining 2787 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 5240 2.89 - 3.39: 10670 3.39 - 3.90: 24962 3.90 - 4.40: 24280 4.40 - 4.90: 44299 Nonbonded interactions: 109451 Sorted by model distance: nonbonded pdb=" OG1 THR B 591 " pdb=" OD1 ASP B 594 " model vdw 2.392 3.040 nonbonded pdb=" OG SER B 136 " pdb=" OE1 GLU B 138 " model vdw 2.392 3.040 nonbonded pdb=" OG SER A 136 " pdb=" OE1 GLU A 138 " model vdw 2.393 3.040 nonbonded pdb=" OD1 ASP A 300 " pdb=" OH TYR A 304 " model vdw 2.395 3.040 nonbonded pdb=" OD2 ASP A 535 " pdb=" OG1 THR A 537 " model vdw 2.396 3.040 ... (remaining 109446 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 42.440 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.340 ------------------------------------------------------------------------------- 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 15590 Z= 0.691 Angle : 1.244 19.953 21250 Z= 0.670 Chirality : 0.070 1.011 2370 Planarity : 0.011 0.129 2780 Dihedral : 12.634 86.704 5990 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.17), residues: 1936 helix: None (None), residues: 0 sheet: -0.33 (0.18), residues: 792 loop : -1.91 (0.16), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.120 0.005 TRP B 168 HIS 0.018 0.002 HIS B 534 PHE 0.031 0.003 PHE A 35 TYR 0.035 0.003 TYR A 71 ARG 0.028 0.001 ARG B 580 *********************** 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 fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 TRP cc_start: 0.6220 (m100) cc_final: 0.5750 (m100) REVERT: A 506 ARG cc_start: 0.7456 (mmt180) cc_final: 0.5498 (mmt-90) REVERT: A 949 MET cc_start: 0.1596 (ttp) cc_final: 0.1389 (ttp) REVERT: B 46 VAL cc_start: 0.7952 (m) cc_final: 0.7549 (p) REVERT: B 161 TYR cc_start: 0.7451 (t80) cc_final: 0.6731 (t80) REVERT: B 213 MET cc_start: 0.4323 (mtt) cc_final: 0.4059 (mtt) REVERT: B 244 ARG cc_start: 0.7590 (ttt-90) cc_final: 0.7068 (tpt-90) REVERT: B 245 PHE cc_start: 0.7549 (p90) cc_final: 0.6494 (p90) REVERT: B 336 THR cc_start: 0.8040 (m) cc_final: 0.7810 (p) REVERT: B 420 ARG cc_start: 0.6783 (mpp80) cc_final: 0.6501 (mpp80) REVERT: B 454 LYS cc_start: 0.8171 (tttp) cc_final: 0.7946 (ttmm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3505 time to fit residues: 77.1825 Evaluate side-chains 148 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.6980 chunk 147 optimal weight: 0.0670 chunk 81 optimal weight: 7.9990 chunk 50 optimal weight: 0.0370 chunk 99 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15590 Z= 0.227 Angle : 0.618 11.227 21250 Z= 0.316 Chirality : 0.043 0.227 2370 Planarity : 0.006 0.053 2780 Dihedral : 6.020 37.376 2454 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.37 % Allowed : 5.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 1936 helix: -4.71 (0.56), residues: 12 sheet: 0.19 (0.17), residues: 860 loop : -1.35 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 168 HIS 0.003 0.001 HIS A 160 PHE 0.015 0.001 PHE B 245 TYR 0.015 0.001 TYR B 109 ARG 0.005 0.001 ARG A 476 *********************** 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 161 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 506 ARG cc_start: 0.7702 (mmt180) cc_final: 0.5850 (mmt-90) REVERT: A 628 TRP cc_start: 0.5963 (p90) cc_final: 0.5497 (p90) REVERT: A 949 MET cc_start: 0.1756 (ttp) cc_final: 0.1543 (ttp) REVERT: B 98 MET cc_start: 0.6756 (mpp) cc_final: 0.6254 (mpp) REVERT: B 244 ARG cc_start: 0.7597 (ttt-90) cc_final: 0.6984 (tpt-90) REVERT: B 454 LYS cc_start: 0.8092 (tttp) cc_final: 0.7474 (tttm) REVERT: B 599 GLU cc_start: 0.6863 (tm-30) cc_final: 0.6661 (tm-30) outliers start: 6 outliers final: 4 residues processed: 156 average time/residue: 0.3534 time to fit residues: 76.1045 Evaluate side-chains 154 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 97 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 176 optimal weight: 40.0000 chunk 190 optimal weight: 50.0000 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 141 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15590 Z= 0.269 Angle : 0.583 12.038 21250 Z= 0.293 Chirality : 0.043 0.253 2370 Planarity : 0.005 0.046 2780 Dihedral : 5.489 37.700 2454 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.74 % Allowed : 6.51 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1936 helix: -3.79 (1.16), residues: 12 sheet: 0.37 (0.18), residues: 866 loop : -1.19 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 168 HIS 0.004 0.001 HIS B 635 PHE 0.014 0.001 PHE B 245 TYR 0.016 0.001 TYR B 560 ARG 0.007 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 506 ARG cc_start: 0.7855 (mmt180) cc_final: 0.5658 (mpt180) REVERT: A 593 VAL cc_start: 0.6607 (OUTLIER) cc_final: 0.6278 (m) REVERT: A 628 TRP cc_start: 0.6012 (p90) cc_final: 0.5553 (p90) REVERT: A 675 LEU cc_start: 0.6899 (mp) cc_final: 0.6245 (tp) REVERT: B 71 TYR cc_start: 0.7207 (m-80) cc_final: 0.6944 (m-10) REVERT: B 105 ASP cc_start: 0.7444 (m-30) cc_final: 0.7198 (m-30) REVERT: B 244 ARG cc_start: 0.7487 (ttt-90) cc_final: 0.7019 (tpt-90) REVERT: B 475 ILE cc_start: 0.6282 (mt) cc_final: 0.5587 (mm) REVERT: B 491 GLU cc_start: 0.6834 (tp30) cc_final: 0.6627 (tp30) REVERT: B 549 PHE cc_start: 0.7574 (m-10) cc_final: 0.7357 (m-80) REVERT: B 625 GLN cc_start: 0.6950 (tp40) cc_final: 0.6231 (tp-100) REVERT: B 640 LYS cc_start: 0.4675 (pttt) cc_final: 0.4449 (pttt) outliers start: 12 outliers final: 8 residues processed: 162 average time/residue: 0.3596 time to fit residues: 81.5335 Evaluate side-chains 162 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 840 MET Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 949 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 91 optimal weight: 40.0000 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 30.0000 chunk 118 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 187 optimal weight: 40.0000 chunk 92 optimal weight: 0.5980 chunk 167 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 GLN B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15590 Z= 0.359 Angle : 0.608 11.496 21250 Z= 0.306 Chirality : 0.045 0.284 2370 Planarity : 0.005 0.039 2780 Dihedral : 5.473 41.878 2454 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.12 % Allowed : 7.69 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 1936 helix: -3.71 (1.33), residues: 12 sheet: 0.31 (0.17), residues: 874 loop : -1.02 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 168 HIS 0.007 0.001 HIS A 559 PHE 0.016 0.001 PHE A 542 TYR 0.020 0.002 TYR B 560 ARG 0.008 0.000 ARG A 426 *********************** 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 194 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 1.497 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 385 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6591 (mt) REVERT: A 420 ARG cc_start: 0.7105 (mtm180) cc_final: 0.6722 (mtm180) REVERT: A 476 ARG cc_start: 0.7253 (mpp-170) cc_final: 0.6955 (mtm110) REVERT: A 506 ARG cc_start: 0.7983 (mmt180) cc_final: 0.6416 (mmt180) REVERT: A 525 ASN cc_start: 0.6806 (OUTLIER) cc_final: 0.3917 (p0) REVERT: A 628 TRP cc_start: 0.6198 (p90) cc_final: 0.5866 (p90) REVERT: B 71 TYR cc_start: 0.7281 (m-80) cc_final: 0.6912 (m-10) REVERT: B 189 THR cc_start: 0.7484 (m) cc_final: 0.7263 (t) REVERT: B 213 MET cc_start: 0.4290 (mtt) cc_final: 0.4082 (mtt) REVERT: B 244 ARG cc_start: 0.7487 (ttt-90) cc_final: 0.7034 (tpt-90) REVERT: B 331 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8543 (mtpp) REVERT: B 475 ILE cc_start: 0.6500 (mt) cc_final: 0.5830 (mm) REVERT: B 476 ARG cc_start: 0.7225 (mtm110) cc_final: 0.6865 (mtm110) REVERT: B 496 LYS cc_start: 0.6872 (mttt) cc_final: 0.6641 (ptpp) REVERT: B 506 ARG cc_start: 0.8045 (mtt-85) cc_final: 0.6650 (mtt-85) REVERT: B 525 ASN cc_start: 0.6511 (OUTLIER) cc_final: 0.3708 (p0) REVERT: B 549 PHE cc_start: 0.7615 (m-10) cc_final: 0.7394 (m-10) REVERT: B 625 GLN cc_start: 0.6956 (tp-100) cc_final: 0.6337 (tp40) REVERT: B 734 MET cc_start: 0.5945 (ppp) cc_final: 0.5592 (tpp) outliers start: 18 outliers final: 11 residues processed: 184 average time/residue: 0.3560 time to fit residues: 89.5865 Evaluate side-chains 178 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 400 LYS 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 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 525 ASN Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 908 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 160 optimal weight: 0.5980 chunk 129 optimal weight: 0.3980 chunk 0 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15590 Z= 0.247 Angle : 0.556 11.926 21250 Z= 0.278 Chirality : 0.043 0.264 2370 Planarity : 0.004 0.040 2780 Dihedral : 5.236 42.703 2454 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.24 % Allowed : 8.50 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.19), residues: 1936 helix: -3.64 (1.36), residues: 12 sheet: 0.37 (0.18), residues: 874 loop : -0.90 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 168 HIS 0.003 0.000 HIS A 559 PHE 0.013 0.001 PHE B 245 TYR 0.014 0.001 TYR B 71 ARG 0.004 0.000 ARG B 506 *********************** 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 186 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 1.615 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 102 LYS cc_start: 0.8223 (tttm) cc_final: 0.7997 (tttm) REVERT: A 420 ARG cc_start: 0.7092 (mtm180) cc_final: 0.6745 (mtm180) REVERT: A 476 ARG cc_start: 0.7248 (mpp-170) cc_final: 0.6943 (mtm110) REVERT: A 506 ARG cc_start: 0.7973 (mmt180) cc_final: 0.6253 (mmt180) REVERT: A 525 ASN cc_start: 0.6747 (OUTLIER) cc_final: 0.3892 (p0) REVERT: A 628 TRP cc_start: 0.6188 (p90) cc_final: 0.5877 (p90) REVERT: A 675 LEU cc_start: 0.6880 (mp) cc_final: 0.6289 (tp) REVERT: B 46 VAL cc_start: 0.8258 (m) cc_final: 0.7847 (p) REVERT: B 71 TYR cc_start: 0.7215 (m-80) cc_final: 0.6864 (m-10) REVERT: B 75 MET cc_start: 0.6622 (tmm) cc_final: 0.6327 (tmm) REVERT: B 213 MET cc_start: 0.4451 (mtt) cc_final: 0.4211 (mtt) REVERT: B 244 ARG cc_start: 0.7481 (ttt-90) cc_final: 0.7032 (tpt-90) REVERT: B 331 LYS cc_start: 0.8754 (mtmt) cc_final: 0.8236 (mtmm) REVERT: B 475 ILE cc_start: 0.6464 (mt) cc_final: 0.6147 (mm) REVERT: B 476 ARG cc_start: 0.7214 (mtm110) cc_final: 0.6838 (mtm110) REVERT: B 506 ARG cc_start: 0.8034 (mtt-85) cc_final: 0.6270 (mtt-85) REVERT: B 525 ASN cc_start: 0.6395 (OUTLIER) cc_final: 0.3505 (p0) REVERT: B 549 PHE cc_start: 0.7639 (m-10) cc_final: 0.7428 (m-10) REVERT: B 625 GLN cc_start: 0.6920 (tp-100) cc_final: 0.6258 (tp40) outliers start: 20 outliers final: 15 residues processed: 177 average time/residue: 0.3971 time to fit residues: 98.9503 Evaluate side-chains 179 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 400 LYS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 840 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 545 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 0.0970 chunk 168 optimal weight: 9.9990 chunk 37 optimal weight: 0.1980 chunk 110 optimal weight: 0.0870 chunk 46 optimal weight: 0.6980 chunk 187 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 50.0000 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15590 Z= 0.186 Angle : 0.536 11.608 21250 Z= 0.267 Chirality : 0.042 0.246 2370 Planarity : 0.004 0.041 2780 Dihedral : 5.027 41.597 2454 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.43 % Allowed : 8.75 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 1936 helix: -3.55 (1.39), residues: 12 sheet: 0.37 (0.17), residues: 884 loop : -0.80 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP A 168 HIS 0.002 0.000 HIS B 160 PHE 0.012 0.001 PHE B 245 TYR 0.011 0.001 TYR B 71 ARG 0.003 0.000 ARG B 657 *********************** 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 190 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8188 (tttm) cc_final: 0.7967 (tttm) REVERT: A 244 ARG cc_start: 0.7631 (tpp80) cc_final: 0.7069 (tpp-160) REVERT: A 273 TRP cc_start: 0.6324 (m100) cc_final: 0.6043 (m100) REVERT: A 420 ARG cc_start: 0.7082 (mtm180) cc_final: 0.6733 (mtm180) REVERT: A 476 ARG cc_start: 0.7260 (mpp-170) cc_final: 0.6660 (mtm110) REVERT: A 506 ARG cc_start: 0.7980 (mmt180) cc_final: 0.5690 (mmt180) REVERT: A 525 ASN cc_start: 0.6725 (OUTLIER) cc_final: 0.3831 (p0) REVERT: A 628 TRP cc_start: 0.6189 (p90) cc_final: 0.5800 (p90) REVERT: B 46 VAL cc_start: 0.8285 (m) cc_final: 0.7879 (p) REVERT: B 213 MET cc_start: 0.4507 (mtt) cc_final: 0.4249 (mtt) REVERT: B 244 ARG cc_start: 0.7479 (ttt-90) cc_final: 0.7025 (tpt-90) REVERT: B 475 ILE cc_start: 0.6380 (mt) cc_final: 0.5706 (mm) REVERT: B 476 ARG cc_start: 0.7232 (mtm110) cc_final: 0.6811 (mtm110) REVERT: B 480 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7621 (ttm-80) REVERT: B 506 ARG cc_start: 0.8007 (mtt-85) cc_final: 0.5892 (mtt-85) REVERT: B 525 ASN cc_start: 0.6290 (OUTLIER) cc_final: 0.3338 (p0) REVERT: B 549 PHE cc_start: 0.7615 (m-10) cc_final: 0.7397 (m-10) REVERT: B 625 GLN cc_start: 0.6881 (tp-100) cc_final: 0.6198 (tp-100) outliers start: 23 outliers final: 12 residues processed: 181 average time/residue: 0.3696 time to fit residues: 90.5967 Evaluate side-chains 177 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 949 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 40.0000 chunk 21 optimal weight: 0.0370 chunk 106 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 158 optimal weight: 0.0770 chunk 104 optimal weight: 2.9990 chunk 186 optimal weight: 30.0000 chunk 117 optimal weight: 0.2980 chunk 113 optimal weight: 8.9990 chunk 86 optimal weight: 50.0000 chunk 115 optimal weight: 9.9990 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15590 Z= 0.354 Angle : 0.600 11.731 21250 Z= 0.299 Chirality : 0.044 0.294 2370 Planarity : 0.004 0.043 2780 Dihedral : 5.227 42.524 2454 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.55 % Allowed : 9.24 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 1936 helix: -3.88 (1.22), residues: 12 sheet: 0.46 (0.18), residues: 848 loop : -0.86 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 168 HIS 0.006 0.001 HIS A 559 PHE 0.018 0.001 PHE A 129 TYR 0.018 0.001 TYR B 560 ARG 0.013 0.000 ARG A 426 *********************** 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 189 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.727 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 71 TYR cc_start: 0.7548 (m-80) cc_final: 0.7254 (m-80) REVERT: A 102 LYS cc_start: 0.8276 (tttm) cc_final: 0.8021 (tttm) REVERT: A 244 ARG cc_start: 0.7721 (tpp80) cc_final: 0.7253 (tpp-160) REVERT: A 385 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6521 (mt) REVERT: A 420 ARG cc_start: 0.7104 (mtm180) cc_final: 0.6762 (mtm180) REVERT: A 476 ARG cc_start: 0.7352 (mpp-170) cc_final: 0.6848 (mtm110) REVERT: A 506 ARG cc_start: 0.8051 (mmt180) cc_final: 0.6056 (mmt180) REVERT: A 525 ASN cc_start: 0.6912 (OUTLIER) cc_final: 0.4106 (p0) REVERT: A 628 TRP cc_start: 0.6185 (p90) cc_final: 0.5941 (p90) REVERT: B 46 VAL cc_start: 0.8422 (m) cc_final: 0.8047 (p) REVERT: B 71 TYR cc_start: 0.7305 (m-80) cc_final: 0.6904 (m-10) REVERT: B 213 MET cc_start: 0.4543 (mtt) cc_final: 0.4298 (mtt) REVERT: B 244 ARG cc_start: 0.7432 (ttt-90) cc_final: 0.7014 (tpt-90) REVERT: B 273 TRP cc_start: 0.5779 (m100) cc_final: 0.5051 (m100) REVERT: B 454 LYS cc_start: 0.8426 (ttmm) cc_final: 0.7117 (tmtt) REVERT: B 475 ILE cc_start: 0.6391 (mt) cc_final: 0.5791 (mm) REVERT: B 476 ARG cc_start: 0.7222 (mtm110) cc_final: 0.6844 (mtm110) REVERT: B 506 ARG cc_start: 0.8001 (mtt-85) cc_final: 0.5866 (mtt-85) REVERT: B 525 ASN cc_start: 0.6663 (OUTLIER) cc_final: 0.3838 (p0) REVERT: B 549 PHE cc_start: 0.7622 (m-10) cc_final: 0.7408 (m-10) REVERT: B 625 GLN cc_start: 0.6922 (tp-100) cc_final: 0.6241 (tp40) REVERT: B 734 MET cc_start: 0.6380 (tmm) cc_final: 0.4669 (pmm) outliers start: 25 outliers final: 18 residues processed: 178 average time/residue: 0.3786 time to fit residues: 92.1358 Evaluate side-chains 187 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 179 optimal weight: 50.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15590 Z= 0.252 Angle : 0.561 12.232 21250 Z= 0.279 Chirality : 0.043 0.267 2370 Planarity : 0.004 0.044 2780 Dihedral : 5.076 43.122 2454 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.30 % Allowed : 9.62 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 1936 helix: -3.84 (1.25), residues: 12 sheet: 0.41 (0.18), residues: 864 loop : -0.77 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 168 HIS 0.003 0.000 HIS A 559 PHE 0.014 0.001 PHE A 129 TYR 0.013 0.001 TYR B 560 ARG 0.009 0.000 ARG B 704 *********************** 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 188 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 1.712 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 71 TYR cc_start: 0.7473 (m-80) cc_final: 0.7174 (m-80) REVERT: A 102 LYS cc_start: 0.8270 (tttm) cc_final: 0.8009 (tttm) REVERT: A 244 ARG cc_start: 0.7724 (tpp80) cc_final: 0.7251 (tpp-160) REVERT: A 385 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6446 (mt) REVERT: A 420 ARG cc_start: 0.7090 (mtm180) cc_final: 0.6756 (mtm180) REVERT: A 476 ARG cc_start: 0.7356 (mpp-170) cc_final: 0.6859 (mtm110) REVERT: A 506 ARG cc_start: 0.7987 (mmt180) cc_final: 0.6290 (mmt180) REVERT: A 525 ASN cc_start: 0.6838 (OUTLIER) cc_final: 0.3956 (p0) REVERT: A 628 TRP cc_start: 0.6113 (p90) cc_final: 0.5869 (p90) REVERT: B 46 VAL cc_start: 0.8395 (m) cc_final: 0.8015 (p) REVERT: B 71 TYR cc_start: 0.7229 (m-80) cc_final: 0.6874 (m-10) REVERT: B 213 MET cc_start: 0.4564 (mtt) cc_final: 0.4317 (mtt) REVERT: B 244 ARG cc_start: 0.7464 (ttt-90) cc_final: 0.7024 (tpt-90) REVERT: B 273 TRP cc_start: 0.5829 (m100) cc_final: 0.5059 (m100) REVERT: B 454 LYS cc_start: 0.8384 (ttmm) cc_final: 0.7108 (tmtt) REVERT: B 475 ILE cc_start: 0.6451 (mt) cc_final: 0.6143 (mm) REVERT: B 476 ARG cc_start: 0.7239 (mtm110) cc_final: 0.6880 (mtm110) REVERT: B 506 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.6350 (mtt-85) REVERT: B 525 ASN cc_start: 0.6421 (OUTLIER) cc_final: 0.3535 (p0) REVERT: B 625 GLN cc_start: 0.6850 (tp-100) cc_final: 0.6130 (tp-100) REVERT: B 734 MET cc_start: 0.6289 (tmm) cc_final: 0.4727 (pmm) outliers start: 21 outliers final: 16 residues processed: 178 average time/residue: 0.3816 time to fit residues: 92.9323 Evaluate side-chains 183 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.3980 chunk 174 optimal weight: 6.9990 chunk 179 optimal weight: 50.0000 chunk 104 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 164 optimal weight: 0.7980 chunk 173 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 GLN B 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15590 Z= 0.246 Angle : 0.561 11.942 21250 Z= 0.279 Chirality : 0.043 0.262 2370 Planarity : 0.004 0.044 2780 Dihedral : 4.972 42.115 2454 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.30 % Allowed : 9.99 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 1936 helix: -3.81 (1.25), residues: 12 sheet: 0.21 (0.17), residues: 900 loop : -0.65 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP B 168 HIS 0.003 0.000 HIS A 559 PHE 0.015 0.001 PHE A 129 TYR 0.012 0.001 TYR B 791 ARG 0.008 0.000 ARG B 704 *********************** 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 189 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8269 (tttm) cc_final: 0.7996 (tttm) REVERT: A 244 ARG cc_start: 0.7728 (tpp80) cc_final: 0.7255 (tpp-160) REVERT: A 273 TRP cc_start: 0.6277 (m100) cc_final: 0.6021 (m100) REVERT: A 385 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6456 (mt) REVERT: A 420 ARG cc_start: 0.7091 (mtm180) cc_final: 0.6759 (mtm180) REVERT: A 476 ARG cc_start: 0.7352 (mpp-170) cc_final: 0.6882 (mtm110) REVERT: A 506 ARG cc_start: 0.8037 (mmt180) cc_final: 0.6112 (mmt180) REVERT: A 525 ASN cc_start: 0.6820 (OUTLIER) cc_final: 0.3980 (p0) REVERT: A 628 TRP cc_start: 0.6087 (p90) cc_final: 0.5830 (p90) REVERT: A 675 LEU cc_start: 0.6564 (mp) cc_final: 0.5752 (tt) REVERT: A 689 ASN cc_start: 0.5921 (m110) cc_final: 0.5563 (m-40) REVERT: B 46 VAL cc_start: 0.8374 (m) cc_final: 0.7992 (p) REVERT: B 71 TYR cc_start: 0.7228 (m-80) cc_final: 0.6880 (m-10) REVERT: B 213 MET cc_start: 0.4579 (mtt) cc_final: 0.4329 (mtt) REVERT: B 244 ARG cc_start: 0.7471 (ttt-90) cc_final: 0.7033 (tpt-90) REVERT: B 273 TRP cc_start: 0.5878 (m100) cc_final: 0.5123 (m100) REVERT: B 454 LYS cc_start: 0.8348 (ttmm) cc_final: 0.7165 (tmtt) REVERT: B 475 ILE cc_start: 0.6492 (mt) cc_final: 0.6239 (mm) REVERT: B 476 ARG cc_start: 0.7245 (mtm110) cc_final: 0.6904 (mtm110) REVERT: B 506 ARG cc_start: 0.7974 (mtt-85) cc_final: 0.6111 (mtt-85) REVERT: B 525 ASN cc_start: 0.6408 (OUTLIER) cc_final: 0.3526 (p0) REVERT: B 625 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6106 (tp40) outliers start: 21 outliers final: 14 residues processed: 180 average time/residue: 0.3708 time to fit residues: 91.2634 Evaluate side-chains 184 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 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 625 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 40.0000 chunk 112 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 193 optimal weight: 50.0000 chunk 177 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 94 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.100 15590 Z= 0.644 Angle : 0.748 12.914 21250 Z= 0.376 Chirality : 0.050 0.355 2370 Planarity : 0.005 0.050 2780 Dihedral : 5.688 44.874 2454 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.36 % Allowed : 10.24 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 1936 helix: None (None), residues: 0 sheet: 0.11 (0.18), residues: 864 loop : -0.92 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP B 168 HIS 0.010 0.001 HIS A 559 PHE 0.022 0.002 PHE B 553 TYR 0.028 0.002 TYR A 560 ARG 0.008 0.001 ARG B 123 ********************** 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 193 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 1.642 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 385 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6708 (mt) REVERT: A 420 ARG cc_start: 0.7119 (mtm180) cc_final: 0.6772 (mtm180) REVERT: A 506 ARG cc_start: 0.8030 (mmt180) cc_final: 0.6211 (mmt180) REVERT: A 525 ASN cc_start: 0.7041 (OUTLIER) cc_final: 0.6535 (m110) REVERT: B 71 TYR cc_start: 0.7382 (m-80) cc_final: 0.7038 (m-10) REVERT: B 213 MET cc_start: 0.4517 (mtt) cc_final: 0.4259 (mtt) REVERT: B 244 ARG cc_start: 0.7446 (ttt-90) cc_final: 0.7143 (ttt180) REVERT: B 435 GLU cc_start: 0.7367 (tp30) cc_final: 0.7130 (tp30) REVERT: B 454 LYS cc_start: 0.8353 (ttmm) cc_final: 0.7089 (tmtt) REVERT: B 475 ILE cc_start: 0.6476 (mt) cc_final: 0.6059 (mm) REVERT: B 476 ARG cc_start: 0.7185 (mtm110) cc_final: 0.6793 (mtm110) REVERT: B 506 ARG cc_start: 0.8069 (mtt-85) cc_final: 0.6430 (mtt-85) REVERT: B 525 ASN cc_start: 0.6889 (OUTLIER) cc_final: 0.4207 (p0) REVERT: B 625 GLN cc_start: 0.6781 (tp-100) cc_final: 0.6183 (tp-100) REVERT: B 640 LYS cc_start: 0.4460 (pttt) cc_final: 0.4129 (pttt) REVERT: B 734 MET cc_start: 0.6371 (tpt) cc_final: 0.4080 (mmt) outliers start: 22 outliers final: 16 residues processed: 183 average time/residue: 0.3691 time to fit residues: 92.8244 Evaluate side-chains 187 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 671 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.0030 chunk 47 optimal weight: 0.9980 chunk 141 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 256 GLN B 326 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.246036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.202835 restraints weight = 24751.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.197393 restraints weight = 25826.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.200015 restraints weight = 20924.881| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.183 15590 Z= 0.518 Angle : 0.909 59.196 21250 Z= 0.517 Chirality : 0.048 0.434 2370 Planarity : 0.005 0.050 2780 Dihedral : 5.670 45.112 2454 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.49 % Allowed : 10.73 % Favored : 87.78 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 1936 helix: None (None), residues: 0 sheet: 0.08 (0.18), residues: 864 loop : -0.94 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP B 168 HIS 0.008 0.001 HIS A 559 PHE 0.019 0.002 PHE A 129 TYR 0.024 0.002 TYR A 560 ARG 0.006 0.000 ARG B 704 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3591.04 seconds wall clock time: 64 minutes 37.18 seconds (3877.18 seconds total)