Starting phenix.real_space_refine on Wed Mar 4 12:34:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lbe_23252/03_2026/7lbe_23252.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lbe_23252/03_2026/7lbe_23252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lbe_23252/03_2026/7lbe_23252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lbe_23252/03_2026/7lbe_23252.map" model { file = "/net/cci-nas-00/data/ceres_data/7lbe_23252/03_2026/7lbe_23252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lbe_23252/03_2026/7lbe_23252.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.033 sd= 0.634 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 8597 2.51 5 N 2258 2.21 5 O 2593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13511 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5234 Classifications: {'peptide': 652} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 618} Chain breaks: 3 Chain: "B" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1845 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 214} Chain breaks: 1 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2484 Classifications: {'peptide': 299} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 280} Chain breaks: 3 Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "F" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 927 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 850 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1001 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 151 Unusual residues: {'MAN': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 3.19, per 1000 atoms: 0.24 Number of scatterers: 13511 At special positions: 0 Unit cell: (98.6522, 177.033, 166.222, 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 63 16.00 O 2593 8.00 N 2258 7.00 C 8597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS B 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 141 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 167 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 111 " distance=2.03 Simple disulfide: pdb=" SG CYS F 45 " - pdb=" SG CYS F 119 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 45 " - pdb=" SG CYS H 119 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 801 " - " ASN A 192 " " NAG A 802 " - " ASN A 55 " " NAG A 803 " - " ASN A 700 " " NAG A 804 " - " ASN A 62 " " NAG A 805 " - " ASN A 67 " " NAG B 301 " - " ASN B 74 " " NAG C 601 " - " ASN C 155 " " NAG C 602 " - " ASN C 217 " " NAG C 603 " - " ASN C 240 " " NAG C 604 " - " ASN C 365 " " NAG C 605 " - " ASN C 452 " " NAG C 606 " - " ASN C 128 " " NAG C 607 " - " ASN C 85 " " NAG C 608 " - " ASN C 101 " " NAG C 610 " - " ASN C 383 " " NAG C 611 " - " ASN C 169 " " NAG D 1 " - " ASN C 160 " " NAG I 1 " - " ASN C 348 " " NAG J 1 " - " ASN C 431 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 609.9 milliseconds 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3138 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 24 sheets defined 31.3% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 95 through 98 Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.639A pdb=" N GLU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.772A pdb=" N SER A 290 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR A 291 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.716A pdb=" N TYR A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.975A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 358 " --> pdb=" O GLN A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 358' Processing helix chain 'A' and resid 363 through 385 Processing helix chain 'A' and resid 396 through 408 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.669A pdb=" N LEU A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 6.000A pdb=" N HIS A 433 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 435 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.644A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 3.676A pdb=" N HIS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 495 removed outlier: 3.729A pdb=" N CYS A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 644 through 648 removed outlier: 4.333A pdb=" N CYS A 647 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'B' and resid 46 through 56 removed outlier: 3.775A pdb=" N LEU B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.834A pdb=" N LEU B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 163 through 167 removed outlier: 4.080A pdb=" N LEU B 167 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 3.689A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 146 through 159 Processing helix chain 'C' and resid 198 through 215 Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.703A pdb=" N ARG C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 251 Processing helix chain 'C' and resid 321 through 335 Processing helix chain 'C' and resid 336 through 343 removed outlier: 6.553A pdb=" N GLU C 340 " --> pdb=" O TYR C 337 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 361 through 364 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 413 through 436 Processing helix chain 'C' and resid 452 through 457 removed outlier: 3.624A pdb=" N LEU C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.750A pdb=" N VAL E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 55 removed outlier: 3.906A pdb=" N TYR F 55 " --> pdb=" O PHE F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 88 Processing helix chain 'F' and resid 110 through 114 Processing helix chain 'G' and resid 107 through 111 removed outlier: 3.959A pdb=" N VAL G 111 " --> pdb=" O THR G 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 88 Processing helix chain 'H' and resid 110 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 66 removed outlier: 4.006A pdb=" N SER A 64 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLN A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ALA A 75 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N PHE B 181 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL B 178 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 194 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 removed outlier: 5.674A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 270 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 182 through 184 Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 197 Processing sheet with id=AA7, first strand: chain 'A' and resid 527 through 528 removed outlier: 4.460A pdb=" N LEU A 613 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 637 through 638 removed outlier: 7.158A pdb=" N THR A 637 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER A 652 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR A 668 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 654 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 666 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLU A 656 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.760A pdb=" N LEU B 82 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 100 removed outlier: 6.980A pdb=" N VAL B 99 " --> pdb=" O ARG C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 151 through 155 Processing sheet with id=AB3, first strand: chain 'C' and resid 93 through 95 Processing sheet with id=AB4, first strand: chain 'C' and resid 171 through 172 removed outlier: 3.529A pdb=" N ILE C 319 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 184 through 189 Processing sheet with id=AB6, first strand: chain 'E' and resid 27 through 30 Processing sheet with id=AB7, first strand: chain 'E' and resid 33 through 36 removed outlier: 6.489A pdb=" N LEU E 56 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR E 72 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP E 58 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 26 through 29 Processing sheet with id=AB9, first strand: chain 'F' and resid 33 through 34 removed outlier: 6.834A pdb=" N ILE F 57 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE F 73 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP F 59 " --> pdb=" O MET F 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 33 through 34 removed outlier: 4.061A pdb=" N ASP F 135 " --> pdb=" O ARG F 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 29 through 30 removed outlier: 3.670A pdb=" N ASP G 98 " --> pdb=" O SER G 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 33 through 35 removed outlier: 5.924A pdb=" N LEU G 34 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY G 112 " --> pdb=" O VAL G 132 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU G 61 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR G 77 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP G 63 " --> pdb=" O LEU G 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 26 through 30 Processing sheet with id=AC5, first strand: chain 'H' and resid 34 through 35 removed outlier: 3.870A pdb=" N SER H 56 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL H 57 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER H 73 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP H 59 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 34 through 35 removed outlier: 3.932A pdb=" N VAL H 142 " --> pdb=" O ARG H 121 " (cutoff:3.500A) 549 hydrogen bonds defined for protein. 1413 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: 2.33 Time building geometry restraints manager: 1.37 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: 4275 1.34 - 1.46: 3433 1.46 - 1.58: 6022 1.58 - 1.70: 0 1.70 - 1.82: 95 Bond restraints: 13825 Sorted by residual: bond pdb=" N ASP A 241 " pdb=" CA ASP A 241 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.51e-02 4.39e+03 4.21e+00 bond pdb=" C1 MAN D 6 " pdb=" C2 MAN D 6 " ideal model delta sigma weight residual 1.526 1.563 -0.037 2.00e-02 2.50e+03 3.48e+00 bond pdb=" N THR B 38 " pdb=" CA THR B 38 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N ASN C 81 " pdb=" CA ASN C 81 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N ASP G 24 " pdb=" CA ASP G 24 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 ... (remaining 13820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 18272 1.29 - 2.58: 393 2.58 - 3.87: 116 3.87 - 5.16: 20 5.16 - 6.45: 8 Bond angle restraints: 18809 Sorted by residual: angle pdb=" N ASP A 241 " pdb=" CA ASP A 241 " pdb=" C ASP A 241 " ideal model delta sigma weight residual 111.39 106.93 4.46 1.38e+00 5.25e-01 1.05e+01 angle pdb=" CA ASP A 241 " pdb=" C ASP A 241 " pdb=" O ASP A 241 " ideal model delta sigma weight residual 121.84 118.67 3.17 1.16e+00 7.43e-01 7.45e+00 angle pdb=" C ASN E 53 " pdb=" N ASN E 54 " pdb=" CA ASN E 54 " ideal model delta sigma weight residual 121.54 125.70 -4.16 1.91e+00 2.74e-01 4.75e+00 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 106.50 6.45 3.00e+00 1.11e-01 4.62e+00 angle pdb=" C3 MAN D 4 " pdb=" C2 MAN D 4 " pdb=" O2 MAN D 4 " ideal model delta sigma weight residual 111.77 105.38 6.39 3.00e+00 1.11e-01 4.54e+00 ... (remaining 18804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 8165 22.40 - 44.80: 386 44.80 - 67.20: 58 67.20 - 89.60: 27 89.60 - 112.00: 4 Dihedral angle restraints: 8640 sinusoidal: 3776 harmonic: 4864 Sorted by residual: dihedral pdb=" CB CYS A 571 " pdb=" SG CYS A 571 " pdb=" SG CYS A 624 " pdb=" CB CYS A 624 " ideal model delta sinusoidal sigma weight residual -86.00 -154.60 68.60 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS B 54 " pdb=" CB CYS B 54 " ideal model delta sinusoidal sigma weight residual -86.00 -147.75 61.75 1 1.00e+01 1.00e-02 5.06e+01 dihedral pdb=" CB CYS C 167 " pdb=" SG CYS C 167 " pdb=" SG CYS C 218 " pdb=" CB CYS C 218 " ideal model delta sinusoidal sigma weight residual 93.00 55.98 37.02 1 1.00e+01 1.00e-02 1.94e+01 ... (remaining 8637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1868 0.052 - 0.104: 259 0.104 - 0.156: 79 0.156 - 0.208: 4 0.208 - 0.260: 1 Chirality restraints: 2211 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C1 NAG C 610 " pdb=" ND2 ASN C 383 " pdb=" C2 NAG C 610 " pdb=" O5 NAG C 610 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" C1 NAG C 604 " pdb=" ND2 ASN C 365 " pdb=" C2 NAG C 604 " pdb=" O5 NAG C 604 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 2208 not shown) Planarity restraints: 2377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 124 " -0.152 9.50e-02 1.11e+02 6.86e-02 3.34e+00 pdb=" NE ARG F 124 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG F 124 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG F 124 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 124 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 92 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO B 93 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 180 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO C 181 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " -0.018 5.00e-02 4.00e+02 ... (remaining 2374 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1078 2.74 - 3.28: 13668 3.28 - 3.82: 21854 3.82 - 4.36: 27222 4.36 - 4.90: 46951 Nonbonded interactions: 110773 Sorted by model distance: nonbonded pdb=" NH2 ARG H 90 " pdb=" OD2 ASP H 113 " model vdw 2.200 3.120 nonbonded pdb=" O PHE H 52 " pdb=" NH2 ARG H 95 " model vdw 2.202 3.120 nonbonded pdb=" O VAL A 256 " pdb=" NH2 ARG A 264 " model vdw 2.222 3.120 nonbonded pdb=" OD2 ASP A 445 " pdb=" OH TYR H 125 " model vdw 2.271 3.040 nonbonded pdb=" O TRP A 167 " pdb=" NE2 GLN A 442 " model vdw 2.281 3.120 ... (remaining 110768 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 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.780 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.003 0.037 13865 Z= 0.148 Angle : 0.525 6.446 18915 Z= 0.247 Chirality : 0.042 0.260 2211 Planarity : 0.003 0.069 2358 Dihedral : 13.441 111.996 5460 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.22), residues: 1625 helix: 1.96 (0.27), residues: 391 sheet: 0.89 (0.27), residues: 381 loop : 0.30 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 124 TYR 0.015 0.001 TYR B 226 PHE 0.010 0.001 PHE F 123 TRP 0.009 0.001 TRP C 330 HIS 0.002 0.000 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00312 (13825) covalent geometry : angle 0.51485 (18809) SS BOND : bond 0.00198 ( 14) SS BOND : angle 0.82704 ( 28) hydrogen bonds : bond 0.17640 ( 538) hydrogen bonds : angle 7.06985 ( 1413) link_ALPHA1-2 : bond 0.00616 ( 1) link_ALPHA1-2 : angle 2.42962 ( 3) link_ALPHA1-3 : bond 0.00601 ( 1) link_ALPHA1-3 : angle 1.43327 ( 3) link_ALPHA1-6 : bond 0.00846 ( 1) link_ALPHA1-6 : angle 1.54189 ( 3) link_BETA1-4 : bond 0.00294 ( 4) link_BETA1-4 : angle 2.28198 ( 12) link_NAG-ASN : bond 0.00252 ( 19) link_NAG-ASN : angle 1.42368 ( 57) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8383 (mmm) cc_final: 0.8170 (mmm) REVERT: A 107 ASN cc_start: 0.8516 (m-40) cc_final: 0.8257 (m-40) REVERT: A 329 ARG cc_start: 0.8151 (mmp-170) cc_final: 0.7832 (mmp-170) REVERT: B 239 ASP cc_start: 0.8062 (t0) cc_final: 0.7783 (t0) REVERT: F 85 GLN cc_start: 0.7996 (tp40) cc_final: 0.7570 (tp40) REVERT: G 53 LEU cc_start: 0.9211 (tp) cc_final: 0.8965 (tp) REVERT: G 100 THR cc_start: 0.8549 (m) cc_final: 0.8289 (t) REVERT: H 96 ASP cc_start: 0.8217 (t70) cc_final: 0.7549 (t70) REVERT: H 100 ASN cc_start: 0.8980 (t0) cc_final: 0.8720 (t0) REVERT: H 128 PHE cc_start: 0.8751 (t80) cc_final: 0.8546 (t80) REVERT: H 141 ASP cc_start: 0.8859 (p0) cc_final: 0.8522 (p0) REVERT: H 145 GLN cc_start: 0.8422 (mm110) cc_final: 0.8208 (mm-40) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.5560 time to fit residues: 188.8757 Evaluate side-chains 232 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 451 HIS C 91 GLN C 215 GLN C 226 ASN C 358 ASN E 54 ASN F 26 GLN G 66 GLN G 81 ASN H 107 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.092034 restraints weight = 25099.434| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.60 r_work: 0.3064 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13865 Z= 0.198 Angle : 0.611 8.098 18915 Z= 0.309 Chirality : 0.045 0.190 2211 Planarity : 0.005 0.042 2358 Dihedral : 8.307 90.757 2378 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.04 % Allowed : 12.00 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.22), residues: 1625 helix: 1.86 (0.27), residues: 378 sheet: 0.80 (0.27), residues: 383 loop : 0.28 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 255 TYR 0.015 0.002 TYR B 226 PHE 0.017 0.002 PHE C 412 TRP 0.012 0.001 TRP C 330 HIS 0.008 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00467 (13825) covalent geometry : angle 0.59790 (18809) SS BOND : bond 0.00368 ( 14) SS BOND : angle 1.80315 ( 28) hydrogen bonds : bond 0.04233 ( 538) hydrogen bonds : angle 5.60235 ( 1413) link_ALPHA1-2 : bond 0.00241 ( 1) link_ALPHA1-2 : angle 1.89113 ( 3) link_ALPHA1-3 : bond 0.00440 ( 1) link_ALPHA1-3 : angle 2.25945 ( 3) link_ALPHA1-6 : bond 0.00486 ( 1) link_ALPHA1-6 : angle 2.29622 ( 3) link_BETA1-4 : bond 0.00288 ( 4) link_BETA1-4 : angle 2.10374 ( 12) link_NAG-ASN : bond 0.00475 ( 19) link_NAG-ASN : angle 1.62954 ( 57) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.8422 (mmp-170) cc_final: 0.8079 (mmp-170) REVERT: A 507 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8883 (tt) REVERT: A 598 LYS cc_start: 0.8269 (mtpt) cc_final: 0.8048 (mmmt) REVERT: A 619 ASP cc_start: 0.8212 (t0) cc_final: 0.7808 (t70) REVERT: A 669 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8828 (mtp) REVERT: A 680 ASP cc_start: 0.8661 (t0) cc_final: 0.8288 (t0) REVERT: B 46 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8432 (pm20) REVERT: B 225 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9014 (mm) REVERT: C 435 GLN cc_start: 0.8636 (tp40) cc_final: 0.8338 (tt0) REVERT: E 27 MET cc_start: 0.9077 (mmm) cc_final: 0.8851 (mmt) REVERT: E 29 GLN cc_start: 0.8757 (tt0) cc_final: 0.8184 (tt0) REVERT: E 47 ARG cc_start: 0.8638 (ttm-80) cc_final: 0.8368 (mtp-110) REVERT: E 65 LYS cc_start: 0.8262 (mtpt) cc_final: 0.8029 (mtmt) REVERT: F 42 LYS cc_start: 0.9319 (tptm) cc_final: 0.9041 (tptp) REVERT: F 85 GLN cc_start: 0.8614 (tp40) cc_final: 0.8146 (tp40) REVERT: F 124 ARG cc_start: 0.8487 (mmt-90) cc_final: 0.7715 (mmt180) REVERT: G 53 LEU cc_start: 0.9025 (tp) cc_final: 0.8816 (tp) REVERT: G 81 ASN cc_start: 0.8000 (m110) cc_final: 0.7598 (m110) REVERT: G 100 THR cc_start: 0.8556 (m) cc_final: 0.8147 (t) REVERT: H 100 ASN cc_start: 0.8880 (t0) cc_final: 0.8559 (t0) REVERT: H 128 PHE cc_start: 0.8791 (t80) cc_final: 0.8584 (t80) REVERT: H 141 ASP cc_start: 0.9005 (p0) cc_final: 0.8756 (p0) REVERT: H 145 GLN cc_start: 0.8976 (mm110) cc_final: 0.8685 (mm-40) outliers start: 30 outliers final: 14 residues processed: 255 average time/residue: 0.5334 time to fit residues: 150.0726 Evaluate side-chains 250 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain H residue 44 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.1980 chunk 81 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 0.0020 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 431 GLN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN C 360 HIS E 54 ASN F 54 ASN H 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.091187 restraints weight = 24997.527| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.58 r_work: 0.3096 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13865 Z= 0.154 Angle : 0.564 8.393 18915 Z= 0.284 Chirality : 0.044 0.186 2211 Planarity : 0.004 0.034 2358 Dihedral : 7.657 78.055 2378 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.86 % Allowed : 13.16 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.22), residues: 1625 helix: 1.74 (0.27), residues: 379 sheet: 0.61 (0.27), residues: 383 loop : 0.20 (0.23), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 124 TYR 0.021 0.001 TYR A 682 PHE 0.016 0.002 PHE B 105 TRP 0.012 0.001 TRP C 330 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00359 (13825) covalent geometry : angle 0.55181 (18809) SS BOND : bond 0.00248 ( 14) SS BOND : angle 1.50117 ( 28) hydrogen bonds : bond 0.03551 ( 538) hydrogen bonds : angle 5.15911 ( 1413) link_ALPHA1-2 : bond 0.00020 ( 1) link_ALPHA1-2 : angle 2.11435 ( 3) link_ALPHA1-3 : bond 0.00914 ( 1) link_ALPHA1-3 : angle 2.20531 ( 3) link_ALPHA1-6 : bond 0.00465 ( 1) link_ALPHA1-6 : angle 1.93964 ( 3) link_BETA1-4 : bond 0.00219 ( 4) link_BETA1-4 : angle 1.76182 ( 12) link_NAG-ASN : bond 0.00379 ( 19) link_NAG-ASN : angle 1.65428 ( 57) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.8593 (mmp-170) cc_final: 0.8226 (mmp-170) REVERT: A 507 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8947 (tt) REVERT: A 598 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7972 (mmmt) REVERT: A 619 ASP cc_start: 0.8246 (t0) cc_final: 0.7889 (t70) REVERT: A 680 ASP cc_start: 0.8604 (t0) cc_final: 0.8201 (t0) REVERT: B 64 LYS cc_start: 0.9372 (ttmt) cc_final: 0.9162 (ttpp) REVERT: B 117 ASP cc_start: 0.8376 (t0) cc_final: 0.8060 (t0) REVERT: B 225 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8983 (mm) REVERT: C 105 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8889 (p) REVERT: C 238 TYR cc_start: 0.7824 (t80) cc_final: 0.7622 (t80) REVERT: C 435 GLN cc_start: 0.8747 (tp40) cc_final: 0.8409 (tt0) REVERT: E 27 MET cc_start: 0.9171 (mmm) cc_final: 0.8926 (mmt) REVERT: E 29 GLN cc_start: 0.8725 (tt0) cc_final: 0.8307 (tt0) REVERT: E 47 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8267 (mtp-110) REVERT: E 65 LYS cc_start: 0.8330 (mtpt) cc_final: 0.8101 (mtmt) REVERT: E 77 LEU cc_start: 0.9356 (tp) cc_final: 0.9120 (tm) REVERT: F 85 GLN cc_start: 0.8617 (tp40) cc_final: 0.8181 (tp40) REVERT: F 124 ARG cc_start: 0.8558 (mmt-90) cc_final: 0.7715 (mmt180) REVERT: G 53 LEU cc_start: 0.9077 (tp) cc_final: 0.8876 (tp) REVERT: G 81 ASN cc_start: 0.8199 (m110) cc_final: 0.7785 (m110) REVERT: G 100 THR cc_start: 0.8524 (m) cc_final: 0.8080 (t) REVERT: H 100 ASN cc_start: 0.8956 (t0) cc_final: 0.8633 (t0) REVERT: H 141 ASP cc_start: 0.9014 (p0) cc_final: 0.8771 (p0) REVERT: H 145 GLN cc_start: 0.8963 (mm110) cc_final: 0.8722 (mm-40) outliers start: 42 outliers final: 22 residues processed: 257 average time/residue: 0.5359 time to fit residues: 152.0274 Evaluate side-chains 238 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 68 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 128 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 60 optimal weight: 0.0270 chunk 152 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN F 54 ASN H 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.095753 restraints weight = 25450.463| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.62 r_work: 0.3120 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13865 Z= 0.112 Angle : 0.541 12.809 18915 Z= 0.269 Chirality : 0.042 0.184 2211 Planarity : 0.004 0.033 2358 Dihedral : 7.091 62.772 2378 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.79 % Allowed : 14.79 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.22), residues: 1625 helix: 1.62 (0.27), residues: 388 sheet: 0.58 (0.27), residues: 381 loop : 0.19 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.013 0.001 TYR B 226 PHE 0.016 0.001 PHE B 105 TRP 0.009 0.001 TRP C 330 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00260 (13825) covalent geometry : angle 0.53091 (18809) SS BOND : bond 0.00219 ( 14) SS BOND : angle 0.93931 ( 28) hydrogen bonds : bond 0.03092 ( 538) hydrogen bonds : angle 4.94213 ( 1413) link_ALPHA1-2 : bond 0.00207 ( 1) link_ALPHA1-2 : angle 1.82401 ( 3) link_ALPHA1-3 : bond 0.01028 ( 1) link_ALPHA1-3 : angle 2.21865 ( 3) link_ALPHA1-6 : bond 0.00526 ( 1) link_ALPHA1-6 : angle 1.95457 ( 3) link_BETA1-4 : bond 0.00287 ( 4) link_BETA1-4 : angle 1.67650 ( 12) link_NAG-ASN : bond 0.00313 ( 19) link_NAG-ASN : angle 1.57894 ( 57) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.8599 (mmp-170) cc_final: 0.8216 (mmp-170) REVERT: A 527 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8246 (mmm160) REVERT: A 529 ASP cc_start: 0.8984 (p0) cc_final: 0.8746 (p0) REVERT: A 598 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7998 (mmmt) REVERT: A 619 ASP cc_start: 0.8252 (t0) cc_final: 0.7907 (t70) REVERT: A 680 ASP cc_start: 0.8532 (t0) cc_final: 0.8101 (t0) REVERT: B 64 LYS cc_start: 0.9374 (ttmt) cc_final: 0.9167 (ttpp) REVERT: C 320 MET cc_start: 0.8457 (mtt) cc_final: 0.8237 (mtm) REVERT: C 332 TYR cc_start: 0.9043 (m-80) cc_final: 0.8842 (m-10) REVERT: C 435 GLN cc_start: 0.8732 (tp40) cc_final: 0.8449 (tt0) REVERT: E 27 MET cc_start: 0.9191 (mmm) cc_final: 0.8890 (mmt) REVERT: E 29 GLN cc_start: 0.8680 (tt0) cc_final: 0.8350 (tt0) REVERT: E 47 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8266 (mtp-110) REVERT: E 65 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8135 (mtmt) REVERT: E 77 LEU cc_start: 0.9357 (tp) cc_final: 0.9116 (tm) REVERT: E 102 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8032 (mm-40) REVERT: F 42 LYS cc_start: 0.9112 (tptm) cc_final: 0.8676 (tptp) REVERT: F 85 GLN cc_start: 0.8593 (tp40) cc_final: 0.8171 (tp40) REVERT: G 28 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7954 (p) REVERT: G 53 LEU cc_start: 0.9082 (tp) cc_final: 0.8863 (tp) REVERT: G 81 ASN cc_start: 0.8239 (m110) cc_final: 0.7922 (m110) REVERT: G 100 THR cc_start: 0.8457 (m) cc_final: 0.7983 (t) REVERT: H 100 ASN cc_start: 0.8967 (t0) cc_final: 0.8636 (t0) REVERT: H 141 ASP cc_start: 0.8986 (p0) cc_final: 0.8742 (p0) outliers start: 41 outliers final: 15 residues processed: 245 average time/residue: 0.5338 time to fit residues: 144.1368 Evaluate side-chains 239 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 222 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 68 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 14 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 chunk 136 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN E 54 ASN H 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.112627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094025 restraints weight = 25350.822| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.61 r_work: 0.3104 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13865 Z= 0.135 Angle : 0.553 12.086 18915 Z= 0.275 Chirality : 0.043 0.196 2211 Planarity : 0.004 0.045 2358 Dihedral : 6.769 58.952 2378 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.14 % Allowed : 15.95 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.22), residues: 1625 helix: 1.64 (0.27), residues: 386 sheet: 0.53 (0.27), residues: 386 loop : 0.19 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 124 TYR 0.021 0.001 TYR A 682 PHE 0.015 0.001 PHE B 105 TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00317 (13825) covalent geometry : angle 0.54186 (18809) SS BOND : bond 0.00255 ( 14) SS BOND : angle 1.27727 ( 28) hydrogen bonds : bond 0.03187 ( 538) hydrogen bonds : angle 4.88645 ( 1413) link_ALPHA1-2 : bond 0.00188 ( 1) link_ALPHA1-2 : angle 1.94095 ( 3) link_ALPHA1-3 : bond 0.00992 ( 1) link_ALPHA1-3 : angle 2.04794 ( 3) link_ALPHA1-6 : bond 0.00439 ( 1) link_ALPHA1-6 : angle 2.08040 ( 3) link_BETA1-4 : bond 0.00162 ( 4) link_BETA1-4 : angle 1.50049 ( 12) link_NAG-ASN : bond 0.00354 ( 19) link_NAG-ASN : angle 1.60357 ( 57) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.8626 (mmp-170) cc_final: 0.8275 (mmp-170) REVERT: A 527 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8475 (mmm160) REVERT: A 529 ASP cc_start: 0.9015 (p0) cc_final: 0.8788 (p0) REVERT: A 598 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7894 (mmmt) REVERT: A 619 ASP cc_start: 0.8276 (t0) cc_final: 0.7920 (t70) REVERT: A 680 ASP cc_start: 0.8504 (t0) cc_final: 0.8083 (t0) REVERT: B 46 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8115 (pm20) REVERT: B 64 LYS cc_start: 0.9368 (ttmt) cc_final: 0.9159 (ttpp) REVERT: B 146 ASP cc_start: 0.8388 (p0) cc_final: 0.8153 (p0) REVERT: C 320 MET cc_start: 0.8550 (mtt) cc_final: 0.8339 (mtm) REVERT: C 332 TYR cc_start: 0.9098 (m-80) cc_final: 0.8871 (m-10) REVERT: C 435 GLN cc_start: 0.8735 (tp40) cc_final: 0.8454 (tt0) REVERT: E 27 MET cc_start: 0.9210 (mmm) cc_final: 0.8893 (mmt) REVERT: E 29 GLN cc_start: 0.8685 (tt0) cc_final: 0.8409 (tt0) REVERT: E 47 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.8240 (mtp-110) REVERT: E 50 GLN cc_start: 0.8692 (mt0) cc_final: 0.8447 (mm-40) REVERT: E 65 LYS cc_start: 0.8357 (mtpt) cc_final: 0.8112 (mtmt) REVERT: E 77 LEU cc_start: 0.9367 (tp) cc_final: 0.9126 (tm) REVERT: F 42 LYS cc_start: 0.9239 (tptm) cc_final: 0.8917 (tptp) REVERT: F 85 GLN cc_start: 0.8607 (tp40) cc_final: 0.8177 (tp40) REVERT: F 124 ARG cc_start: 0.8625 (mmt-90) cc_final: 0.7768 (mmt180) REVERT: F 138 GLN cc_start: 0.9083 (pm20) cc_final: 0.8832 (pm20) REVERT: G 53 LEU cc_start: 0.9103 (tp) cc_final: 0.8873 (tp) REVERT: G 81 ASN cc_start: 0.8287 (m110) cc_final: 0.7994 (m110) REVERT: G 100 THR cc_start: 0.8490 (m) cc_final: 0.8013 (t) REVERT: H 100 ASN cc_start: 0.8981 (t0) cc_final: 0.8628 (t0) REVERT: H 141 ASP cc_start: 0.8984 (p0) cc_final: 0.8756 (p0) outliers start: 46 outliers final: 22 residues processed: 255 average time/residue: 0.5577 time to fit residues: 156.9904 Evaluate side-chains 240 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 68 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 50 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 126 optimal weight: 0.0570 chunk 80 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN E 102 GLN H 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.113934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.095208 restraints weight = 25319.587| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.66 r_work: 0.3119 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13865 Z= 0.114 Angle : 0.550 12.098 18915 Z= 0.272 Chirality : 0.043 0.250 2211 Planarity : 0.004 0.031 2358 Dihedral : 6.432 59.870 2378 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.14 % Allowed : 16.56 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.22), residues: 1625 helix: 1.64 (0.27), residues: 386 sheet: 0.56 (0.27), residues: 386 loop : 0.20 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 124 TYR 0.013 0.001 TYR B 226 PHE 0.015 0.001 PHE B 105 TRP 0.010 0.001 TRP C 330 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00266 (13825) covalent geometry : angle 0.53936 (18809) SS BOND : bond 0.00218 ( 14) SS BOND : angle 1.30683 ( 28) hydrogen bonds : bond 0.03082 ( 538) hydrogen bonds : angle 4.80057 ( 1413) link_ALPHA1-2 : bond 0.00257 ( 1) link_ALPHA1-2 : angle 1.94756 ( 3) link_ALPHA1-3 : bond 0.01174 ( 1) link_ALPHA1-3 : angle 1.95314 ( 3) link_ALPHA1-6 : bond 0.00513 ( 1) link_ALPHA1-6 : angle 1.87125 ( 3) link_BETA1-4 : bond 0.00274 ( 4) link_BETA1-4 : angle 1.40481 ( 12) link_NAG-ASN : bond 0.00316 ( 19) link_NAG-ASN : angle 1.55987 ( 57) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 GLU cc_start: 0.8705 (mp0) cc_final: 0.8250 (mp0) REVERT: A 329 ARG cc_start: 0.8619 (mmp-170) cc_final: 0.8263 (mmp-170) REVERT: A 527 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8239 (mmm160) REVERT: A 598 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7858 (mmmt) REVERT: A 619 ASP cc_start: 0.8259 (t0) cc_final: 0.7906 (t70) REVERT: A 656 GLU cc_start: 0.8712 (tt0) cc_final: 0.8497 (tt0) REVERT: A 679 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8203 (mp) REVERT: A 680 ASP cc_start: 0.8483 (t0) cc_final: 0.8048 (t0) REVERT: B 46 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8201 (pm20) REVERT: B 64 LYS cc_start: 0.9351 (ttmt) cc_final: 0.9137 (ttpp) REVERT: C 84 MET cc_start: 0.7449 (ptm) cc_final: 0.7193 (ptt) REVERT: C 332 TYR cc_start: 0.9090 (m-80) cc_final: 0.8852 (m-10) REVERT: C 435 GLN cc_start: 0.8751 (tp40) cc_final: 0.8486 (tt0) REVERT: E 27 MET cc_start: 0.9210 (mmm) cc_final: 0.8884 (mmt) REVERT: E 29 GLN cc_start: 0.8693 (tt0) cc_final: 0.8477 (tt0) REVERT: E 47 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.8198 (mtp-110) REVERT: E 50 GLN cc_start: 0.8728 (mt0) cc_final: 0.8384 (mm-40) REVERT: E 65 LYS cc_start: 0.8397 (mtpt) cc_final: 0.8143 (mtmt) REVERT: E 77 LEU cc_start: 0.9359 (tp) cc_final: 0.9122 (tm) REVERT: F 42 LYS cc_start: 0.9233 (tptm) cc_final: 0.8904 (tptp) REVERT: F 85 GLN cc_start: 0.8582 (tp40) cc_final: 0.8153 (tp40) REVERT: F 124 ARG cc_start: 0.8621 (mmt-90) cc_final: 0.7746 (mmt180) REVERT: F 138 GLN cc_start: 0.9017 (pm20) cc_final: 0.8812 (pm20) REVERT: G 53 LEU cc_start: 0.9089 (tp) cc_final: 0.8857 (tp) REVERT: G 81 ASN cc_start: 0.8283 (m110) cc_final: 0.7985 (m110) REVERT: G 100 THR cc_start: 0.8469 (m) cc_final: 0.7990 (t) REVERT: H 141 ASP cc_start: 0.8973 (p0) cc_final: 0.8742 (p0) outliers start: 46 outliers final: 21 residues processed: 263 average time/residue: 0.5419 time to fit residues: 157.6190 Evaluate side-chains 249 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 68 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 109 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN C 447 HIS E 54 ASN H 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.113183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094520 restraints weight = 25463.884| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.61 r_work: 0.3106 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13865 Z= 0.150 Angle : 0.564 11.630 18915 Z= 0.281 Chirality : 0.044 0.211 2211 Planarity : 0.004 0.034 2358 Dihedral : 6.408 58.943 2378 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.86 % Allowed : 16.97 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.21), residues: 1625 helix: 1.59 (0.27), residues: 386 sheet: 0.50 (0.27), residues: 388 loop : 0.14 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 42 TYR 0.021 0.001 TYR A 682 PHE 0.013 0.001 PHE B 105 TRP 0.010 0.001 TRP C 330 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00354 (13825) covalent geometry : angle 0.55252 (18809) SS BOND : bond 0.00265 ( 14) SS BOND : angle 1.44390 ( 28) hydrogen bonds : bond 0.03253 ( 538) hydrogen bonds : angle 4.86644 ( 1413) link_ALPHA1-2 : bond 0.00034 ( 1) link_ALPHA1-2 : angle 1.91009 ( 3) link_ALPHA1-3 : bond 0.01086 ( 1) link_ALPHA1-3 : angle 2.53768 ( 3) link_ALPHA1-6 : bond 0.00349 ( 1) link_ALPHA1-6 : angle 2.07546 ( 3) link_BETA1-4 : bond 0.00154 ( 4) link_BETA1-4 : angle 1.42261 ( 12) link_NAG-ASN : bond 0.00344 ( 19) link_NAG-ASN : angle 1.64110 ( 57) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: A 329 ARG cc_start: 0.8573 (mmp-170) cc_final: 0.8278 (mmp-170) REVERT: A 507 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8960 (tt) REVERT: A 527 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8478 (mmm160) REVERT: A 619 ASP cc_start: 0.8266 (t0) cc_final: 0.7923 (t70) REVERT: A 679 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8226 (mp) REVERT: A 680 ASP cc_start: 0.8457 (t0) cc_final: 0.8050 (t0) REVERT: B 46 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8043 (pm20) REVERT: B 64 LYS cc_start: 0.9349 (ttmt) cc_final: 0.9137 (ttpp) REVERT: C 84 MET cc_start: 0.7523 (ptm) cc_final: 0.7247 (ptt) REVERT: C 435 GLN cc_start: 0.8748 (tp40) cc_final: 0.8458 (tt0) REVERT: E 27 MET cc_start: 0.9208 (mmm) cc_final: 0.8862 (mmt) REVERT: E 47 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.8187 (mtp-110) REVERT: E 50 GLN cc_start: 0.8633 (mt0) cc_final: 0.8267 (mm-40) REVERT: E 65 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8066 (mtmt) REVERT: E 77 LEU cc_start: 0.9371 (tp) cc_final: 0.9125 (tm) REVERT: F 85 GLN cc_start: 0.8597 (tp40) cc_final: 0.8169 (tp40) REVERT: F 138 GLN cc_start: 0.9068 (pm20) cc_final: 0.8755 (pm20) REVERT: G 53 LEU cc_start: 0.9084 (tp) cc_final: 0.8857 (tp) REVERT: G 81 ASN cc_start: 0.8306 (m110) cc_final: 0.8025 (m110) REVERT: G 100 THR cc_start: 0.8538 (m) cc_final: 0.8081 (t) REVERT: G 105 ARG cc_start: 0.7031 (mmp80) cc_final: 0.6775 (mtm110) REVERT: H 141 ASP cc_start: 0.8978 (p0) cc_final: 0.8706 (p0) outliers start: 42 outliers final: 24 residues processed: 260 average time/residue: 0.5531 time to fit residues: 158.4094 Evaluate side-chains 250 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 68 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 59 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 115 optimal weight: 0.0020 chunk 160 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 145 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.113534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.095174 restraints weight = 25059.706| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.63 r_work: 0.3122 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13865 Z= 0.117 Angle : 0.559 11.722 18915 Z= 0.278 Chirality : 0.043 0.194 2211 Planarity : 0.004 0.046 2358 Dihedral : 6.270 57.967 2378 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.39 % Allowed : 17.93 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.22), residues: 1625 helix: 1.64 (0.27), residues: 385 sheet: 0.52 (0.27), residues: 388 loop : 0.16 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 124 TYR 0.012 0.001 TYR B 226 PHE 0.015 0.001 PHE B 105 TRP 0.011 0.001 TRP C 330 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00275 (13825) covalent geometry : angle 0.54990 (18809) SS BOND : bond 0.00208 ( 14) SS BOND : angle 1.18473 ( 28) hydrogen bonds : bond 0.03006 ( 538) hydrogen bonds : angle 4.76789 ( 1413) link_ALPHA1-2 : bond 0.00023 ( 1) link_ALPHA1-2 : angle 2.00346 ( 3) link_ALPHA1-3 : bond 0.01166 ( 1) link_ALPHA1-3 : angle 1.59001 ( 3) link_ALPHA1-6 : bond 0.00520 ( 1) link_ALPHA1-6 : angle 1.72361 ( 3) link_BETA1-4 : bond 0.00236 ( 4) link_BETA1-4 : angle 1.35513 ( 12) link_NAG-ASN : bond 0.00296 ( 19) link_NAG-ASN : angle 1.56873 ( 57) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: A 329 ARG cc_start: 0.8556 (mmp-170) cc_final: 0.8260 (mmp-170) REVERT: A 527 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8259 (mmm160) REVERT: A 619 ASP cc_start: 0.8262 (t0) cc_final: 0.7934 (t70) REVERT: A 679 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8228 (mp) REVERT: A 680 ASP cc_start: 0.8392 (t0) cc_final: 0.7982 (t0) REVERT: C 84 MET cc_start: 0.7438 (ptm) cc_final: 0.7179 (ptt) REVERT: C 435 GLN cc_start: 0.8746 (tp40) cc_final: 0.8462 (tt0) REVERT: E 27 MET cc_start: 0.9199 (mmm) cc_final: 0.8870 (mmt) REVERT: E 47 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.8158 (mtp-110) REVERT: E 50 GLN cc_start: 0.8725 (mt0) cc_final: 0.8390 (mm-40) REVERT: E 65 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8094 (mtmt) REVERT: E 77 LEU cc_start: 0.9364 (tp) cc_final: 0.9123 (tm) REVERT: F 42 LYS cc_start: 0.9034 (tptm) cc_final: 0.8714 (tptp) REVERT: F 85 GLN cc_start: 0.8574 (tp40) cc_final: 0.8141 (tp40) REVERT: F 138 GLN cc_start: 0.9002 (pm20) cc_final: 0.8787 (pm20) REVERT: G 32 LEU cc_start: 0.9089 (mt) cc_final: 0.8832 (mm) REVERT: G 53 LEU cc_start: 0.9074 (tp) cc_final: 0.8841 (tp) REVERT: G 81 ASN cc_start: 0.8277 (m110) cc_final: 0.8070 (m110) REVERT: G 100 THR cc_start: 0.8518 (m) cc_final: 0.8066 (t) REVERT: H 141 ASP cc_start: 0.8968 (p0) cc_final: 0.8620 (p0) outliers start: 35 outliers final: 21 residues processed: 250 average time/residue: 0.5226 time to fit residues: 143.9842 Evaluate side-chains 244 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 68 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 140 optimal weight: 0.0870 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN E 54 ASN E 102 GLN G 56 ASN G 66 GLN H 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.092772 restraints weight = 25497.875| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.64 r_work: 0.3086 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13865 Z= 0.174 Angle : 0.595 11.047 18915 Z= 0.295 Chirality : 0.044 0.215 2211 Planarity : 0.004 0.038 2358 Dihedral : 6.408 56.827 2378 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.52 % Allowed : 18.47 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.21), residues: 1625 helix: 1.58 (0.27), residues: 387 sheet: 0.45 (0.27), residues: 385 loop : 0.10 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 124 TYR 0.021 0.001 TYR A 682 PHE 0.013 0.001 PHE B 105 TRP 0.013 0.001 TRP C 330 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00410 (13825) covalent geometry : angle 0.58401 (18809) SS BOND : bond 0.00293 ( 14) SS BOND : angle 1.30180 ( 28) hydrogen bonds : bond 0.03336 ( 538) hydrogen bonds : angle 4.85095 ( 1413) link_ALPHA1-2 : bond 0.00295 ( 1) link_ALPHA1-2 : angle 2.05722 ( 3) link_ALPHA1-3 : bond 0.00959 ( 1) link_ALPHA1-3 : angle 1.75294 ( 3) link_ALPHA1-6 : bond 0.00290 ( 1) link_ALPHA1-6 : angle 2.10138 ( 3) link_BETA1-4 : bond 0.00097 ( 4) link_BETA1-4 : angle 1.48404 ( 12) link_NAG-ASN : bond 0.00430 ( 19) link_NAG-ASN : angle 1.71916 ( 57) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.8633 (mmp-170) cc_final: 0.8305 (mmp-170) REVERT: A 507 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8967 (tt) REVERT: A 527 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8430 (mmm160) REVERT: A 619 ASP cc_start: 0.8277 (t0) cc_final: 0.7930 (t70) REVERT: A 680 ASP cc_start: 0.8434 (t0) cc_final: 0.8030 (t0) REVERT: B 46 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8050 (pm20) REVERT: E 27 MET cc_start: 0.9234 (mmm) cc_final: 0.8930 (mmt) REVERT: E 50 GLN cc_start: 0.8631 (mt0) cc_final: 0.8259 (mm-40) REVERT: E 65 LYS cc_start: 0.8373 (mtpt) cc_final: 0.8086 (mtmt) REVERT: E 77 LEU cc_start: 0.9366 (tp) cc_final: 0.9117 (tm) REVERT: F 42 LYS cc_start: 0.9138 (tptm) cc_final: 0.8851 (tptp) REVERT: F 85 GLN cc_start: 0.8577 (tp40) cc_final: 0.8103 (tp40) REVERT: F 124 ARG cc_start: 0.8600 (mmt90) cc_final: 0.8353 (mmt-90) REVERT: F 138 GLN cc_start: 0.9078 (pm20) cc_final: 0.8775 (pm20) REVERT: G 32 LEU cc_start: 0.9092 (mt) cc_final: 0.8854 (mm) REVERT: G 53 LEU cc_start: 0.9083 (tp) cc_final: 0.8848 (tp) REVERT: G 100 THR cc_start: 0.8555 (m) cc_final: 0.8098 (t) REVERT: G 105 ARG cc_start: 0.7047 (mmp80) cc_final: 0.6816 (mtm110) REVERT: H 141 ASP cc_start: 0.8984 (p0) cc_final: 0.8737 (p0) outliers start: 37 outliers final: 26 residues processed: 241 average time/residue: 0.5491 time to fit residues: 146.0279 Evaluate side-chains 245 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 68 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 99 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 151 optimal weight: 0.0370 chunk 16 optimal weight: 0.9990 chunk 103 optimal weight: 0.0060 chunk 20 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 overall best weight: 0.5274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN G 56 ASN G 66 GLN H 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.113488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.094871 restraints weight = 25254.177| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.63 r_work: 0.3121 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13865 Z= 0.117 Angle : 0.575 10.354 18915 Z= 0.287 Chirality : 0.043 0.203 2211 Planarity : 0.004 0.039 2358 Dihedral : 6.215 55.737 2378 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.04 % Allowed : 19.02 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.21), residues: 1625 helix: 1.64 (0.27), residues: 386 sheet: 0.47 (0.27), residues: 385 loop : 0.14 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 124 TYR 0.011 0.001 TYR B 226 PHE 0.014 0.001 PHE B 105 TRP 0.010 0.001 TRP C 462 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00275 (13825) covalent geometry : angle 0.56645 (18809) SS BOND : bond 0.00189 ( 14) SS BOND : angle 1.14316 ( 28) hydrogen bonds : bond 0.02973 ( 538) hydrogen bonds : angle 4.71794 ( 1413) link_ALPHA1-2 : bond 0.00026 ( 1) link_ALPHA1-2 : angle 2.07181 ( 3) link_ALPHA1-3 : bond 0.01255 ( 1) link_ALPHA1-3 : angle 1.53311 ( 3) link_ALPHA1-6 : bond 0.00547 ( 1) link_ALPHA1-6 : angle 1.65936 ( 3) link_BETA1-4 : bond 0.00331 ( 4) link_BETA1-4 : angle 1.36531 ( 12) link_NAG-ASN : bond 0.00296 ( 19) link_NAG-ASN : angle 1.54213 ( 57) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8272 (mp0) REVERT: A 329 ARG cc_start: 0.8590 (mmp-170) cc_final: 0.8275 (mmp-170) REVERT: A 527 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8240 (mmm160) REVERT: A 619 ASP cc_start: 0.8258 (t0) cc_final: 0.7936 (t70) REVERT: A 656 GLU cc_start: 0.8634 (tt0) cc_final: 0.8411 (tt0) REVERT: A 680 ASP cc_start: 0.8405 (t0) cc_final: 0.7996 (t0) REVERT: B 46 GLU cc_start: 0.8738 (mm-30) cc_final: 0.7953 (pm20) REVERT: C 84 MET cc_start: 0.7506 (ptm) cc_final: 0.7289 (ptt) REVERT: C 91 GLN cc_start: 0.8728 (tt0) cc_final: 0.8488 (tt0) REVERT: C 435 GLN cc_start: 0.8713 (tp40) cc_final: 0.8412 (tt0) REVERT: E 27 MET cc_start: 0.9187 (mmm) cc_final: 0.8879 (mmt) REVERT: E 50 GLN cc_start: 0.8694 (mt0) cc_final: 0.8395 (mm-40) REVERT: E 65 LYS cc_start: 0.8411 (mtpt) cc_final: 0.8113 (mtmt) REVERT: E 77 LEU cc_start: 0.9351 (tp) cc_final: 0.9113 (tm) REVERT: F 42 LYS cc_start: 0.9013 (tptm) cc_final: 0.8717 (tptp) REVERT: F 85 GLN cc_start: 0.8545 (tp40) cc_final: 0.8091 (tp40) REVERT: F 124 ARG cc_start: 0.8567 (mmt90) cc_final: 0.8324 (mmt-90) REVERT: F 138 GLN cc_start: 0.9001 (pm20) cc_final: 0.8801 (pm20) REVERT: G 32 LEU cc_start: 0.9034 (mt) cc_final: 0.8795 (mm) REVERT: G 100 THR cc_start: 0.8524 (m) cc_final: 0.8071 (t) REVERT: G 105 ARG cc_start: 0.6990 (mmp80) cc_final: 0.6767 (mtm110) REVERT: H 51 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8482 (t) REVERT: H 106 MET cc_start: 0.8950 (mtm) cc_final: 0.8738 (mtp) REVERT: H 141 ASP cc_start: 0.8975 (p0) cc_final: 0.8747 (p0) outliers start: 30 outliers final: 19 residues processed: 245 average time/residue: 0.5555 time to fit residues: 149.8883 Evaluate side-chains 238 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 68 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 111 optimal weight: 0.0570 chunk 121 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 145 optimal weight: 0.0070 chunk 115 optimal weight: 0.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS C 358 ASN E 54 ASN G 56 ASN H 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097189 restraints weight = 25538.584| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.60 r_work: 0.3134 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13865 Z= 0.111 Angle : 0.565 12.171 18915 Z= 0.280 Chirality : 0.043 0.192 2211 Planarity : 0.004 0.040 2358 Dihedral : 6.127 53.254 2378 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.84 % Allowed : 19.36 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.22), residues: 1625 helix: 1.66 (0.27), residues: 384 sheet: 0.51 (0.27), residues: 385 loop : 0.19 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 124 TYR 0.024 0.001 TYR A 682 PHE 0.011 0.001 PHE B 105 TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00261 (13825) covalent geometry : angle 0.55596 (18809) SS BOND : bond 0.00189 ( 14) SS BOND : angle 1.13656 ( 28) hydrogen bonds : bond 0.02896 ( 538) hydrogen bonds : angle 4.64195 ( 1413) link_ALPHA1-2 : bond 0.00028 ( 1) link_ALPHA1-2 : angle 2.03131 ( 3) link_ALPHA1-3 : bond 0.01151 ( 1) link_ALPHA1-3 : angle 1.49234 ( 3) link_ALPHA1-6 : bond 0.00462 ( 1) link_ALPHA1-6 : angle 1.59704 ( 3) link_BETA1-4 : bond 0.00271 ( 4) link_BETA1-4 : angle 1.33667 ( 12) link_NAG-ASN : bond 0.00308 ( 19) link_NAG-ASN : angle 1.53577 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5345.74 seconds wall clock time: 91 minutes 40.45 seconds (5500.45 seconds total)