Starting phenix.real_space_refine on Thu Jul 31 17:04:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lbe_23252/07_2025/7lbe_23252.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lbe_23252/07_2025/7lbe_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_23252/07_2025/7lbe_23252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lbe_23252/07_2025/7lbe_23252.map" model { file = "/net/cci-nas-00/data/ceres_data/7lbe_23252/07_2025/7lbe_23252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lbe_23252/07_2025/7lbe_23252.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.033 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.99, per 1000 atoms: 0.59 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: 3.97 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.94 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: 5.09 Time building geometry restraints manager: 4.65 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.680 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.230 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (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 TRP 0.009 0.001 TRP C 330 HIS 0.002 0.000 HIS A 289 PHE 0.010 0.001 PHE F 123 TYR 0.015 0.001 TYR B 226 ARG 0.012 0.000 ARG F 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 19) link_NAG-ASN : angle 1.42368 ( 57) 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_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) hydrogen bonds : bond 0.17640 ( 538) hydrogen bonds : angle 7.06985 ( 1413) SS BOND : bond 0.00198 ( 14) SS BOND : angle 0.82704 ( 28) covalent geometry : bond 0.00312 (13825) covalent geometry : angle 0.51485 (18809) *********************** 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 : 1.539 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: 0.8966 (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: 1.1771 time to fit residues: 401.4269 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 : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 126 optimal weight: 0.0870 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 431 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.111005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.092900 restraints weight = 24918.217| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.61 r_work: 0.3079 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13865 Z= 0.168 Angle : 0.605 8.347 18915 Z= 0.305 Chirality : 0.045 0.190 2211 Planarity : 0.005 0.050 2358 Dihedral : 8.160 86.660 2378 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.98 % Allowed : 11.93 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.22), residues: 1625 helix: 1.87 (0.27), residues: 378 sheet: 0.81 (0.27), residues: 383 loop : 0.30 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 330 HIS 0.008 0.001 HIS A 451 PHE 0.017 0.002 PHE C 412 TYR 0.015 0.002 TYR B 226 ARG 0.008 0.001 ARG B 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 19) link_NAG-ASN : angle 1.58991 ( 57) link_ALPHA1-6 : bond 0.00137 ( 1) link_ALPHA1-6 : angle 2.33450 ( 3) link_BETA1-4 : bond 0.00340 ( 4) link_BETA1-4 : angle 2.04760 ( 12) link_ALPHA1-2 : bond 0.00231 ( 1) link_ALPHA1-2 : angle 1.95370 ( 3) link_ALPHA1-3 : bond 0.00849 ( 1) link_ALPHA1-3 : angle 2.59158 ( 3) hydrogen bonds : bond 0.03869 ( 538) hydrogen bonds : angle 5.52765 ( 1413) SS BOND : bond 0.00353 ( 14) SS BOND : angle 1.77241 ( 28) covalent geometry : bond 0.00391 (13825) covalent geometry : angle 0.59217 (18809) *********************** 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 271 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.8409 (mmp-170) cc_final: 0.8068 (mmp-170) REVERT: A 507 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8871 (tt) REVERT: A 619 ASP cc_start: 0.8201 (t0) cc_final: 0.7813 (t70) REVERT: A 680 ASP cc_start: 0.8669 (t0) cc_final: 0.8296 (t0) REVERT: B 46 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8427 (pm20) REVERT: B 225 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9017 (mm) REVERT: C 435 GLN cc_start: 0.8687 (tp40) cc_final: 0.8365 (tt0) REVERT: E 27 MET cc_start: 0.9068 (mmm) cc_final: 0.8837 (mmt) REVERT: E 29 GLN cc_start: 0.8745 (tt0) cc_final: 0.8176 (tt0) REVERT: E 47 ARG cc_start: 0.8618 (ttm-80) cc_final: 0.8370 (mtp-110) REVERT: E 65 LYS cc_start: 0.8243 (mtpt) cc_final: 0.8009 (mtmt) REVERT: F 42 LYS cc_start: 0.9291 (tptm) cc_final: 0.9006 (tptp) REVERT: F 85 GLN cc_start: 0.8590 (tp40) cc_final: 0.8120 (tp40) REVERT: F 123 PHE cc_start: 0.7935 (t80) cc_final: 0.7686 (t80) REVERT: F 124 ARG cc_start: 0.8597 (mmt-90) cc_final: 0.7723 (mmt180) REVERT: G 53 LEU cc_start: 0.9019 (tp) cc_final: 0.8810 (tp) REVERT: G 81 ASN cc_start: 0.7993 (m110) cc_final: 0.7569 (m110) REVERT: G 100 THR cc_start: 0.8508 (m) cc_final: 0.8100 (t) REVERT: H 100 ASN cc_start: 0.8861 (t0) cc_final: 0.8550 (t0) REVERT: H 128 PHE cc_start: 0.8763 (t80) cc_final: 0.8548 (t80) REVERT: H 141 ASP cc_start: 0.9006 (p0) cc_final: 0.8753 (p0) REVERT: H 145 GLN cc_start: 0.8979 (mm110) cc_final: 0.8683 (mm-40) outliers start: 29 outliers final: 12 residues processed: 256 average time/residue: 1.1297 time to fit residues: 319.9602 Evaluate side-chains 246 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 232 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 B residue 72 LEU 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 146 SER 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 H residue 44 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 60 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 73 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 119 GLN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN E 54 ASN F 54 ASN H 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.092760 restraints weight = 24844.207| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.59 r_work: 0.3090 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13865 Z= 0.125 Angle : 0.547 8.480 18915 Z= 0.275 Chirality : 0.043 0.180 2211 Planarity : 0.004 0.034 2358 Dihedral : 7.482 73.096 2378 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.39 % Allowed : 13.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.22), residues: 1625 helix: 1.80 (0.27), residues: 379 sheet: 0.66 (0.27), residues: 383 loop : 0.25 (0.23), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 330 HIS 0.004 0.001 HIS A 213 PHE 0.014 0.001 PHE B 105 TYR 0.020 0.001 TYR A 682 ARG 0.006 0.000 ARG F 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 19) link_NAG-ASN : angle 1.58451 ( 57) link_ALPHA1-6 : bond 0.00570 ( 1) link_ALPHA1-6 : angle 1.86012 ( 3) link_BETA1-4 : bond 0.00301 ( 4) link_BETA1-4 : angle 1.72261 ( 12) link_ALPHA1-2 : bond 0.00158 ( 1) link_ALPHA1-2 : angle 2.05738 ( 3) link_ALPHA1-3 : bond 0.01035 ( 1) link_ALPHA1-3 : angle 2.16146 ( 3) hydrogen bonds : bond 0.03386 ( 538) hydrogen bonds : angle 5.10405 ( 1413) SS BOND : bond 0.00243 ( 14) SS BOND : angle 1.30879 ( 28) covalent geometry : bond 0.00291 (13825) covalent geometry : angle 0.53542 (18809) *********************** 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 267 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.8444 (mmp-170) cc_final: 0.8079 (mmp-170) REVERT: A 619 ASP cc_start: 0.8225 (t0) cc_final: 0.7873 (t70) REVERT: A 680 ASP cc_start: 0.8567 (t0) cc_final: 0.8149 (t0) REVERT: B 64 LYS cc_start: 0.9360 (ttmt) cc_final: 0.9146 (ttpp) REVERT: B 117 ASP cc_start: 0.8469 (t0) cc_final: 0.7933 (t0) REVERT: B 247 ASP cc_start: 0.8937 (m-30) cc_final: 0.8726 (m-30) REVERT: C 435 GLN cc_start: 0.8758 (tp40) cc_final: 0.8405 (tt0) REVERT: E 27 MET cc_start: 0.9139 (mmm) cc_final: 0.8864 (mmt) REVERT: E 29 GLN cc_start: 0.8712 (tt0) cc_final: 0.8235 (tt0) REVERT: E 47 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8243 (mtp-110) REVERT: E 65 LYS cc_start: 0.8303 (mtpt) cc_final: 0.8060 (mtmt) REVERT: E 77 LEU cc_start: 0.9367 (tp) cc_final: 0.9109 (tm) REVERT: F 85 GLN cc_start: 0.8554 (tp40) cc_final: 0.8049 (tp40) REVERT: G 81 ASN cc_start: 0.8049 (m110) cc_final: 0.7646 (m110) REVERT: G 100 THR cc_start: 0.8453 (m) cc_final: 0.8004 (t) REVERT: H 100 ASN cc_start: 0.8891 (t0) cc_final: 0.8591 (t0) REVERT: H 128 PHE cc_start: 0.8715 (t80) cc_final: 0.8506 (t80) REVERT: H 141 ASP cc_start: 0.9004 (p0) cc_final: 0.8755 (p0) REVERT: H 145 GLN cc_start: 0.8987 (mm110) cc_final: 0.8702 (mm-40) outliers start: 35 outliers final: 18 residues processed: 257 average time/residue: 1.0363 time to fit residues: 295.9743 Evaluate side-chains 238 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR 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 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 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 G residue 121 GLN Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 51 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 6 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 54 optimal weight: 0.0980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.113722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.095276 restraints weight = 25097.049| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.63 r_work: 0.3118 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1899 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= 0.125 Angle : 0.543 12.125 18915 Z= 0.270 Chirality : 0.043 0.181 2211 Planarity : 0.004 0.041 2358 Dihedral : 7.085 62.406 2378 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.27 % Allowed : 14.86 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1625 helix: 1.70 (0.27), residues: 385 sheet: 0.58 (0.27), residues: 381 loop : 0.19 (0.23), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 330 HIS 0.003 0.001 HIS A 213 PHE 0.015 0.001 PHE B 105 TYR 0.013 0.001 TYR B 226 ARG 0.008 0.000 ARG F 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 19) link_NAG-ASN : angle 1.55542 ( 57) link_ALPHA1-6 : bond 0.00582 ( 1) link_ALPHA1-6 : angle 2.10888 ( 3) link_BETA1-4 : bond 0.00246 ( 4) link_BETA1-4 : angle 1.65165 ( 12) link_ALPHA1-2 : bond 0.00231 ( 1) link_ALPHA1-2 : angle 1.83226 ( 3) link_ALPHA1-3 : bond 0.00997 ( 1) link_ALPHA1-3 : angle 2.13820 ( 3) hydrogen bonds : bond 0.03179 ( 538) hydrogen bonds : angle 4.96243 ( 1413) SS BOND : bond 0.00266 ( 14) SS BOND : angle 1.14750 ( 28) covalent geometry : bond 0.00292 (13825) covalent geometry : angle 0.53295 (18809) *********************** 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 267 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.8577 (mmp-170) cc_final: 0.8202 (mmp-170) REVERT: A 507 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8959 (tt) REVERT: A 527 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8195 (mmm160) REVERT: A 529 ASP cc_start: 0.8957 (p0) cc_final: 0.8737 (p0) REVERT: A 619 ASP cc_start: 0.8229 (t0) cc_final: 0.7884 (t70) REVERT: A 679 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8307 (mp) REVERT: A 680 ASP cc_start: 0.8557 (t0) cc_final: 0.8132 (t0) REVERT: B 64 LYS cc_start: 0.9371 (ttmt) cc_final: 0.9159 (ttpp) REVERT: C 320 MET cc_start: 0.8457 (mtt) cc_final: 0.8235 (mtm) REVERT: C 435 GLN cc_start: 0.8737 (tp40) cc_final: 0.8450 (tt0) REVERT: E 27 MET cc_start: 0.9100 (mmm) cc_final: 0.8790 (mmt) REVERT: E 29 GLN cc_start: 0.8693 (tt0) cc_final: 0.8357 (tt0) REVERT: E 47 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8222 (mtp-110) REVERT: E 65 LYS cc_start: 0.8374 (mtpt) cc_final: 0.8133 (mtmt) REVERT: E 77 LEU cc_start: 0.9360 (tp) cc_final: 0.9110 (tm) REVERT: E 102 GLN cc_start: 0.8484 (mm-40) cc_final: 0.7978 (mm-40) REVERT: F 42 LYS cc_start: 0.9232 (tptm) cc_final: 0.8817 (tptp) REVERT: F 85 GLN cc_start: 0.8583 (tp40) cc_final: 0.8094 (tp40) REVERT: F 124 ARG cc_start: 0.8551 (mmt-90) cc_final: 0.7782 (mmt180) REVERT: G 81 ASN cc_start: 0.8215 (m110) cc_final: 0.7897 (m110) REVERT: G 100 THR cc_start: 0.8439 (m) cc_final: 0.7981 (t) REVERT: H 100 ASN cc_start: 0.8945 (t0) cc_final: 0.8628 (t0) REVERT: H 128 PHE cc_start: 0.8739 (t80) cc_final: 0.8522 (t80) REVERT: H 141 ASP cc_start: 0.8984 (p0) cc_final: 0.8743 (p0) REVERT: H 145 GLN cc_start: 0.9009 (mm110) cc_final: 0.8784 (mm-40) outliers start: 48 outliers final: 22 residues processed: 249 average time/residue: 1.0903 time to fit residues: 299.8281 Evaluate side-chains 253 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 507 LEU Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain A residue 679 LEU 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 97 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 69 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 115 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 145 optimal weight: 0.0470 chunk 42 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 138 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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** C 358 ASN E 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 = 0.3549 r_free = 0.3549 target = 0.114223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096174 restraints weight = 25166.584| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.61 r_work: 0.3136 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13865 Z= 0.106 Angle : 0.537 12.207 18915 Z= 0.266 Chirality : 0.042 0.199 2211 Planarity : 0.004 0.035 2358 Dihedral : 6.570 59.255 2378 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.45 % Allowed : 16.09 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.22), residues: 1625 helix: 1.71 (0.27), residues: 386 sheet: 0.65 (0.27), residues: 381 loop : 0.21 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS A 213 PHE 0.014 0.001 PHE B 105 TYR 0.021 0.001 TYR A 682 ARG 0.006 0.000 ARG F 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 19) link_NAG-ASN : angle 1.53032 ( 57) link_ALPHA1-6 : bond 0.00544 ( 1) link_ALPHA1-6 : angle 1.91359 ( 3) link_BETA1-4 : bond 0.00284 ( 4) link_BETA1-4 : angle 1.47691 ( 12) link_ALPHA1-2 : bond 0.00321 ( 1) link_ALPHA1-2 : angle 1.91285 ( 3) link_ALPHA1-3 : bond 0.01191 ( 1) link_ALPHA1-3 : angle 1.94531 ( 3) hydrogen bonds : bond 0.03011 ( 538) hydrogen bonds : angle 4.80330 ( 1413) SS BOND : bond 0.00189 ( 14) SS BOND : angle 1.45221 ( 28) covalent geometry : bond 0.00244 (13825) covalent geometry : angle 0.52554 (18809) *********************** 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 276 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.8583 (mmp-170) cc_final: 0.8197 (mmp-170) REVERT: A 619 ASP cc_start: 0.8230 (t0) cc_final: 0.7914 (t70) REVERT: A 679 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8177 (mp) REVERT: A 680 ASP cc_start: 0.8517 (t0) cc_final: 0.8060 (t0) REVERT: B 46 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8278 (pm20) REVERT: B 64 LYS cc_start: 0.9354 (ttmt) cc_final: 0.9143 (ttpp) REVERT: B 102 ASP cc_start: 0.9132 (p0) cc_final: 0.8764 (p0) REVERT: B 117 ASP cc_start: 0.8328 (t0) cc_final: 0.8048 (t0) REVERT: B 146 ASP cc_start: 0.8294 (p0) cc_final: 0.8026 (p0) REVERT: B 247 ASP cc_start: 0.8943 (m-30) cc_final: 0.8701 (m-30) REVERT: C 320 MET cc_start: 0.8458 (mtt) cc_final: 0.8213 (mtm) REVERT: C 435 GLN cc_start: 0.8696 (tp40) cc_final: 0.8455 (tt0) REVERT: E 27 MET cc_start: 0.9131 (mmm) cc_final: 0.8794 (mmt) REVERT: E 29 GLN cc_start: 0.8681 (tt0) cc_final: 0.8428 (tt0) REVERT: E 47 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.8242 (mtp-110) REVERT: E 50 GLN cc_start: 0.8801 (mt0) cc_final: 0.8582 (mm-40) REVERT: E 65 LYS cc_start: 0.8379 (mtpt) cc_final: 0.8132 (mtmt) REVERT: E 77 LEU cc_start: 0.9355 (tp) cc_final: 0.9115 (tm) REVERT: F 42 LYS cc_start: 0.9203 (tptm) cc_final: 0.8884 (tptp) REVERT: F 85 GLN cc_start: 0.8582 (tp40) cc_final: 0.8093 (tp40) REVERT: F 124 ARG cc_start: 0.8562 (mmt-90) cc_final: 0.7760 (mmt180) REVERT: F 138 GLN cc_start: 0.8971 (pm20) cc_final: 0.8749 (pm20) REVERT: G 81 ASN cc_start: 0.8214 (m110) cc_final: 0.7904 (m110) REVERT: G 100 THR cc_start: 0.8444 (m) cc_final: 0.7979 (t) REVERT: H 100 ASN cc_start: 0.8959 (t0) cc_final: 0.8571 (t0) REVERT: H 128 PHE cc_start: 0.8700 (t80) cc_final: 0.8471 (t80) REVERT: H 141 ASP cc_start: 0.8971 (p0) cc_final: 0.8738 (p0) outliers start: 36 outliers final: 17 residues processed: 261 average time/residue: 1.0682 time to fit residues: 308.5070 Evaluate side-chains 234 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 209 THR 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 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 80 SER Chi-restraints excluded: chain G residue 97 THR 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 24 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 11 optimal weight: 0.0470 chunk 56 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- 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 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 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 = 0.3516 r_free = 0.3516 target = 0.111917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.093420 restraints weight = 25360.364| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.62 r_work: 0.3094 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2114 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= 0.171 Angle : 0.577 11.893 18915 Z= 0.287 Chirality : 0.044 0.208 2211 Planarity : 0.004 0.033 2358 Dihedral : 6.565 59.875 2378 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.14 % Allowed : 16.50 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.22), residues: 1625 helix: 1.66 (0.27), residues: 386 sheet: 0.52 (0.27), residues: 388 loop : 0.15 (0.23), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 330 HIS 0.003 0.001 HIS A 451 PHE 0.013 0.001 PHE B 105 TYR 0.017 0.001 TYR C 332 ARG 0.006 0.000 ARG H 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 19) link_NAG-ASN : angle 1.68205 ( 57) link_ALPHA1-6 : bond 0.00279 ( 1) link_ALPHA1-6 : angle 2.02156 ( 3) link_BETA1-4 : bond 0.00131 ( 4) link_BETA1-4 : angle 1.51052 ( 12) link_ALPHA1-2 : bond 0.00165 ( 1) link_ALPHA1-2 : angle 1.92062 ( 3) link_ALPHA1-3 : bond 0.01023 ( 1) link_ALPHA1-3 : angle 2.08313 ( 3) hydrogen bonds : bond 0.03409 ( 538) hydrogen bonds : angle 4.91529 ( 1413) SS BOND : bond 0.00302 ( 14) SS BOND : angle 1.36488 ( 28) covalent geometry : bond 0.00404 (13825) covalent geometry : angle 0.56592 (18809) *********************** 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 263 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: A 329 ARG cc_start: 0.8643 (mmp-170) cc_final: 0.8278 (mmp-170) REVERT: A 507 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8975 (tt) REVERT: A 527 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8262 (mmm160) REVERT: A 619 ASP cc_start: 0.8286 (t0) cc_final: 0.7945 (t70) REVERT: A 680 ASP cc_start: 0.8480 (t0) cc_final: 0.8052 (t0) REVERT: B 46 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8261 (pm20) REVERT: B 64 LYS cc_start: 0.9357 (ttmt) cc_final: 0.9144 (ttpp) REVERT: C 435 GLN cc_start: 0.8773 (tp40) cc_final: 0.8485 (tt0) REVERT: E 27 MET cc_start: 0.9210 (mmm) cc_final: 0.8882 (mmt) REVERT: E 29 GLN cc_start: 0.8697 (tt0) cc_final: 0.8429 (tt0) REVERT: E 47 ARG cc_start: 0.8515 (ttm-80) cc_final: 0.8217 (mtp-110) REVERT: E 50 GLN cc_start: 0.8691 (mt0) cc_final: 0.8333 (mm-40) REVERT: E 65 LYS cc_start: 0.8418 (mtpt) cc_final: 0.8169 (mtmt) REVERT: E 77 LEU cc_start: 0.9373 (tp) cc_final: 0.9121 (tm) REVERT: F 85 GLN cc_start: 0.8601 (tp40) cc_final: 0.8168 (tp40) REVERT: G 81 ASN cc_start: 0.8224 (m110) cc_final: 0.7966 (m110) REVERT: G 100 THR cc_start: 0.8556 (m) cc_final: 0.8107 (t) REVERT: H 100 ASN cc_start: 0.8919 (t0) cc_final: 0.8557 (t0) REVERT: H 123 ARG cc_start: 0.9072 (tpt90) cc_final: 0.8626 (tpt90) REVERT: H 141 ASP cc_start: 0.8988 (p0) cc_final: 0.8771 (p0) outliers start: 46 outliers final: 22 residues processed: 249 average time/residue: 1.1059 time to fit residues: 305.9558 Evaluate side-chains 245 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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 378 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain B residue 151 VAL 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 240 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 63 optimal weight: 6.9990 chunk 145 optimal weight: 0.4980 chunk 143 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 65 optimal weight: 0.0070 chunk 142 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS E 54 ASN G 50 GLN H 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.113303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094917 restraints weight = 25312.138| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.60 r_work: 0.3106 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2204 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= 0.134 Angle : 0.566 11.916 18915 Z= 0.281 Chirality : 0.043 0.221 2211 Planarity : 0.004 0.038 2358 Dihedral : 6.378 59.616 2378 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.73 % Allowed : 16.84 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1625 helix: 1.62 (0.27), residues: 385 sheet: 0.46 (0.27), residues: 390 loop : 0.15 (0.23), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 330 HIS 0.004 0.001 HIS A 213 PHE 0.013 0.001 PHE B 105 TYR 0.021 0.001 TYR A 682 ARG 0.006 0.000 ARG H 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 19) link_NAG-ASN : angle 1.59794 ( 57) link_ALPHA1-6 : bond 0.00325 ( 1) link_ALPHA1-6 : angle 1.95850 ( 3) link_BETA1-4 : bond 0.00162 ( 4) link_BETA1-4 : angle 1.37924 ( 12) link_ALPHA1-2 : bond 0.00056 ( 1) link_ALPHA1-2 : angle 1.94127 ( 3) link_ALPHA1-3 : bond 0.01208 ( 1) link_ALPHA1-3 : angle 2.55289 ( 3) hydrogen bonds : bond 0.03150 ( 538) hydrogen bonds : angle 4.85209 ( 1413) SS BOND : bond 0.00236 ( 14) SS BOND : angle 1.20959 ( 28) covalent geometry : bond 0.00316 (13825) covalent geometry : angle 0.55566 (18809) *********************** 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 261 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8300 (mp0) REVERT: A 329 ARG cc_start: 0.8635 (mmp-170) cc_final: 0.8272 (mmp-170) REVERT: A 527 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8272 (mmm160) REVERT: A 619 ASP cc_start: 0.8269 (t0) cc_final: 0.7932 (t70) REVERT: A 680 ASP cc_start: 0.8476 (t0) cc_final: 0.8045 (t0) REVERT: B 64 LYS cc_start: 0.9351 (ttmt) cc_final: 0.9138 (ttpp) REVERT: B 102 ASP cc_start: 0.9112 (p0) cc_final: 0.8749 (p0) REVERT: B 247 ASP cc_start: 0.8985 (m-30) cc_final: 0.8734 (m-30) REVERT: C 435 GLN cc_start: 0.8760 (tp40) cc_final: 0.8482 (tt0) REVERT: E 27 MET cc_start: 0.9205 (mmm) cc_final: 0.8881 (mmt) REVERT: E 47 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.8181 (mtp-110) REVERT: E 50 GLN cc_start: 0.8743 (mt0) cc_final: 0.8402 (mm-40) REVERT: E 65 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8121 (mtmt) REVERT: E 77 LEU cc_start: 0.9365 (tp) cc_final: 0.9123 (tm) REVERT: F 42 LYS cc_start: 0.9063 (tptm) cc_final: 0.8775 (tptp) REVERT: F 85 GLN cc_start: 0.8585 (tp40) cc_final: 0.8155 (tp40) REVERT: G 32 LEU cc_start: 0.9052 (mt) cc_final: 0.8824 (mm) REVERT: G 81 ASN cc_start: 0.8237 (m110) cc_final: 0.7970 (m110) REVERT: G 100 THR cc_start: 0.8538 (m) cc_final: 0.8086 (t) REVERT: H 100 ASN cc_start: 0.8862 (t0) cc_final: 0.8459 (t0) REVERT: H 141 ASP cc_start: 0.8979 (p0) cc_final: 0.8688 (p0) outliers start: 40 outliers final: 21 residues processed: 250 average time/residue: 1.0568 time to fit residues: 292.7459 Evaluate side-chains 236 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 527 ARG Chi-restraints excluded: chain B residue 151 VAL 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 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 139 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 360 HIS ** 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 = 0.3518 r_free = 0.3518 target = 0.112779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.094189 restraints weight = 25530.193| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.61 r_work: 0.3090 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13865 Z= 0.165 Angle : 0.576 10.933 18915 Z= 0.286 Chirality : 0.044 0.206 2211 Planarity : 0.004 0.038 2358 Dihedral : 6.465 58.718 2378 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.52 % Allowed : 17.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1625 helix: 1.58 (0.27), residues: 386 sheet: 0.43 (0.27), residues: 390 loop : 0.11 (0.23), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 330 HIS 0.004 0.001 HIS A 213 PHE 0.013 0.001 PHE B 105 TYR 0.012 0.001 TYR B 226 ARG 0.006 0.000 ARG H 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 19) link_NAG-ASN : angle 1.67614 ( 57) link_ALPHA1-6 : bond 0.00360 ( 1) link_ALPHA1-6 : angle 2.05442 ( 3) link_BETA1-4 : bond 0.00125 ( 4) link_BETA1-4 : angle 1.44485 ( 12) link_ALPHA1-2 : bond 0.00205 ( 1) link_ALPHA1-2 : angle 2.07343 ( 3) link_ALPHA1-3 : bond 0.00979 ( 1) link_ALPHA1-3 : angle 1.59078 ( 3) hydrogen bonds : bond 0.03304 ( 538) hydrogen bonds : angle 4.89917 ( 1413) SS BOND : bond 0.00300 ( 14) SS BOND : angle 1.39883 ( 28) covalent geometry : bond 0.00389 (13825) covalent geometry : angle 0.56516 (18809) *********************** 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 249 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: A 329 ARG cc_start: 0.8611 (mmp-170) cc_final: 0.8303 (mmp-170) REVERT: A 507 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8990 (tt) REVERT: A 527 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8285 (mmm160) REVERT: A 619 ASP cc_start: 0.8282 (t0) cc_final: 0.7943 (t70) REVERT: A 680 ASP cc_start: 0.8439 (t0) cc_final: 0.8006 (t0) REVERT: B 46 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8137 (pm20) REVERT: B 64 LYS cc_start: 0.9343 (ttmt) cc_final: 0.9126 (ttpp) REVERT: C 435 GLN cc_start: 0.8740 (tp40) cc_final: 0.8485 (tt0) REVERT: E 27 MET cc_start: 0.9209 (mmm) cc_final: 0.8884 (mmt) REVERT: E 50 GLN cc_start: 0.8748 (mt0) cc_final: 0.8406 (mm-40) REVERT: E 65 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8142 (mtmt) REVERT: E 77 LEU cc_start: 0.9365 (tp) cc_final: 0.9121 (tm) REVERT: F 42 LYS cc_start: 0.9075 (tptm) cc_final: 0.8663 (tptp) REVERT: F 85 GLN cc_start: 0.8570 (tp40) cc_final: 0.8094 (tp40) REVERT: G 32 LEU cc_start: 0.9053 (mt) cc_final: 0.8828 (mm) REVERT: G 81 ASN cc_start: 0.8283 (m110) cc_final: 0.8050 (m110) REVERT: G 100 THR cc_start: 0.8556 (m) cc_final: 0.8100 (t) REVERT: H 36 LYS cc_start: 0.6267 (mmpt) cc_final: 0.5982 (mmpt) REVERT: H 100 ASN cc_start: 0.8844 (t0) cc_final: 0.8456 (t0) REVERT: H 141 ASP cc_start: 0.8986 (p0) cc_final: 0.8733 (p0) outliers start: 37 outliers final: 25 residues processed: 240 average time/residue: 1.1459 time to fit residues: 303.5800 Evaluate side-chains 243 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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 A residue 696 MET Chi-restraints excluded: chain B residue 151 VAL 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 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 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 109 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 G 50 GLN 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 = 0.3533 r_free = 0.3533 target = 0.113049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.094382 restraints weight = 25152.268| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.63 r_work: 0.3112 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13865 Z= 0.124 Angle : 0.564 10.637 18915 Z= 0.281 Chirality : 0.043 0.205 2211 Planarity : 0.004 0.038 2358 Dihedral : 6.285 57.641 2378 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.25 % Allowed : 18.13 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1625 helix: 1.64 (0.27), residues: 385 sheet: 0.48 (0.27), residues: 387 loop : 0.13 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS A 213 PHE 0.014 0.001 PHE B 105 TYR 0.022 0.001 TYR A 682 ARG 0.006 0.000 ARG H 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 19) link_NAG-ASN : angle 1.56934 ( 57) link_ALPHA1-6 : bond 0.00496 ( 1) link_ALPHA1-6 : angle 1.78376 ( 3) link_BETA1-4 : bond 0.00188 ( 4) link_BETA1-4 : angle 1.36161 ( 12) link_ALPHA1-2 : bond 0.00064 ( 1) link_ALPHA1-2 : angle 2.08524 ( 3) link_ALPHA1-3 : bond 0.01176 ( 1) link_ALPHA1-3 : angle 1.69877 ( 3) hydrogen bonds : bond 0.03062 ( 538) hydrogen bonds : angle 4.79194 ( 1413) SS BOND : bond 0.00239 ( 14) SS BOND : angle 1.28144 ( 28) covalent geometry : bond 0.00291 (13825) covalent geometry : angle 0.55376 (18809) *********************** 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 253 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: A 329 ARG cc_start: 0.8586 (mmp-170) cc_final: 0.8280 (mmp-170) REVERT: A 527 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8320 (mmm160) REVERT: A 619 ASP cc_start: 0.8267 (t0) cc_final: 0.7941 (t70) REVERT: A 680 ASP cc_start: 0.8432 (t0) cc_final: 0.7996 (t0) REVERT: B 46 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8062 (pm20) REVERT: B 102 ASP cc_start: 0.9058 (p0) cc_final: 0.8824 (p0) REVERT: B 247 ASP cc_start: 0.8995 (m-30) cc_final: 0.8744 (m-30) REVERT: C 84 MET cc_start: 0.7574 (ptm) cc_final: 0.7333 (ptt) REVERT: C 435 GLN cc_start: 0.8775 (tp40) cc_final: 0.8472 (tt0) REVERT: E 27 MET cc_start: 0.9214 (mmm) cc_final: 0.8914 (mmt) REVERT: E 28 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8614 (p) REVERT: E 50 GLN cc_start: 0.8727 (mt0) cc_final: 0.8387 (mm-40) REVERT: E 65 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8114 (mtmt) REVERT: E 77 LEU cc_start: 0.9352 (tp) cc_final: 0.9113 (tm) REVERT: F 42 LYS cc_start: 0.9053 (tptm) cc_final: 0.8650 (tptp) REVERT: F 85 GLN cc_start: 0.8542 (tp40) cc_final: 0.8083 (tp40) REVERT: F 138 GLN cc_start: 0.9054 (pm20) cc_final: 0.8841 (pm20) REVERT: G 32 LEU cc_start: 0.9023 (mt) cc_final: 0.8810 (mm) REVERT: G 81 ASN cc_start: 0.8273 (m110) cc_final: 0.8047 (m110) REVERT: G 100 THR cc_start: 0.8530 (m) cc_final: 0.8082 (t) REVERT: H 36 LYS cc_start: 0.6270 (mmpt) cc_final: 0.6021 (mmpt) REVERT: H 100 ASN cc_start: 0.8824 (t0) cc_final: 0.8454 (t0) REVERT: H 141 ASP cc_start: 0.8972 (p0) cc_final: 0.8566 (p0) outliers start: 33 outliers final: 23 residues processed: 244 average time/residue: 1.1106 time to fit residues: 300.3022 Evaluate side-chains 242 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 527 ARG Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain B residue 151 VAL 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 240 ASN Chi-restraints excluded: chain C residue 414 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 30 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN G 56 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 = 0.3528 r_free = 0.3528 target = 0.112738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.094206 restraints weight = 25209.761| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.63 r_work: 0.3107 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13865 Z= 0.137 Angle : 0.568 11.640 18915 Z= 0.283 Chirality : 0.043 0.206 2211 Planarity : 0.004 0.036 2358 Dihedral : 6.276 55.949 2378 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.11 % Allowed : 18.68 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1625 helix: 1.63 (0.27), residues: 385 sheet: 0.46 (0.27), residues: 387 loop : 0.10 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 330 HIS 0.003 0.001 HIS A 213 PHE 0.012 0.001 PHE B 105 TYR 0.011 0.001 TYR H 137 ARG 0.007 0.000 ARG E 47 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 19) link_NAG-ASN : angle 1.61057 ( 57) link_ALPHA1-6 : bond 0.00408 ( 1) link_ALPHA1-6 : angle 1.85461 ( 3) link_BETA1-4 : bond 0.00161 ( 4) link_BETA1-4 : angle 1.40147 ( 12) link_ALPHA1-2 : bond 0.00128 ( 1) link_ALPHA1-2 : angle 2.07280 ( 3) link_ALPHA1-3 : bond 0.01072 ( 1) link_ALPHA1-3 : angle 1.62447 ( 3) hydrogen bonds : bond 0.03126 ( 538) hydrogen bonds : angle 4.77460 ( 1413) SS BOND : bond 0.00245 ( 14) SS BOND : angle 1.33518 ( 28) covalent geometry : bond 0.00322 (13825) covalent geometry : angle 0.55812 (18809) ********************** 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 248 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: A 329 ARG cc_start: 0.8600 (mmp-170) cc_final: 0.8278 (mmp-170) REVERT: A 527 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8325 (mmm160) REVERT: A 619 ASP cc_start: 0.8280 (t0) cc_final: 0.7957 (t70) REVERT: A 680 ASP cc_start: 0.8429 (t0) cc_final: 0.8026 (t0) REVERT: B 46 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8038 (pm20) REVERT: B 247 ASP cc_start: 0.8998 (m-30) cc_final: 0.8748 (m-30) REVERT: C 84 MET cc_start: 0.7579 (ptm) cc_final: 0.7346 (ptt) REVERT: C 435 GLN cc_start: 0.8748 (tp40) cc_final: 0.8505 (tt0) REVERT: E 27 MET cc_start: 0.9229 (mmm) cc_final: 0.8885 (mmt) REVERT: E 50 GLN cc_start: 0.8723 (mt0) cc_final: 0.8385 (mm-40) REVERT: E 65 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8124 (mtmt) REVERT: E 77 LEU cc_start: 0.9356 (tp) cc_final: 0.9112 (tm) REVERT: F 42 LYS cc_start: 0.9120 (tptm) cc_final: 0.8634 (tptp) REVERT: F 85 GLN cc_start: 0.8557 (tp40) cc_final: 0.8098 (tp40) REVERT: G 32 LEU cc_start: 0.9017 (mt) cc_final: 0.8812 (mm) REVERT: G 81 ASN cc_start: 0.8287 (m110) cc_final: 0.8066 (m110) REVERT: G 100 THR cc_start: 0.8540 (m) cc_final: 0.8099 (t) REVERT: H 36 LYS cc_start: 0.6304 (mmpt) cc_final: 0.6062 (mmpt) REVERT: H 100 ASN cc_start: 0.8828 (t0) cc_final: 0.8459 (t0) REVERT: H 141 ASP cc_start: 0.9002 (p0) cc_final: 0.8776 (p0) outliers start: 31 outliers final: 25 residues processed: 241 average time/residue: 1.0557 time to fit residues: 282.7109 Evaluate side-chains 240 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 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 414 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 140 optimal weight: 0.1980 chunk 116 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 358 ASN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN G 56 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 = 0.3534 r_free = 0.3534 target = 0.113219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.094717 restraints weight = 25237.133| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.63 r_work: 0.3113 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2400 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= 0.125 Angle : 0.568 11.198 18915 Z= 0.283 Chirality : 0.043 0.205 2211 Planarity : 0.004 0.038 2358 Dihedral : 6.209 54.652 2378 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.39 % Allowed : 18.13 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1625 helix: 1.63 (0.27), residues: 385 sheet: 0.48 (0.27), residues: 387 loop : 0.14 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 462 HIS 0.003 0.001 HIS A 213 PHE 0.014 0.001 PHE B 105 TYR 0.024 0.001 TYR A 682 ARG 0.007 0.000 ARG H 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 19) link_NAG-ASN : angle 1.56663 ( 57) link_ALPHA1-6 : bond 0.00428 ( 1) link_ALPHA1-6 : angle 1.74095 ( 3) link_BETA1-4 : bond 0.00198 ( 4) link_BETA1-4 : angle 1.36559 ( 12) link_ALPHA1-2 : bond 0.00078 ( 1) link_ALPHA1-2 : angle 2.08604 ( 3) link_ALPHA1-3 : bond 0.01136 ( 1) link_ALPHA1-3 : angle 1.58873 ( 3) hydrogen bonds : bond 0.03038 ( 538) hydrogen bonds : angle 4.73516 ( 1413) SS BOND : bond 0.00227 ( 14) SS BOND : angle 1.19079 ( 28) covalent geometry : bond 0.00296 (13825) covalent geometry : angle 0.55862 (18809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10803.06 seconds wall clock time: 184 minutes 32.68 seconds (11072.68 seconds total)