Starting phenix.real_space_refine on Wed Mar 4 15:51:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lbg_23254/03_2026/7lbg_23254.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lbg_23254/03_2026/7lbg_23254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lbg_23254/03_2026/7lbg_23254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lbg_23254/03_2026/7lbg_23254.map" model { file = "/net/cci-nas-00/data/ceres_data/7lbg_23254/03_2026/7lbg_23254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lbg_23254/03_2026/7lbg_23254.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.027 sd= 0.763 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 65 5.16 5 C 9289 2.51 5 N 2453 2.21 5 O 2779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14586 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5118 Classifications: {'peptide': 635} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 602} Chain breaks: 6 Chain: "B" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1843 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2462 Classifications: {'peptide': 296} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 278} Chain breaks: 3 Chain: "D" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1235 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain breaks: 1 Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} 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: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 3.19, per 1000 atoms: 0.22 Number of scatterers: 14586 At special positions: 0 Unit cell: (96.7788, 174.441, 163.688, 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 65 16.00 O 2779 8.00 N 2453 7.00 C 9289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 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=2.02 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 167 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 197 " 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 J 4 " - " MAN J 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " MAN J 6 " - " MAN J 7 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 801 " - " ASN A 192 " " NAG A 802 " - " ASN A 67 " " NAG A 803 " - " ASN A 62 " " NAG A 804 " - " ASN A 55 " " NAG A 805 " - " ASN A 700 " " NAG B 301 " - " ASN B 74 " " NAG C 601 " - " ASN C 85 " " NAG C 602 " - " ASN C 101 " " NAG C 603 " - " ASN C 155 " " NAG C 604 " - " ASN C 217 " " NAG C 605 " - " ASN C 240 " " NAG C 606 " - " ASN C 348 " " NAG C 607 " - " ASN C 365 " " NAG C 608 " - " ASN C 383 " " NAG C 609 " - " ASN C 452 " " NAG C 610 " - " ASN C 128 " " NAG C 611 " - " ASN C 169 " " NAG J 1 " - " ASN C 160 " Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 561.2 milliseconds 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3394 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 27 sheets defined 29.4% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.710A pdb=" N PHE A 105 " --> pdb=" O LEU A 101 " (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: 4.221A pdb=" N SER A 290 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.054A 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 Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.586A pdb=" N LEU A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.709A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 3.816A pdb=" N HIS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 494 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 538 removed outlier: 3.598A pdb=" N LEU A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'A' and resid 707 through 710 removed outlier: 3.788A pdb=" N VAL A 710 " --> pdb=" O THR A 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 707 through 710' Processing helix chain 'B' and resid 46 through 56 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 113 removed outlier: 3.575A 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: 3.835A pdb=" N LEU B 167 " --> pdb=" O LEU B 164 " (cutoff:3.500A) 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: 3.974A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 252 removed outlier: 3.952A pdb=" N ARG B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 146 through 159 Processing helix chain 'C' and resid 198 through 214 removed outlier: 3.640A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.555A 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: 6.741A 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 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 413 through 435 Processing helix chain 'C' and resid 452 through 458 removed outlier: 3.555A pdb=" N LEU C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 458 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.829A pdb=" N GLY D 59 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.525A pdb=" N VAL E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 88 removed outlier: 3.555A pdb=" N GLN F 88 " --> pdb=" O GLN F 85 " (cutoff:3.500A) No H-bonds generated for '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: 3.884A pdb=" N VAL G 111 " --> pdb=" O THR G 108 " (cutoff:3.500A) 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 64 through 66 removed outlier: 4.220A pdb=" N SER A 64 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR A 88 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N PHE A 81 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 90 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ASN A 79 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N MET A 92 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N SER A 77 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS B 177 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 192 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE B 181 " --> pdb=" O ASN B 190 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN B 190 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU B 183 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 188 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 5.797A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 270 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 197 Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA6, first strand: chain 'A' and resid 637 through 638 removed outlier: 6.647A pdb=" N THR A 637 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP A 658 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL A 663 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.507A pdb=" N LEU B 82 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 100 removed outlier: 6.328A pdb=" N VAL B 99 " --> pdb=" O ARG C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 155 Processing sheet with id=AB1, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.675A pdb=" N TYR C 124 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N TYR C 122 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 117 through 118 removed outlier: 6.632A pdb=" N VAL D 83 " --> pdb=" O HIS D 113 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LYS D 115 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU D 85 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN D 88 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AB4, first strand: chain 'C' and resid 184 through 189 removed outlier: 3.838A pdb=" N THR C 192 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 369 through 370 Processing sheet with id=AB6, first strand: chain 'C' and resid 381 through 382 Processing sheet with id=AB7, first strand: chain 'D' and resid 50 through 51 removed outlier: 6.334A pdb=" N GLU D 63 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU D 103 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N HIS D 65 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ASN D 105 " --> pdb=" O HIS D 65 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU D 67 " --> pdb=" O ASN D 105 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL D 100 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU D 128 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE D 102 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 27 through 30 Processing sheet with id=AB9, first strand: chain 'E' and resid 33 through 35 removed outlier: 6.524A pdb=" N LEU E 56 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR E 72 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP E 58 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 26 through 29 Processing sheet with id=AC2, first strand: chain 'F' and resid 33 through 34 removed outlier: 6.600A pdb=" N ARG F 61 " --> pdb=" O TRP F 70 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TRP F 70 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 33 through 34 removed outlier: 3.928A pdb=" N ASP F 135 " --> pdb=" O ARG F 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 27 through 30 Processing sheet with id=AC5, first strand: chain 'G' and resid 33 through 35 removed outlier: 5.939A pdb=" N LEU G 34 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY G 112 " --> pdb=" O VAL G 132 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU G 61 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR G 77 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TRP G 63 " --> pdb=" O LEU G 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 33 through 35 removed outlier: 5.939A pdb=" N LEU G 34 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY G 112 " --> pdb=" O VAL G 132 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR G 125 " --> pdb=" O GLN G 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 26 through 30 Processing sheet with id=AC8, first strand: chain 'H' and resid 34 through 35 removed outlier: 4.013A pdb=" N SER H 56 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL H 57 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER H 73 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP H 59 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 34 through 35 removed outlier: 3.874A pdb=" N VAL H 142 " --> pdb=" O ARG H 121 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 1.75 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: 4621 1.34 - 1.46: 3656 1.46 - 1.58: 6549 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 14923 Sorted by residual: bond pdb=" C1 NAG C 605 " pdb=" O5 NAG C 605 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.22e+00 bond pdb=" C1 NAG C 603 " pdb=" O5 NAG C 603 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.81e+00 bond pdb=" C1 MAN J 7 " pdb=" C2 MAN J 7 " ideal model delta sigma weight residual 1.526 1.569 -0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" C1 NAG C 610 " pdb=" O5 NAG C 610 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 MAN J 5 " pdb=" C2 MAN J 5 " ideal model delta sigma weight residual 1.526 1.564 -0.038 2.00e-02 2.50e+03 3.64e+00 ... (remaining 14918 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 19592 1.39 - 2.77: 540 2.77 - 4.16: 135 4.16 - 5.55: 17 5.55 - 6.94: 6 Bond angle restraints: 20290 Sorted by residual: angle pdb=" CB LYS B 64 " pdb=" CG LYS B 64 " pdb=" CD LYS B 64 " ideal model delta sigma weight residual 111.30 116.61 -5.31 2.30e+00 1.89e-01 5.32e+00 angle pdb=" CA ASN C 101 " pdb=" CB ASN C 101 " pdb=" CG ASN C 101 " ideal model delta sigma weight residual 112.60 114.88 -2.28 1.00e+00 1.00e+00 5.19e+00 angle pdb=" C3 MAN J 4 " pdb=" C2 MAN J 4 " pdb=" O2 MAN J 4 " ideal model delta sigma weight residual 111.77 104.94 6.83 3.00e+00 1.11e-01 5.19e+00 angle pdb=" C ASN A 85 " pdb=" CA ASN A 85 " pdb=" CB ASN A 85 " ideal model delta sigma weight residual 111.80 108.48 3.32 1.46e+00 4.69e-01 5.16e+00 angle pdb=" C3 MAN J 6 " pdb=" C2 MAN J 6 " pdb=" O2 MAN J 6 " ideal model delta sigma weight residual 111.77 105.24 6.53 3.00e+00 1.11e-01 4.74e+00 ... (remaining 20285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 8839 22.35 - 44.70: 331 44.70 - 67.04: 59 67.04 - 89.39: 27 89.39 - 111.74: 4 Dihedral angle restraints: 9260 sinusoidal: 4007 harmonic: 5253 Sorted by residual: dihedral pdb=" CB CYS D 52 " pdb=" SG CYS D 52 " pdb=" SG CYS D 197 " pdb=" CB CYS D 197 " ideal model delta sinusoidal sigma weight residual -86.00 -167.27 81.27 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CA PRO C 145 " pdb=" C PRO C 145 " pdb=" N SER C 146 " pdb=" CA SER C 146 " ideal model delta harmonic sigma weight residual 180.00 153.60 26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ALA B 194 " pdb=" C ALA B 194 " pdb=" N ILE B 195 " pdb=" CA ILE B 195 " ideal model delta harmonic sigma weight residual 180.00 155.35 24.65 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 9257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2011 0.053 - 0.105: 278 0.105 - 0.158: 86 0.158 - 0.210: 1 0.210 - 0.263: 3 Chirality restraints: 2379 Sorted by residual: chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 NAG C 611 " pdb=" ND2 ASN C 169 " pdb=" C2 NAG C 611 " pdb=" O5 NAG C 611 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN C 101 " pdb=" N ASN C 101 " pdb=" C ASN C 101 " pdb=" CB ASN C 101 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2376 not shown) Planarity restraints: 2560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 344 " 0.059 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO C 345 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 345 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 345 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 94 " 0.236 9.50e-02 1.11e+02 1.06e-01 7.47e+00 pdb=" NE ARG A 94 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 94 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 94 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 94 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 253 " -0.229 9.50e-02 1.11e+02 1.03e-01 7.25e+00 pdb=" NE ARG C 253 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG C 253 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 253 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 253 " -0.003 2.00e-02 2.50e+03 ... (remaining 2557 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 189 2.65 - 3.21: 13461 3.21 - 3.77: 22227 3.77 - 4.34: 33742 4.34 - 4.90: 53996 Nonbonded interactions: 123615 Sorted by model distance: nonbonded pdb=" NH2 ARG A 365 " pdb=" OD2 ASP A 368 " model vdw 2.085 3.120 nonbonded pdb=" ND1 HIS C 360 " pdb=" O LEU C 459 " model vdw 2.192 3.120 nonbonded pdb=" O LEU G 34 " pdb=" N GLU G 133 " model vdw 2.209 3.120 nonbonded pdb=" OG SER B 83 " pdb=" OE1 GLU B 176 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP E 128 " pdb=" N ILE E 129 " model vdw 2.283 3.120 ... (remaining 123610 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.140 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 0.057 14961 Z= 0.160 Angle : 0.610 10.320 20391 Z= 0.289 Chirality : 0.043 0.263 2379 Planarity : 0.006 0.106 2542 Dihedral : 12.952 111.738 5827 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.20), residues: 1750 helix: 0.45 (0.25), residues: 402 sheet: 0.37 (0.24), residues: 432 loop : 0.34 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG C 253 TYR 0.020 0.002 TYR A 344 PHE 0.027 0.002 PHE H 52 TRP 0.026 0.002 TRP C 460 HIS 0.005 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00343 (14923) covalent geometry : angle 0.57966 (20290) SS BOND : bond 0.00387 ( 13) SS BOND : angle 0.81153 ( 26) hydrogen bonds : bond 0.14035 ( 571) hydrogen bonds : angle 6.05404 ( 1509) link_ALPHA1-2 : bond 0.00705 ( 1) link_ALPHA1-2 : angle 1.77179 ( 3) link_ALPHA1-3 : bond 0.00493 ( 2) link_ALPHA1-3 : angle 2.59910 ( 6) link_ALPHA1-6 : bond 0.00928 ( 1) link_ALPHA1-6 : angle 1.44628 ( 3) link_BETA1-4 : bond 0.00521 ( 3) link_BETA1-4 : angle 2.66635 ( 9) link_NAG-ASN : bond 0.00306 ( 18) link_NAG-ASN : angle 3.40662 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 317 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7694 (mmtm) REVERT: D 96 HIS cc_start: 0.7843 (t70) cc_final: 0.7576 (t70) REVERT: D 115 LYS cc_start: 0.7382 (mmpt) cc_final: 0.6495 (pttp) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.7376 time to fit residues: 225.5819 Evaluate side-chains 217 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0020 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 480 HIS B 203 ASN C 215 GLN D 155 HIS D 157 ASN D 202 ASN D 207 ASN E 26 GLN G 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.088489 restraints weight = 20203.909| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.93 r_work: 0.2860 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14961 Z= 0.204 Angle : 0.657 7.650 20391 Z= 0.330 Chirality : 0.046 0.280 2379 Planarity : 0.005 0.057 2542 Dihedral : 8.063 84.473 2490 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.70 % Allowed : 8.81 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.20), residues: 1750 helix: 1.26 (0.25), residues: 405 sheet: 0.47 (0.24), residues: 428 loop : 0.35 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 216 TYR 0.028 0.002 TYR A 84 PHE 0.036 0.002 PHE H 52 TRP 0.015 0.002 TRP C 460 HIS 0.008 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00477 (14923) covalent geometry : angle 0.63715 (20290) SS BOND : bond 0.00499 ( 13) SS BOND : angle 1.00615 ( 26) hydrogen bonds : bond 0.04361 ( 571) hydrogen bonds : angle 4.89922 ( 1509) link_ALPHA1-2 : bond 0.00327 ( 1) link_ALPHA1-2 : angle 1.69318 ( 3) link_ALPHA1-3 : bond 0.00513 ( 2) link_ALPHA1-3 : angle 1.79949 ( 6) link_ALPHA1-6 : bond 0.00865 ( 1) link_ALPHA1-6 : angle 1.31484 ( 3) link_BETA1-4 : bond 0.00274 ( 3) link_BETA1-4 : angle 2.58122 ( 9) link_NAG-ASN : bond 0.00439 ( 18) link_NAG-ASN : angle 2.83343 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8246 (tm-30) REVERT: A 393 LEU cc_start: 0.9023 (mt) cc_final: 0.8819 (mm) REVERT: A 627 THR cc_start: 0.7003 (m) cc_final: 0.6765 (p) REVERT: C 317 LYS cc_start: 0.8453 (mmtt) cc_final: 0.7750 (mmpt) REVERT: C 375 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8244 (mp) REVERT: E 68 LYS cc_start: 0.9165 (tttt) cc_final: 0.8865 (ttpt) REVERT: F 112 GLU cc_start: 0.8477 (mp0) cc_final: 0.8249 (mp0) REVERT: H 96 ASP cc_start: 0.8507 (t70) cc_final: 0.7826 (t70) REVERT: H 99 GLU cc_start: 0.8031 (mp0) cc_final: 0.7582 (mp0) outliers start: 27 outliers final: 11 residues processed: 234 average time/residue: 0.7503 time to fit residues: 189.8213 Evaluate side-chains 229 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 217 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 94 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.0980 chunk 128 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN D 96 HIS D 155 HIS E 26 GLN G 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.092561 restraints weight = 19955.169| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.85 r_work: 0.2926 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14961 Z= 0.127 Angle : 0.554 7.292 20391 Z= 0.280 Chirality : 0.043 0.225 2379 Planarity : 0.004 0.046 2542 Dihedral : 7.652 80.491 2490 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.89 % Allowed : 10.44 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.20), residues: 1750 helix: 1.62 (0.26), residues: 405 sheet: 0.48 (0.24), residues: 432 loop : 0.41 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 249 TYR 0.014 0.001 TYR C 188 PHE 0.020 0.002 PHE H 52 TRP 0.012 0.001 TRP C 460 HIS 0.004 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00290 (14923) covalent geometry : angle 0.53951 (20290) SS BOND : bond 0.00360 ( 13) SS BOND : angle 0.67561 ( 26) hydrogen bonds : bond 0.03551 ( 571) hydrogen bonds : angle 4.58361 ( 1509) link_ALPHA1-2 : bond 0.00495 ( 1) link_ALPHA1-2 : angle 1.46786 ( 3) link_ALPHA1-3 : bond 0.00548 ( 2) link_ALPHA1-3 : angle 1.51787 ( 6) link_ALPHA1-6 : bond 0.00898 ( 1) link_ALPHA1-6 : angle 1.26854 ( 3) link_BETA1-4 : bond 0.00362 ( 3) link_BETA1-4 : angle 2.26287 ( 9) link_NAG-ASN : bond 0.00297 ( 18) link_NAG-ASN : angle 2.21333 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: A 143 LYS cc_start: 0.8539 (ttmt) cc_final: 0.7985 (ptpt) REVERT: B 63 ASP cc_start: 0.8627 (p0) cc_final: 0.8196 (p0) REVERT: C 126 GLN cc_start: 0.8736 (pt0) cc_final: 0.8348 (pt0) REVERT: C 161 ASP cc_start: 0.8423 (p0) cc_final: 0.8219 (p0) REVERT: C 249 ARG cc_start: 0.8469 (mtt90) cc_final: 0.8231 (mtt180) REVERT: C 317 LYS cc_start: 0.8491 (mmtt) cc_final: 0.7818 (mmpt) REVERT: D 55 ARG cc_start: 0.8458 (ptt-90) cc_final: 0.8007 (ptt-90) REVERT: D 115 LYS cc_start: 0.7169 (mmpt) cc_final: 0.6014 (pttp) REVERT: D 131 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8064 (tt0) REVERT: D 149 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7540 (mm-30) REVERT: F 112 GLU cc_start: 0.8422 (mp0) cc_final: 0.8099 (mp0) REVERT: G 47 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7806 (ttp-110) REVERT: H 96 ASP cc_start: 0.8488 (t70) cc_final: 0.7806 (t70) REVERT: H 99 GLU cc_start: 0.8046 (mp0) cc_final: 0.7680 (mp0) outliers start: 30 outliers final: 13 residues processed: 257 average time/residue: 0.7075 time to fit residues: 196.9679 Evaluate side-chains 235 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain G residue 47 ARG Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 7 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 HIS B 203 ASN D 155 HIS G 73 GLN G 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.089657 restraints weight = 20001.760| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.85 r_work: 0.2885 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14961 Z= 0.233 Angle : 0.628 7.595 20391 Z= 0.316 Chirality : 0.046 0.238 2379 Planarity : 0.005 0.042 2542 Dihedral : 7.752 81.553 2490 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.20 % Allowed : 11.76 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.20), residues: 1750 helix: 1.38 (0.25), residues: 411 sheet: 0.33 (0.24), residues: 433 loop : 0.22 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 249 TYR 0.016 0.002 TYR C 188 PHE 0.025 0.002 PHE H 52 TRP 0.012 0.002 TRP A 438 HIS 0.008 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00546 (14923) covalent geometry : angle 0.61377 (20290) SS BOND : bond 0.00533 ( 13) SS BOND : angle 0.88905 ( 26) hydrogen bonds : bond 0.04152 ( 571) hydrogen bonds : angle 4.71648 ( 1509) link_ALPHA1-2 : bond 0.00220 ( 1) link_ALPHA1-2 : angle 1.55839 ( 3) link_ALPHA1-3 : bond 0.00281 ( 2) link_ALPHA1-3 : angle 1.77260 ( 6) link_ALPHA1-6 : bond 0.00520 ( 1) link_ALPHA1-6 : angle 1.49358 ( 3) link_BETA1-4 : bond 0.00179 ( 3) link_BETA1-4 : angle 2.39665 ( 9) link_NAG-ASN : bond 0.00432 ( 18) link_NAG-ASN : angle 2.28492 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8239 (tm-30) REVERT: A 119 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: A 168 MET cc_start: 0.8951 (mpt) cc_final: 0.8587 (mmt) REVERT: A 623 LYS cc_start: 0.8220 (tppt) cc_final: 0.7994 (mmmm) REVERT: A 684 GLU cc_start: 0.8436 (mp0) cc_final: 0.8211 (mp0) REVERT: B 63 ASP cc_start: 0.8704 (p0) cc_final: 0.8163 (p0) REVERT: C 82 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6171 (tm) REVERT: C 115 GLN cc_start: 0.7913 (mt0) cc_final: 0.7644 (mp10) REVERT: C 161 ASP cc_start: 0.8523 (p0) cc_final: 0.8263 (p0) REVERT: C 249 ARG cc_start: 0.8493 (mtt90) cc_final: 0.8253 (mtt180) REVERT: C 317 LYS cc_start: 0.8449 (mmtt) cc_final: 0.7978 (mmtm) REVERT: C 375 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8357 (mp) REVERT: D 55 ARG cc_start: 0.8531 (ptt-90) cc_final: 0.8205 (ptt-90) REVERT: D 115 LYS cc_start: 0.7013 (mmpt) cc_final: 0.6772 (mmpt) REVERT: D 131 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8210 (tt0) REVERT: F 86 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8497 (mppt) REVERT: F 124 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8392 (mtt90) outliers start: 35 outliers final: 14 residues processed: 247 average time/residue: 0.7168 time to fit residues: 191.6999 Evaluate side-chains 226 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS B 203 ASN D 155 HIS G 73 GLN G 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.090938 restraints weight = 19901.823| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.85 r_work: 0.2901 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14961 Z= 0.155 Angle : 0.567 7.298 20391 Z= 0.287 Chirality : 0.043 0.212 2379 Planarity : 0.004 0.040 2542 Dihedral : 7.544 77.827 2490 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.64 % Allowed : 11.89 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1750 helix: 1.62 (0.26), residues: 405 sheet: 0.33 (0.24), residues: 438 loop : 0.31 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 249 TYR 0.013 0.001 TYR C 188 PHE 0.015 0.002 PHE A 379 TRP 0.011 0.001 TRP A 438 HIS 0.005 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00358 (14923) covalent geometry : angle 0.55431 (20290) SS BOND : bond 0.00391 ( 13) SS BOND : angle 0.67626 ( 26) hydrogen bonds : bond 0.03645 ( 571) hydrogen bonds : angle 4.56242 ( 1509) link_ALPHA1-2 : bond 0.00407 ( 1) link_ALPHA1-2 : angle 1.44755 ( 3) link_ALPHA1-3 : bond 0.00444 ( 2) link_ALPHA1-3 : angle 1.62000 ( 6) link_ALPHA1-6 : bond 0.00642 ( 1) link_ALPHA1-6 : angle 1.39784 ( 3) link_BETA1-4 : bond 0.00212 ( 3) link_BETA1-4 : angle 2.30833 ( 9) link_NAG-ASN : bond 0.00293 ( 18) link_NAG-ASN : angle 2.09773 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8626 (tt0) cc_final: 0.8313 (tp40) REVERT: A 103 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 119 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7760 (mp10) REVERT: A 143 LYS cc_start: 0.8555 (ttmt) cc_final: 0.8007 (ptpt) REVERT: A 168 MET cc_start: 0.8957 (mpt) cc_final: 0.8603 (mmt) REVERT: A 623 LYS cc_start: 0.8256 (tppt) cc_final: 0.8030 (mmmm) REVERT: A 684 GLU cc_start: 0.8437 (mp0) cc_final: 0.8174 (mp0) REVERT: C 115 GLN cc_start: 0.7916 (mt0) cc_final: 0.7649 (mp10) REVERT: C 126 GLN cc_start: 0.8722 (pt0) cc_final: 0.8362 (pt0) REVERT: C 161 ASP cc_start: 0.8556 (p0) cc_final: 0.8264 (p0) REVERT: C 249 ARG cc_start: 0.8494 (mtt90) cc_final: 0.8260 (mtt180) REVERT: C 317 LYS cc_start: 0.8506 (mmtt) cc_final: 0.7951 (mmtm) REVERT: C 375 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8332 (mp) REVERT: D 55 ARG cc_start: 0.8502 (ptt-90) cc_final: 0.8130 (ptt-90) REVERT: D 115 LYS cc_start: 0.6936 (mmpt) cc_final: 0.5809 (pttp) REVERT: D 131 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8222 (tt0) REVERT: E 68 LYS cc_start: 0.9107 (ttpt) cc_final: 0.8759 (tttm) REVERT: F 112 GLU cc_start: 0.8433 (mp0) cc_final: 0.8206 (mp0) REVERT: F 124 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8354 (mtt90) REVERT: H 96 ASP cc_start: 0.8538 (t70) cc_final: 0.7639 (t70) REVERT: H 99 GLU cc_start: 0.8092 (mp0) cc_final: 0.7632 (mp0) outliers start: 42 outliers final: 19 residues processed: 238 average time/residue: 0.7298 time to fit residues: 188.3658 Evaluate side-chains 228 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 78 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 511 HIS B 203 ASN D 108 HIS D 155 HIS E 53 ASN G 29 GLN G 73 GLN G 81 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.088406 restraints weight = 19976.158| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.85 r_work: 0.2860 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 14961 Z= 0.289 Angle : 0.674 8.510 20391 Z= 0.339 Chirality : 0.048 0.240 2379 Planarity : 0.005 0.050 2542 Dihedral : 7.787 79.817 2490 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.89 % Allowed : 12.08 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1750 helix: 1.19 (0.25), residues: 417 sheet: 0.14 (0.24), residues: 440 loop : 0.07 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 249 TYR 0.015 0.002 TYR E 109 PHE 0.022 0.002 PHE H 52 TRP 0.013 0.002 TRP A 438 HIS 0.009 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00674 (14923) covalent geometry : angle 0.66055 (20290) SS BOND : bond 0.00613 ( 13) SS BOND : angle 1.21610 ( 26) hydrogen bonds : bond 0.04435 ( 571) hydrogen bonds : angle 4.84856 ( 1509) link_ALPHA1-2 : bond 0.00155 ( 1) link_ALPHA1-2 : angle 1.57918 ( 3) link_ALPHA1-3 : bond 0.00185 ( 2) link_ALPHA1-3 : angle 1.88603 ( 6) link_ALPHA1-6 : bond 0.00301 ( 1) link_ALPHA1-6 : angle 1.61738 ( 3) link_BETA1-4 : bond 0.00058 ( 3) link_BETA1-4 : angle 2.52702 ( 9) link_NAG-ASN : bond 0.00486 ( 18) link_NAG-ASN : angle 2.30855 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8660 (tp40) cc_final: 0.8329 (tp40) REVERT: A 103 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8095 (tm-30) REVERT: A 119 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7806 (mp10) REVERT: A 168 MET cc_start: 0.8953 (mpt) cc_final: 0.8585 (mmt) REVERT: A 623 LYS cc_start: 0.8472 (tppt) cc_final: 0.8260 (mmmm) REVERT: A 625 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: A 684 GLU cc_start: 0.8461 (mp0) cc_final: 0.8194 (mp0) REVERT: C 115 GLN cc_start: 0.7900 (mt0) cc_final: 0.7629 (mp10) REVERT: C 161 ASP cc_start: 0.8611 (p0) cc_final: 0.8296 (p0) REVERT: C 249 ARG cc_start: 0.8589 (mtt90) cc_final: 0.8326 (mtt180) REVERT: C 317 LYS cc_start: 0.8472 (mmtt) cc_final: 0.7960 (mmtm) REVERT: D 55 ARG cc_start: 0.8504 (ptt-90) cc_final: 0.8201 (ptt-90) REVERT: D 115 LYS cc_start: 0.6991 (mmpt) cc_final: 0.6004 (pttp) REVERT: F 112 GLU cc_start: 0.8469 (mp0) cc_final: 0.8232 (mp0) REVERT: F 124 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8367 (mtt90) REVERT: H 110 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7811 (mtt90) outliers start: 46 outliers final: 24 residues processed: 241 average time/residue: 0.6936 time to fit residues: 181.3536 Evaluate side-chains 241 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 110 ARG Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 7 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS B 203 ASN D 155 HIS G 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.090876 restraints weight = 19770.466| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.84 r_work: 0.2901 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14961 Z= 0.146 Angle : 0.567 7.458 20391 Z= 0.288 Chirality : 0.043 0.220 2379 Planarity : 0.004 0.040 2542 Dihedral : 7.433 74.119 2490 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.58 % Allowed : 13.02 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.20), residues: 1750 helix: 1.54 (0.26), residues: 411 sheet: 0.23 (0.24), residues: 438 loop : 0.20 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 249 TYR 0.012 0.001 TYR C 188 PHE 0.016 0.002 PHE A 379 TRP 0.012 0.001 TRP A 438 HIS 0.004 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00338 (14923) covalent geometry : angle 0.55480 (20290) SS BOND : bond 0.00349 ( 13) SS BOND : angle 0.80380 ( 26) hydrogen bonds : bond 0.03557 ( 571) hydrogen bonds : angle 4.60234 ( 1509) link_ALPHA1-2 : bond 0.00427 ( 1) link_ALPHA1-2 : angle 1.39422 ( 3) link_ALPHA1-3 : bond 0.00493 ( 2) link_ALPHA1-3 : angle 1.60297 ( 6) link_ALPHA1-6 : bond 0.00646 ( 1) link_ALPHA1-6 : angle 1.41254 ( 3) link_BETA1-4 : bond 0.00200 ( 3) link_BETA1-4 : angle 2.28647 ( 9) link_NAG-ASN : bond 0.00276 ( 18) link_NAG-ASN : angle 2.06387 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8668 (tp40) cc_final: 0.8350 (tp40) REVERT: A 103 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8047 (tm-30) REVERT: A 143 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8021 (ptpt) REVERT: A 168 MET cc_start: 0.8949 (mpt) cc_final: 0.8608 (mmt) REVERT: A 623 LYS cc_start: 0.8454 (tppt) cc_final: 0.8236 (mmmm) REVERT: A 684 GLU cc_start: 0.8443 (mp0) cc_final: 0.8184 (mp0) REVERT: B 63 ASP cc_start: 0.8757 (p0) cc_final: 0.8242 (p0) REVERT: C 115 GLN cc_start: 0.7897 (mt0) cc_final: 0.7626 (mp10) REVERT: C 249 ARG cc_start: 0.8599 (mtt90) cc_final: 0.8347 (mtt180) REVERT: C 317 LYS cc_start: 0.8509 (mmtt) cc_final: 0.7840 (mmpt) REVERT: C 375 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8328 (mp) REVERT: D 55 ARG cc_start: 0.8381 (ptt-90) cc_final: 0.8128 (ptt-90) REVERT: D 115 LYS cc_start: 0.6859 (mmpt) cc_final: 0.5889 (pttp) REVERT: E 68 LYS cc_start: 0.9107 (ttpt) cc_final: 0.8730 (tttm) REVERT: F 124 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8300 (mtt90) REVERT: F 130 ASP cc_start: 0.8849 (m-30) cc_final: 0.8606 (m-30) REVERT: H 96 ASP cc_start: 0.8556 (t70) cc_final: 0.7833 (t70) outliers start: 41 outliers final: 20 residues processed: 241 average time/residue: 0.7315 time to fit residues: 191.0553 Evaluate side-chains 234 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 51 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS B 203 ASN G 50 GLN G 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.097929 restraints weight = 19861.650| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.84 r_work: 0.3007 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14961 Z= 0.145 Angle : 0.575 7.456 20391 Z= 0.290 Chirality : 0.043 0.367 2379 Planarity : 0.004 0.040 2542 Dihedral : 7.334 70.350 2490 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.08 % Allowed : 14.15 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1750 helix: 1.71 (0.26), residues: 405 sheet: 0.26 (0.24), residues: 440 loop : 0.29 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 249 TYR 0.012 0.001 TYR H 118 PHE 0.015 0.002 PHE A 379 TRP 0.012 0.001 TRP A 438 HIS 0.004 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00335 (14923) covalent geometry : angle 0.56052 (20290) SS BOND : bond 0.00348 ( 13) SS BOND : angle 0.74215 ( 26) hydrogen bonds : bond 0.03476 ( 571) hydrogen bonds : angle 4.52275 ( 1509) link_ALPHA1-2 : bond 0.00483 ( 1) link_ALPHA1-2 : angle 1.43668 ( 3) link_ALPHA1-3 : bond 0.00533 ( 2) link_ALPHA1-3 : angle 1.57957 ( 6) link_ALPHA1-6 : bond 0.00589 ( 1) link_ALPHA1-6 : angle 1.43932 ( 3) link_BETA1-4 : bond 0.00202 ( 3) link_BETA1-4 : angle 2.21019 ( 9) link_NAG-ASN : bond 0.00369 ( 18) link_NAG-ASN : angle 2.29151 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8682 (tp40) cc_final: 0.8348 (tp40) REVERT: A 103 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 119 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7792 (mp10) REVERT: A 143 LYS cc_start: 0.8505 (ttmt) cc_final: 0.7955 (ptpt) REVERT: A 168 MET cc_start: 0.8942 (mpt) cc_final: 0.8566 (mmt) REVERT: A 623 LYS cc_start: 0.8493 (tppt) cc_final: 0.8254 (mmmm) REVERT: A 684 GLU cc_start: 0.8422 (mp0) cc_final: 0.8155 (mp0) REVERT: C 86 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7796 (mtp) REVERT: C 115 GLN cc_start: 0.7907 (mt0) cc_final: 0.7591 (mp10) REVERT: C 126 GLN cc_start: 0.8681 (pt0) cc_final: 0.8316 (pt0) REVERT: C 249 ARG cc_start: 0.8592 (mtt90) cc_final: 0.8313 (mtt180) REVERT: C 317 LYS cc_start: 0.8507 (mmtt) cc_final: 0.7936 (mmtm) REVERT: C 375 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8313 (mp) REVERT: D 114 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8180 (pp) REVERT: D 115 LYS cc_start: 0.6749 (mmpt) cc_final: 0.5776 (pttp) REVERT: E 68 LYS cc_start: 0.9095 (ttpt) cc_final: 0.8669 (tttm) REVERT: F 112 GLU cc_start: 0.8379 (mp0) cc_final: 0.8168 (mp0) REVERT: F 124 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8244 (mtt90) REVERT: F 130 ASP cc_start: 0.8784 (m-30) cc_final: 0.8478 (m-30) outliers start: 33 outliers final: 21 residues processed: 236 average time/residue: 0.7411 time to fit residues: 189.7499 Evaluate side-chains 243 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 33 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 511 HIS B 203 ASN G 81 ASN G 121 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.095919 restraints weight = 19910.729| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.84 r_work: 0.2975 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14961 Z= 0.237 Angle : 0.642 8.327 20391 Z= 0.323 Chirality : 0.046 0.381 2379 Planarity : 0.005 0.043 2542 Dihedral : 7.497 70.458 2490 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.26 % Allowed : 14.03 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1750 helix: 1.41 (0.25), residues: 411 sheet: 0.11 (0.24), residues: 442 loop : 0.16 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 249 TYR 0.014 0.002 TYR G 60 PHE 0.017 0.002 PHE B 105 TRP 0.012 0.002 TRP A 438 HIS 0.007 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00552 (14923) covalent geometry : angle 0.62763 (20290) SS BOND : bond 0.00515 ( 13) SS BOND : angle 0.93986 ( 26) hydrogen bonds : bond 0.04098 ( 571) hydrogen bonds : angle 4.72998 ( 1509) link_ALPHA1-2 : bond 0.00255 ( 1) link_ALPHA1-2 : angle 1.55079 ( 3) link_ALPHA1-3 : bond 0.00370 ( 2) link_ALPHA1-3 : angle 1.73227 ( 6) link_ALPHA1-6 : bond 0.00289 ( 1) link_ALPHA1-6 : angle 1.62061 ( 3) link_BETA1-4 : bond 0.00078 ( 3) link_BETA1-4 : angle 2.31014 ( 9) link_NAG-ASN : bond 0.00501 ( 18) link_NAG-ASN : angle 2.41170 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8696 (tp40) cc_final: 0.8362 (tp40) REVERT: A 103 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 119 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: A 143 LYS cc_start: 0.8514 (ttmt) cc_final: 0.7950 (ptpt) REVERT: A 168 MET cc_start: 0.8937 (mpt) cc_final: 0.8626 (mmt) REVERT: A 623 LYS cc_start: 0.8559 (tppt) cc_final: 0.8334 (mmmm) REVERT: A 684 GLU cc_start: 0.8443 (mp0) cc_final: 0.8170 (mp0) REVERT: C 115 GLN cc_start: 0.7849 (mt0) cc_final: 0.7544 (mp10) REVERT: C 249 ARG cc_start: 0.8597 (mtt90) cc_final: 0.8292 (mtt180) REVERT: C 317 LYS cc_start: 0.8545 (mmtt) cc_final: 0.7887 (mmpt) REVERT: C 375 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8356 (mp) REVERT: D 115 LYS cc_start: 0.6771 (mmpt) cc_final: 0.5861 (pttp) REVERT: E 68 LYS cc_start: 0.9087 (ttpt) cc_final: 0.8669 (tttm) REVERT: F 124 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8271 (mtt90) REVERT: F 130 ASP cc_start: 0.8946 (m-30) cc_final: 0.8613 (m-30) REVERT: H 52 PHE cc_start: 0.9501 (OUTLIER) cc_final: 0.8420 (m-80) outliers start: 36 outliers final: 24 residues processed: 237 average time/residue: 0.7472 time to fit residues: 191.4978 Evaluate side-chains 237 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 62 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 94 optimal weight: 0.0030 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 164 optimal weight: 0.2980 chunk 44 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS B 203 ASN G 50 GLN G 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098964 restraints weight = 19861.504| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.84 r_work: 0.3023 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14961 Z= 0.118 Angle : 0.565 13.032 20391 Z= 0.285 Chirality : 0.043 0.349 2379 Planarity : 0.004 0.039 2542 Dihedral : 7.109 62.160 2490 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.57 % Allowed : 14.72 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.20), residues: 1750 helix: 1.65 (0.26), residues: 411 sheet: 0.23 (0.24), residues: 442 loop : 0.28 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 55 TYR 0.012 0.001 TYR F 56 PHE 0.014 0.001 PHE A 379 TRP 0.012 0.001 TRP A 438 HIS 0.004 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00269 (14923) covalent geometry : angle 0.55204 (20290) SS BOND : bond 0.00284 ( 13) SS BOND : angle 0.64728 ( 26) hydrogen bonds : bond 0.03248 ( 571) hydrogen bonds : angle 4.50058 ( 1509) link_ALPHA1-2 : bond 0.00552 ( 1) link_ALPHA1-2 : angle 1.35059 ( 3) link_ALPHA1-3 : bond 0.00698 ( 2) link_ALPHA1-3 : angle 1.43408 ( 6) link_ALPHA1-6 : bond 0.00638 ( 1) link_ALPHA1-6 : angle 1.46262 ( 3) link_BETA1-4 : bond 0.00196 ( 3) link_BETA1-4 : angle 2.06772 ( 9) link_NAG-ASN : bond 0.00315 ( 18) link_NAG-ASN : angle 2.12301 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8669 (tp40) cc_final: 0.8328 (tp40) REVERT: A 103 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8033 (tm-30) REVERT: A 119 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: A 143 LYS cc_start: 0.8495 (ttmt) cc_final: 0.7967 (ptpt) REVERT: A 168 MET cc_start: 0.8945 (mpt) cc_final: 0.8581 (mmt) REVERT: A 623 LYS cc_start: 0.8504 (tppt) cc_final: 0.8265 (mmmm) REVERT: A 684 GLU cc_start: 0.8423 (mp0) cc_final: 0.8149 (mp0) REVERT: C 115 GLN cc_start: 0.7919 (mt0) cc_final: 0.7576 (mp10) REVERT: C 126 GLN cc_start: 0.8725 (pt0) cc_final: 0.8378 (pt0) REVERT: C 317 LYS cc_start: 0.8530 (mmtt) cc_final: 0.7868 (mmpt) REVERT: C 375 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8316 (mp) REVERT: D 114 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8243 (pp) REVERT: D 115 LYS cc_start: 0.6669 (mmpt) cc_final: 0.5658 (pttp) REVERT: E 68 LYS cc_start: 0.9082 (ttpt) cc_final: 0.8652 (tttm) REVERT: F 130 ASP cc_start: 0.8753 (m-30) cc_final: 0.8553 (m-30) REVERT: H 52 PHE cc_start: 0.9449 (OUTLIER) cc_final: 0.8396 (m-80) outliers start: 25 outliers final: 19 residues processed: 233 average time/residue: 0.7422 time to fit residues: 187.2793 Evaluate side-chains 235 residues out of total 1591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.0370 chunk 148 optimal weight: 0.0010 chunk 11 optimal weight: 0.0270 chunk 93 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN G 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099264 restraints weight = 19799.536| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.84 r_work: 0.3028 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14961 Z= 0.123 Angle : 0.565 13.214 20391 Z= 0.284 Chirality : 0.043 0.333 2379 Planarity : 0.004 0.040 2542 Dihedral : 6.849 59.681 2490 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.51 % Allowed : 15.16 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.20), residues: 1750 helix: 1.79 (0.26), residues: 405 sheet: 0.31 (0.24), residues: 440 loop : 0.32 (0.22), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 249 TYR 0.014 0.001 TYR F 56 PHE 0.013 0.001 PHE A 379 TRP 0.012 0.001 TRP A 438 HIS 0.003 0.001 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.00284 (14923) covalent geometry : angle 0.55365 (20290) SS BOND : bond 0.00305 ( 13) SS BOND : angle 0.64394 ( 26) hydrogen bonds : bond 0.03213 ( 571) hydrogen bonds : angle 4.43692 ( 1509) link_ALPHA1-2 : bond 0.00479 ( 1) link_ALPHA1-2 : angle 1.40023 ( 3) link_ALPHA1-3 : bond 0.00797 ( 2) link_ALPHA1-3 : angle 1.40670 ( 6) link_ALPHA1-6 : bond 0.00590 ( 1) link_ALPHA1-6 : angle 1.55011 ( 3) link_BETA1-4 : bond 0.00215 ( 3) link_BETA1-4 : angle 1.87847 ( 9) link_NAG-ASN : bond 0.00358 ( 18) link_NAG-ASN : angle 2.07186 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6215.93 seconds wall clock time: 106 minutes 23.11 seconds (6383.11 seconds total)