Starting phenix.real_space_refine on Sat Jul 4 15:03:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wld_32582/07_2026/7wld_32582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wld_32582/07_2026/7wld_32582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wld_32582/07_2026/7wld_32582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wld_32582/07_2026/7wld_32582.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wld_32582/07_2026/7wld_32582.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wld_32582/07_2026/7wld_32582.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wld_32582/07_2026/7wld_32582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wld_32582/07_2026/7wld_32582.cif" } resolution = 2.53 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= 0.013 sd= 0.182 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 9 5.49 5 S 76 5.16 5 C 13082 2.51 5 N 3103 2.21 5 O 3461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19732 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 4458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4458 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 27, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 2, 'ASP:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "K" Number of atoms: 2644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2644 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 311} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "S" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3968 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 499} Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 11, 'ASP:plan': 8, 'GLN:plan1': 5, 'HIS:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 144 Chain: "T" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4220 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 41, 'TRANS': 486} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 43 Chain: "U" Number of atoms: 3419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3419 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 399} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 407 Unusual residues: {'AJP': 1, 'BJR': 2, 'PEE': 1, 'Y01': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P5S:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 98 Unusual residues: {'CLR': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'05E': 1, 'NAG': 1, 'PA1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 405 Unusual residues: {'06O': 1, 'CDL': 1, 'CLR': 2, 'DKB': 1, 'Y01': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Time building chain proxies: 4.02, per 1000 atoms: 0.20 Number of scatterers: 19732 At special positions: 0 Unit cell: (102.85, 152.15, 156.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 76 16.00 P 9 15.00 O 3461 8.00 N 3103 7.00 C 13082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 266 " distance=2.03 Simple disulfide: pdb=" SG CYS K 92 " - pdb=" SG CYS T 182 " distance=2.03 Simple disulfide: pdb=" SG CYS T 195 " - pdb=" SG CYS T 272 " distance=2.03 Simple disulfide: pdb=" SG CYS T 226 " - pdb=" SG CYS T 231 " distance=1.96 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=2, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN G 203 " " NAG S 901 " - " ASN S 267 " " NAG T 902 " - " ASN T 327 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 847.4 milliseconds 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4556 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 13 sheets defined 49.6% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'G' and resid 9 through 38 removed outlier: 3.534A pdb=" N LEU G 13 " --> pdb=" O ARG G 9 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA G 14 " --> pdb=" O ARG G 10 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG G 15 " --> pdb=" O ARG G 11 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA G 22 " --> pdb=" O LEU G 18 " (cutoff:3.500A) Proline residue: G 23 - end of helix removed outlier: 3.834A pdb=" N VAL G 26 " --> pdb=" O ALA G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 57 Processing helix chain 'G' and resid 66 through 85 removed outlier: 3.787A pdb=" N ALA G 70 " --> pdb=" O GLY G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 100 Processing helix chain 'G' and resid 156 through 171 Processing helix chain 'G' and resid 189 through 201 Processing helix chain 'G' and resid 241 through 245 removed outlier: 3.596A pdb=" N GLN G 245 " --> pdb=" O LEU G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 262 removed outlier: 4.208A pdb=" N LEU G 252 " --> pdb=" O ASN G 248 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN G 260 " --> pdb=" O GLN G 256 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS G 261 " --> pdb=" O THR G 257 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY G 262 " --> pdb=" O PHE G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 300 removed outlier: 4.029A pdb=" N GLN G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY G 300 " --> pdb=" O ARG G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 310 removed outlier: 4.263A pdb=" N LEU G 308 " --> pdb=" O GLY G 304 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE G 309 " --> pdb=" O SER G 305 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU G 310 " --> pdb=" O HIS G 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 304 through 310' Processing helix chain 'G' and resid 311 through 313 No H-bonds generated for 'chain 'G' and resid 311 through 313' Processing helix chain 'G' and resid 331 through 348 removed outlier: 3.937A pdb=" N VAL G 335 " --> pdb=" O ASP G 331 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS G 348 " --> pdb=" O ARG G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 375 Processing helix chain 'G' and resid 375 through 398 removed outlier: 4.215A pdb=" N LEU G 381 " --> pdb=" O ALA G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 427 through 444 Processing helix chain 'G' and resid 449 through 456 Processing helix chain 'G' and resid 459 through 477 removed outlier: 3.767A pdb=" N VAL G 464 " --> pdb=" O GLU G 460 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL G 465 " --> pdb=" O ALA G 461 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU G 476 " --> pdb=" O TYR G 472 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA G 477 " --> pdb=" O ALA G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 479 through 483 Processing helix chain 'G' and resid 492 through 517 Processing helix chain 'G' and resid 517 through 533 Proline residue: G 530 - end of helix Processing helix chain 'G' and resid 540 through 550 Processing helix chain 'G' and resid 552 through 568 removed outlier: 3.817A pdb=" N LEU G 557 " --> pdb=" O PRO G 553 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU G 558 " --> pdb=" O ALA G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 596 Processing helix chain 'G' and resid 598 through 619 removed outlier: 4.609A pdb=" N TYR G 608 " --> pdb=" O SER G 604 " (cutoff:3.500A) Proline residue: G 609 - end of helix Processing helix chain 'K' and resid 58 through 76 removed outlier: 4.205A pdb=" N VAL K 62 " --> pdb=" O ASN K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing helix chain 'K' and resid 122 through 126 removed outlier: 3.905A pdb=" N VAL K 126 " --> pdb=" O SER K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 137 Processing helix chain 'K' and resid 144 through 148 Processing helix chain 'K' and resid 180 through 193 removed outlier: 3.704A pdb=" N LYS K 193 " --> pdb=" O GLN K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 213 removed outlier: 3.523A pdb=" N TYR K 212 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU K 213 " --> pdb=" O SER K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 257 Processing helix chain 'K' and resid 294 through 299 removed outlier: 6.384A pdb=" N LEU K 299 " --> pdb=" O LYS K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 305 Processing helix chain 'K' and resid 350 through 357 Processing helix chain 'K' and resid 367 through 386 removed outlier: 3.875A pdb=" N LYS K 384 " --> pdb=" O MET K 380 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR K 385 " --> pdb=" O VAL K 381 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 39 removed outlier: 3.964A pdb=" N GLU S 12 " --> pdb=" O ALA S 8 " (cutoff:3.500A) Proline residue: S 33 - end of helix Processing helix chain 'S' and resid 47 through 55 removed outlier: 3.582A pdb=" N ASN S 55 " --> pdb=" O ILE S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 82 removed outlier: 3.689A pdb=" N LYS S 81 " --> pdb=" O ASP S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 121 removed outlier: 3.870A pdb=" N GLU S 116 " --> pdb=" O LEU S 112 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU S 117 " --> pdb=" O ASP S 113 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER S 121 " --> pdb=" O GLU S 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 132 removed outlier: 3.509A pdb=" N ALA S 127 " --> pdb=" O SER S 123 " (cutoff:3.500A) Processing helix chain 'S' and resid 179 through 193 Processing helix chain 'S' and resid 215 through 219 Processing helix chain 'S' and resid 246 through 254 removed outlier: 3.671A pdb=" N ALA S 250 " --> pdb=" O ASP S 246 " (cutoff:3.500A) Processing helix chain 'S' and resid 254 through 263 removed outlier: 3.880A pdb=" N PHE S 258 " --> pdb=" O TYR S 254 " (cutoff:3.500A) Processing helix chain 'S' and resid 299 through 303 Processing helix chain 'S' and resid 307 through 312 Processing helix chain 'S' and resid 330 through 334 Processing helix chain 'S' and resid 366 through 371 removed outlier: 4.261A pdb=" N ALA S 371 " --> pdb=" O THR S 368 " (cutoff:3.500A) Processing helix chain 'S' and resid 381 through 397 removed outlier: 3.738A pdb=" N VAL S 385 " --> pdb=" O ASP S 381 " (cutoff:3.500A) Processing helix chain 'S' and resid 414 through 418 removed outlier: 3.734A pdb=" N GLY S 417 " --> pdb=" O THR S 414 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU S 418 " --> pdb=" O SER S 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 414 through 418' Processing helix chain 'S' and resid 419 through 452 removed outlier: 3.567A pdb=" N LEU S 423 " --> pdb=" O MET S 419 " (cutoff:3.500A) Processing helix chain 'S' and resid 458 through 482 Processing helix chain 'S' and resid 483 through 503 Processing helix chain 'S' and resid 504 through 512 removed outlier: 3.864A pdb=" N LEU S 508 " --> pdb=" O PRO S 505 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS S 509 " --> pdb=" O SER S 506 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU S 510 " --> pdb=" O LEU S 507 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR S 512 " --> pdb=" O HIS S 509 " (cutoff:3.500A) Processing helix chain 'S' and resid 514 through 516 No H-bonds generated for 'chain 'S' and resid 514 through 516' Processing helix chain 'S' and resid 517 through 523 removed outlier: 3.773A pdb=" N ILE S 521 " --> pdb=" O GLN S 517 " (cutoff:3.500A) Processing helix chain 'S' and resid 526 through 531 Processing helix chain 'T' and resid 70 through 75 removed outlier: 3.561A pdb=" N GLN T 75 " --> pdb=" O LYS T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 80 removed outlier: 3.582A pdb=" N LYS T 79 " --> pdb=" O GLN T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 100 Processing helix chain 'T' and resid 122 through 139 removed outlier: 3.680A pdb=" N SER T 126 " --> pdb=" O ASP T 122 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY T 136 " --> pdb=" O ASN T 132 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE T 137 " --> pdb=" O VAL T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 141 through 145 Processing helix chain 'T' and resid 146 through 148 No H-bonds generated for 'chain 'T' and resid 146 through 148' Processing helix chain 'T' and resid 167 through 169 No H-bonds generated for 'chain 'T' and resid 167 through 169' Processing helix chain 'T' and resid 182 through 192 Proline residue: T 188 - end of helix Processing helix chain 'T' and resid 199 through 205 removed outlier: 3.659A pdb=" N SER T 202 " --> pdb=" O ALA T 199 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL T 203 " --> pdb=" O GLY T 200 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 211 Processing helix chain 'T' and resid 260 through 265 Processing helix chain 'T' and resid 490 through 494 removed outlier: 3.516A pdb=" N SER T 494 " --> pdb=" O LEU T 491 " (cutoff:3.500A) Processing helix chain 'T' and resid 526 through 549 removed outlier: 3.637A pdb=" N CYS T 530 " --> pdb=" O TYR T 526 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG T 549 " --> pdb=" O ASN T 545 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 21 removed outlier: 3.672A pdb=" N ARG U 21 " --> pdb=" O ALA U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 29 Processing helix chain 'U' and resid 40 through 53 removed outlier: 3.661A pdb=" N VAL U 44 " --> pdb=" O SER U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 60 removed outlier: 4.192A pdb=" N GLY U 60 " --> pdb=" O PRO U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 76 Processing helix chain 'U' and resid 79 through 116 removed outlier: 3.700A pdb=" N PHE U 84 " --> pdb=" O ALA U 80 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET U 85 " --> pdb=" O GLU U 81 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU U 115 " --> pdb=" O LYS U 111 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU U 116 " --> pdb=" O LEU U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 135 through 146 Processing helix chain 'U' and resid 147 through 156 Processing helix chain 'U' and resid 159 through 176 removed outlier: 3.602A pdb=" N ASN U 163 " --> pdb=" O THR U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 178 through 193 Processing helix chain 'U' and resid 194 through 198 removed outlier: 3.517A pdb=" N LEU U 197 " --> pdb=" O LEU U 194 " (cutoff:3.500A) Processing helix chain 'U' and resid 199 through 212 removed outlier: 3.626A pdb=" N GLY U 203 " --> pdb=" O LEU U 199 " (cutoff:3.500A) Processing helix chain 'U' and resid 220 through 249 removed outlier: 3.818A pdb=" N PHE U 246 " --> pdb=" O CYS U 242 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU U 247 " --> pdb=" O LEU U 243 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU U 248 " --> pdb=" O SER U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 252 through 264 removed outlier: 3.503A pdb=" N ALA U 256 " --> pdb=" O ASP U 252 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE U 260 " --> pdb=" O ALA U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 274 through 280 Processing helix chain 'U' and resid 285 through 300 removed outlier: 4.494A pdb=" N VAL U 297 " --> pdb=" O PHE U 293 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE U 298 " --> pdb=" O GLN U 294 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR U 300 " --> pdb=" O ASN U 296 " (cutoff:3.500A) Processing helix chain 'U' and resid 300 through 308 Processing helix chain 'U' and resid 311 through 327 Processing helix chain 'U' and resid 331 through 340 removed outlier: 3.922A pdb=" N LEU U 337 " --> pdb=" O GLY U 333 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR U 338 " --> pdb=" O ASP U 334 " (cutoff:3.500A) Processing helix chain 'U' and resid 341 through 352 removed outlier: 3.571A pdb=" N ASN U 346 " --> pdb=" O PRO U 343 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N HIS U 347 " --> pdb=" O VAL U 344 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ARG U 350 " --> pdb=" O HIS U 347 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 378 removed outlier: 3.912A pdb=" N LEU U 358 " --> pdb=" O ASN U 354 " (cutoff:3.500A) Proline residue: U 370 - end of helix Processing helix chain 'U' and resid 383 through 419 removed outlier: 4.278A pdb=" N PHE U 387 " --> pdb=" O ASN U 383 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.532A pdb=" N PHE G 368 " --> pdb=" O GLN G 46 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG G 367 " --> pdb=" O PRO G 363 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 208 through 209 removed outlier: 7.417A pdb=" N TYR G 122 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU G 142 " --> pdb=" O ASP G 179 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL G 181 " --> pdb=" O GLU G 142 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU G 144 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU G 183 " --> pdb=" O LEU G 144 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU G 146 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N THR G 185 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL G 148 " --> pdb=" O THR G 185 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N SER G 143 " --> pdb=" O GLN G 220 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA G 222 " --> pdb=" O SER G 143 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL G 145 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA G 224 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR G 147 " --> pdb=" O ALA G 224 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU G 226 " --> pdb=" O THR G 147 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU G 315 " --> pdb=" O GLN G 220 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR G 318 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU G 235 " --> pdb=" O THR G 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 82 through 86 removed outlier: 8.653A pdb=" N VAL K 83 " --> pdb=" O ASN K 45 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA K 47 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N MET K 85 " --> pdb=" O ALA K 47 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU K 49 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR K 162 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU K 198 " --> pdb=" O SER K 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 165 through 166 removed outlier: 3.864A pdb=" N PHE K 169 " --> pdb=" O GLY K 166 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU K 176 " --> pdb=" O PHE K 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 311 through 312 removed outlier: 6.761A pdb=" N TYR S 227 " --> pdb=" O SER S 269 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASP S 271 " --> pdb=" O TYR S 227 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE S 229 " --> pdb=" O ASP S 271 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N GLN S 273 " --> pdb=" O ILE S 229 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE S 231 " --> pdb=" O GLN S 273 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU S 275 " --> pdb=" O PHE S 231 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU S 233 " --> pdb=" O LEU S 275 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N TYR T 66 " --> pdb=" O VAL S 270 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER S 272 " --> pdb=" O TYR T 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 85 through 92 removed outlier: 4.741A pdb=" N ILE S 100 " --> pdb=" O ILE S 92 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU S 59 " --> pdb=" O LYS S 101 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ARG S 103 " --> pdb=" O LEU S 59 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU S 61 " --> pdb=" O ARG S 103 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLN S 105 " --> pdb=" O LEU S 61 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL S 63 " --> pdb=" O GLN S 105 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA S 107 " --> pdb=" O VAL S 63 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL S 65 " --> pdb=" O ALA S 107 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N LEU S 142 " --> pdb=" O MET S 62 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL S 144 " --> pdb=" O PRO S 64 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR S 66 " --> pdb=" O VAL S 144 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL S 146 " --> pdb=" O THR S 66 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL S 68 " --> pdb=" O VAL S 146 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR S 143 " --> pdb=" O ALA S 168 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL S 170 " --> pdb=" O THR S 143 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR S 145 " --> pdb=" O VAL S 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 241 through 244 Processing sheet with id=AA8, first strand: chain 'S' and resid 285 through 287 Processing sheet with id=AA9, first strand: chain 'T' and resid 150 through 151 removed outlier: 6.831A pdb=" N GLY T 109 " --> pdb=" O PHE T 89 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N PHE T 89 " --> pdb=" O GLY T 109 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLU T 111 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU T 87 " --> pdb=" O GLU T 111 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TRP T 113 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU T 85 " --> pdb=" O TRP T 113 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP T 115 " --> pdb=" O ARG T 83 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N ARG T 83 " --> pdb=" O PRO T 224 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR T 215 " --> pdb=" O VAL T 245 " (cutoff:3.500A) removed outlier: 10.168A pdb=" N GLU T 277 " --> pdb=" O ASP T 28 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU T 30 " --> pdb=" O GLU T 277 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N ARG T 279 " --> pdb=" O LEU T 30 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU T 32 " --> pdb=" O ARG T 279 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N TYR T 281 " --> pdb=" O GLU T 32 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU T 34 " --> pdb=" O TYR T 281 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ASP T 283 " --> pdb=" O LEU T 34 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE T 36 " --> pdb=" O ASP T 283 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 258 through 259 Processing sheet with id=AB2, first strand: chain 'T' and resid 352 through 359 removed outlier: 3.813A pdb=" N HIS T 353 " --> pdb=" O TYR T 373 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN T 445 " --> pdb=" O THR T 399 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR T 399 " --> pdb=" O GLN T 445 " (cutoff:3.500A) removed outlier: 12.444A pdb=" N GLU T 447 " --> pdb=" O VAL T 397 " (cutoff:3.500A) removed outlier: 11.260A pdb=" N VAL T 397 " --> pdb=" O GLU T 447 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 413 through 417 removed outlier: 3.996A pdb=" N TYR T 413 " --> pdb=" O LEU T 431 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU T 474 " --> pdb=" O PRO T 382 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 464 through 466 938 hydrogen bonds defined for protein. 2652 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2940 1.30 - 1.44: 5521 1.44 - 1.57: 11683 1.57 - 1.71: 19 1.71 - 1.84: 125 Bond restraints: 20288 Sorted by residual: bond pdb=" C24 06O U 809 " pdb=" C71 06O U 809 " ideal model delta sigma weight residual 2.441 1.541 0.900 2.00e-02 2.50e+03 2.03e+03 bond pdb=" C41 06O U 809 " pdb=" C42 06O U 809 " ideal model delta sigma weight residual 1.337 1.548 -0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C5 PA1 T 903 " pdb=" O5 PA1 T 903 " ideal model delta sigma weight residual 1.417 1.546 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" O69 06O U 809 " pdb=" P26 06O U 809 " ideal model delta sigma weight residual 1.631 1.505 0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C ASP K 152 " pdb=" O ASP K 152 " ideal model delta sigma weight residual 1.236 1.179 0.057 9.90e-03 1.02e+04 3.32e+01 ... (remaining 20283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.52: 27712 16.52 - 33.04: 3 33.04 - 49.56: 0 49.56 - 66.09: 0 66.09 - 82.61: 1 Bond angle restraints: 27716 Sorted by residual: angle pdb=" C24 06O U 809 " pdb=" C71 06O U 809 " pdb=" O72 06O U 809 " ideal model delta sigma weight residual 30.16 112.77 -82.61 3.00e+00 1.11e-01 7.58e+02 angle pdb=" N LEU K 279 " pdb=" CA LEU K 279 " pdb=" C LEU K 279 " ideal model delta sigma weight residual 113.12 104.04 9.08 1.25e+00 6.40e-01 5.28e+01 angle pdb=" N LEU S 153 " pdb=" CA LEU S 153 " pdb=" C LEU S 153 " ideal model delta sigma weight residual 113.41 104.77 8.64 1.22e+00 6.72e-01 5.02e+01 angle pdb=" N VAL K 281 " pdb=" CA VAL K 281 " pdb=" C VAL K 281 " ideal model delta sigma weight residual 113.10 106.41 6.69 9.70e-01 1.06e+00 4.75e+01 angle pdb=" CA2 06O U 809 " pdb=" C71 06O U 809 " pdb=" O72 06O U 809 " ideal model delta sigma weight residual 127.44 107.77 19.67 3.00e+00 1.11e-01 4.30e+01 ... (remaining 27711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 11475 33.37 - 66.74: 356 66.74 - 100.11: 46 100.11 - 133.48: 9 133.48 - 166.85: 8 Dihedral angle restraints: 11894 sinusoidal: 4849 harmonic: 7045 Sorted by residual: dihedral pdb=" CB CYS T 195 " pdb=" SG CYS T 195 " pdb=" SG CYS T 272 " pdb=" CB CYS T 272 " ideal model delta sinusoidal sigma weight residual 93.00 176.30 -83.30 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" O72 06O U 809 " pdb=" C71 06O U 809 " pdb=" CA2 06O U 809 " pdb=" OA3 06O U 809 " ideal model delta sinusoidal sigma weight residual 199.82 32.97 166.85 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C34 BJR G1605 " pdb=" C35 BJR G1605 " pdb=" C36 BJR G1605 " pdb=" C37 BJR G1605 " ideal model delta sinusoidal sigma weight residual 179.73 16.80 162.93 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 11891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.551: 3230 0.551 - 1.103: 2 1.103 - 1.654: 0 1.654 - 2.205: 1 2.205 - 2.756: 1 Chirality restraints: 3234 Sorted by residual: chirality pdb=" C24 06O U 809 " pdb=" C05 06O U 809 " pdb=" C71 06O U 809 " pdb=" O25 06O U 809 " both_signs ideal model delta sigma weight residual False 5.03 2.27 2.76 2.00e-01 2.50e+01 1.90e+02 chirality pdb=" C71 06O U 809 " pdb=" C24 06O U 809 " pdb=" CA2 06O U 809 " pdb=" O72 06O U 809 " both_signs ideal model delta sigma weight residual False -0.62 -2.72 2.10 2.00e-01 2.50e+01 1.10e+02 chirality pdb=" C81 05E T 901 " pdb=" C80 05E T 901 " pdb=" C90 05E T 901 " pdb=" O82 05E T 901 " both_signs ideal model delta sigma weight residual False 2.59 1.90 0.69 2.00e-01 2.50e+01 1.19e+01 ... (remaining 3231 not shown) Planarity restraints: 3332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 902 " -0.346 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG T 902 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG T 902 " -0.110 2.00e-02 2.50e+03 pdb=" N2 NAG T 902 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG T 902 " -0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL S 146 " 0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C VAL S 146 " -0.079 2.00e-02 2.50e+03 pdb=" O VAL S 146 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE S 147 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN T 327 " 0.007 2.00e-02 2.50e+03 3.34e-02 1.40e+01 pdb=" CG ASN T 327 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN T 327 " -0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN T 327 " 0.055 2.00e-02 2.50e+03 pdb=" C1 NAG T 902 " -0.038 2.00e-02 2.50e+03 ... (remaining 3329 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1295 2.74 - 3.28: 18253 3.28 - 3.82: 30317 3.82 - 4.36: 37685 4.36 - 4.90: 65212 Nonbonded interactions: 152762 Sorted by model distance: nonbonded pdb=" OH TYR K 113 " pdb=" OE1 GLU T 184 " model vdw 2.197 3.040 nonbonded pdb=" CD1 ILE S 247 " pdb=" ND1 HIS T 65 " model vdw 2.202 3.540 nonbonded pdb=" O LEU G 349 " pdb=" NH2 ARG K 95 " model vdw 2.220 3.120 nonbonded pdb=" OH TYR U 338 " pdb=" OE1 GLN U 398 " model vdw 2.254 3.040 nonbonded pdb=" O ALA S 8 " pdb=" OE1 GLU S 12 " model vdw 2.270 3.040 ... (remaining 152757 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.660 Find NCS groups from input model: 0.140 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:7.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 : 0.009 0.900 20298 Z= 0.519 Angle : 1.079 82.607 27736 Z= 0.554 Chirality : 0.082 2.756 3234 Planarity : 0.008 0.299 3329 Dihedral : 17.032 166.851 7326 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.19 % Favored : 97.73 % Rotamer: Outliers : 1.87 % Allowed : 1.06 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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: 0.47 (0.17), residues: 2377 helix: 1.44 (0.17), residues: 970 sheet: 0.79 (0.25), residues: 409 loop : -1.04 (0.18), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 11 TYR 0.024 0.002 TYR K 59 PHE 0.057 0.002 PHE G 255 TRP 0.017 0.002 TRP T 127 HIS 0.010 0.001 HIS K 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00931 / 0.51 (20288) covalent geometry : angle 1.07206 / 0.55 (27716) SS BOND : bond 0.03558 / 1.78 ( 4) SS BOND : angle 3.32001 / 1.24 ( 8) hydrogen bonds : bond 0.18886 / 12.63 ( 938) hydrogen bonds : angle 6.02999 / 4.28 ( 2652) Misc. bond : bond 0.05961 / 4.09 ( 2) link_BETA1-4 : bond 0.00748 / 0.50 ( 1) link_BETA1-4 : angle 4.45193 / 3.37 ( 3) link_NAG-ASN : bond 0.04487 / 2.14 ( 3) link_NAG-ASN : angle 5.39884 / 2.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 292 time to evaluate : 0.780 Fit side-chains REVERT: G 9 ARG cc_start: 0.3842 (OUTLIER) cc_final: 0.3397 (mtm-85) REVERT: G 265 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7535 (tp) REVERT: S 98 MET cc_start: 0.6873 (ttm) cc_final: 0.6468 (ttm) REVERT: S 147 ILE cc_start: 0.6146 (OUTLIER) cc_final: 0.5886 (pp) REVERT: S 197 GLU cc_start: 0.6677 (pm20) cc_final: 0.6368 (pm20) REVERT: S 279 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7048 (mmt) REVERT: S 522 TYR cc_start: 0.5863 (p90) cc_final: 0.5423 (p90) REVERT: T 262 ARG cc_start: 0.7580 (mtt90) cc_final: 0.7298 (ttt180) REVERT: U 107 PHE cc_start: 0.8309 (t80) cc_final: 0.8057 (t80) REVERT: U 109 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7267 (ttmt) REVERT: U 134 ARG cc_start: 0.7438 (ttp-170) cc_final: 0.7175 (ttm-80) REVERT: U 228 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6791 (mt-10) outliers start: 37 outliers final: 10 residues processed: 318 average time/residue: 0.6803 time to fit residues: 241.7107 Evaluate side-chains 225 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 ARG Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain S residue 147 ILE Chi-restraints excluded: chain S residue 148 SER Chi-restraints excluded: chain S residue 151 SER Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 279 MET Chi-restraints excluded: chain U residue 109 LYS Chi-restraints excluded: chain U residue 371 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 235 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 44 ASN K 61 HIS S 283 ASN S 298 HIS S 333 HIS T 49 GLN T 143 ASN T 164 ASN T 305 GLN U 110 GLN U 163 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.153723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115242 restraints weight = 21106.195| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.80 r_work: 0.3163 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20298 Z= 0.137 Angle : 0.645 10.778 27736 Z= 0.323 Chirality : 0.044 0.303 3234 Planarity : 0.005 0.046 3329 Dihedral : 16.194 146.974 3186 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.10 % Favored : 97.85 % Rotamer: Outliers : 2.42 % Allowed : 7.97 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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: 0.88 (0.17), residues: 2377 helix: 1.81 (0.17), residues: 996 sheet: 1.06 (0.24), residues: 417 loop : -0.98 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 27 TYR 0.021 0.002 TYR K 59 PHE 0.012 0.001 PHE U 386 TRP 0.017 0.001 TRP T 127 HIS 0.007 0.001 HIS S 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (20288) covalent geometry : angle 0.64122 / 0.32 (27716) SS BOND : bond 0.00478 / 0.28 ( 4) SS BOND : angle 2.28437 / 1.21 ( 8) hydrogen bonds : bond 0.06439 / 4.31 ( 938) hydrogen bonds : angle 4.54991 / 3.18 ( 2652) Misc. bond : bond 0.00390 / 0.28 ( 2) link_BETA1-4 : bond 0.00246 / 0.16 ( 1) link_BETA1-4 : angle 2.30621 / 1.68 ( 3) link_NAG-ASN : bond 0.00663 / 0.34 ( 3) link_NAG-ASN : angle 3.12834 / 1.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 0.794 Fit side-chains REVERT: G 116 ASP cc_start: 0.6113 (t0) cc_final: 0.5862 (t0) REVERT: G 439 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.6865 (mm) REVERT: K 139 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7360 (pp) REVERT: S 109 ARG cc_start: 0.6653 (ppt170) cc_final: 0.6366 (ppt170) REVERT: S 184 ARG cc_start: 0.6147 (mpp80) cc_final: 0.5849 (mmm-85) REVERT: T 262 ARG cc_start: 0.8292 (mtt90) cc_final: 0.7625 (ttt180) REVERT: T 270 GLU cc_start: 0.7891 (pm20) cc_final: 0.7579 (pm20) REVERT: U 30 GLU cc_start: 0.7995 (pt0) cc_final: 0.7341 (pp20) REVERT: U 110 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: U 134 ARG cc_start: 0.7927 (ttp-170) cc_final: 0.7459 (ttm-80) REVERT: U 228 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7516 (mt-10) outliers start: 48 outliers final: 13 residues processed: 250 average time/residue: 0.6509 time to fit residues: 183.5285 Evaluate side-chains 215 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 264 SER Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain K residue 306 SER Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 336 LEU Chi-restraints excluded: chain T residue 511 GLU Chi-restraints excluded: chain U residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 186 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 182 optimal weight: 0.3980 chunk 6 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 44 ASN S 283 ASN S 298 HIS T 49 GLN T 164 ASN T 305 GLN T 355 GLN U 110 GLN U 163 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109575 restraints weight = 21076.926| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.87 r_work: 0.3086 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20298 Z= 0.171 Angle : 0.682 10.181 27736 Z= 0.346 Chirality : 0.046 0.313 3234 Planarity : 0.005 0.047 3329 Dihedral : 15.480 139.032 3166 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.36 % Favored : 97.60 % Rotamer: Outliers : 2.47 % Allowed : 10.39 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.17), residues: 2377 helix: 1.92 (0.17), residues: 987 sheet: 1.13 (0.24), residues: 417 loop : -1.04 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 27 TYR 0.031 0.002 TYR K 212 PHE 0.016 0.002 PHE U 73 TRP 0.020 0.002 TRP T 127 HIS 0.009 0.001 HIS K 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (20288) covalent geometry : angle 0.67807 / 0.34 (27716) SS BOND : bond 0.00776 / 0.40 ( 4) SS BOND : angle 2.39098 / 1.19 ( 8) hydrogen bonds : bond 0.07590 / 5.06 ( 938) hydrogen bonds : angle 4.49451 / 3.15 ( 2652) Misc. bond : bond 0.00485 / 0.34 ( 2) link_BETA1-4 : bond 0.00079 / 0.05 ( 1) link_BETA1-4 : angle 2.67457 / 1.95 ( 3) link_NAG-ASN : bond 0.00181 / 0.13 ( 3) link_NAG-ASN : angle 2.87508 / 1.38 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.804 Fit side-chains REVERT: G 9 ARG cc_start: 0.3899 (OUTLIER) cc_final: 0.3447 (mtm180) REVERT: G 297 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: G 394 MET cc_start: 0.7457 (ttm) cc_final: 0.7157 (mtt) REVERT: G 439 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.6941 (mm) REVERT: K 49 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8713 (mt) REVERT: K 139 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7584 (pp) REVERT: K 248 ARG cc_start: 0.7562 (mmp-170) cc_final: 0.7275 (mmp80) REVERT: K 269 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7914 (m-40) REVERT: K 356 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7364 (m-70) REVERT: S 147 ILE cc_start: 0.5999 (OUTLIER) cc_final: 0.5635 (pp) REVERT: S 184 ARG cc_start: 0.6215 (mpp80) cc_final: 0.5844 (mmt180) REVERT: S 529 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6411 (mpt) REVERT: T 33 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: T 262 ARG cc_start: 0.8219 (mtt90) cc_final: 0.7515 (ttt180) REVERT: T 270 GLU cc_start: 0.7927 (pm20) cc_final: 0.7497 (pm20) REVERT: U 30 GLU cc_start: 0.8026 (pt0) cc_final: 0.7365 (pp20) REVERT: U 110 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6920 (tm-30) REVERT: U 132 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6675 (tm-30) REVERT: U 134 ARG cc_start: 0.7889 (ttp-170) cc_final: 0.7405 (ttm-80) outliers start: 49 outliers final: 17 residues processed: 226 average time/residue: 0.6826 time to fit residues: 172.8856 Evaluate side-chains 215 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 ARG Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 264 SER Chi-restraints excluded: chain K residue 269 ASN Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 306 SER Chi-restraints excluded: chain K residue 356 HIS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 147 ILE Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 463 SER Chi-restraints excluded: chain S residue 523 ILE Chi-restraints excluded: chain S residue 529 MET Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain T residue 302 THR Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 326 ILE Chi-restraints excluded: chain T residue 336 LEU Chi-restraints excluded: chain T residue 511 GLU Chi-restraints excluded: chain U residue 110 GLN Chi-restraints excluded: chain U residue 132 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 0 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 29 optimal weight: 0.0970 chunk 135 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 323 ASN K 292 GLN S 260 ASN S 283 ASN S 298 HIS S 392 GLN T 49 GLN T 164 ASN U 110 GLN U 163 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107778 restraints weight = 20902.176| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.85 r_work: 0.3061 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20298 Z= 0.195 Angle : 0.724 9.933 27736 Z= 0.366 Chirality : 0.047 0.332 3234 Planarity : 0.006 0.050 3329 Dihedral : 15.237 139.441 3163 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.61 % Favored : 97.35 % Rotamer: Outliers : 3.08 % Allowed : 11.09 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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 (0.17), residues: 2377 helix: 1.76 (0.17), residues: 994 sheet: 1.11 (0.25), residues: 406 loop : -1.07 (0.18), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 27 TYR 0.031 0.002 TYR K 59 PHE 0.018 0.002 PHE G 258 TRP 0.021 0.002 TRP T 127 HIS 0.008 0.001 HIS T 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (20288) covalent geometry : angle 0.71908 / 0.36 (27716) SS BOND : bond 0.00478 / 0.24 ( 4) SS BOND : angle 3.09429 / 1.43 ( 8) hydrogen bonds : bond 0.08123 / 5.42 ( 938) hydrogen bonds : angle 4.54332 / 3.19 ( 2652) Misc. bond : bond 0.00464 / 0.33 ( 2) link_BETA1-4 : bond 0.00109 / 0.07 ( 1) link_BETA1-4 : angle 2.84903 / 2.08 ( 3) link_NAG-ASN : bond 0.00111 / 0.08 ( 3) link_NAG-ASN : angle 3.17185 / 1.49 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 195 time to evaluate : 0.713 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU U 125 " (corrupted residue). Skipping it. REVERT: G 9 ARG cc_start: 0.3778 (OUTLIER) cc_final: 0.3378 (mtm180) REVERT: G 62 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: G 297 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: G 394 MET cc_start: 0.7576 (ttm) cc_final: 0.7266 (mtt) REVERT: G 439 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.6917 (mm) REVERT: K 49 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8705 (mt) REVERT: K 122 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7587 (mtt180) REVERT: K 139 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7632 (pp) REVERT: K 248 ARG cc_start: 0.7616 (mmp-170) cc_final: 0.7293 (mmp80) REVERT: K 356 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7320 (m-70) REVERT: K 384 LYS cc_start: 0.5956 (OUTLIER) cc_final: 0.4988 (tttt) REVERT: S 89 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6775 (mm-30) REVERT: S 184 ARG cc_start: 0.6209 (mpp80) cc_final: 0.5695 (mpt90) REVERT: S 454 ASN cc_start: 0.8654 (p0) cc_final: 0.8418 (p0) REVERT: S 529 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6316 (mpt) REVERT: T 33 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7889 (pt0) REVERT: T 262 ARG cc_start: 0.8183 (mtt90) cc_final: 0.7453 (ttt180) REVERT: T 270 GLU cc_start: 0.7969 (pm20) cc_final: 0.7542 (pm20) REVERT: U 30 GLU cc_start: 0.8074 (pt0) cc_final: 0.7359 (pp20) REVERT: U 110 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: U 111 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6984 (tttp) REVERT: U 132 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6813 (tm-30) REVERT: U 134 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.7427 (ttm-80) outliers start: 61 outliers final: 25 residues processed: 232 average time/residue: 0.6567 time to fit residues: 171.3669 Evaluate side-chains 236 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 ARG Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 122 ARG Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 264 SER Chi-restraints excluded: chain K residue 269 ASN Chi-restraints excluded: chain K residue 306 SER Chi-restraints excluded: chain K residue 356 HIS Chi-restraints excluded: chain K residue 384 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 271 ASP Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 463 SER Chi-restraints excluded: chain S residue 522 TYR Chi-restraints excluded: chain S residue 523 ILE Chi-restraints excluded: chain S residue 529 MET Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain T residue 302 THR Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 326 ILE Chi-restraints excluded: chain T residue 336 LEU Chi-restraints excluded: chain T residue 355 GLN Chi-restraints excluded: chain T residue 511 GLU Chi-restraints excluded: chain U residue 110 GLN Chi-restraints excluded: chain U residue 111 LYS Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 357 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 78 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 269 GLN G 323 ASN S 260 ASN S 283 ASN T 49 GLN T 164 ASN U 110 GLN U 163 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108363 restraints weight = 20843.366| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.80 r_work: 0.3070 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20298 Z= 0.178 Angle : 0.695 9.803 27736 Z= 0.350 Chirality : 0.046 0.344 3234 Planarity : 0.006 0.049 3329 Dihedral : 14.969 139.675 3160 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.65 % Favored : 97.31 % Rotamer: Outliers : 3.33 % Allowed : 12.20 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % 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 (0.17), residues: 2377 helix: 1.76 (0.17), residues: 997 sheet: 1.10 (0.25), residues: 406 loop : -1.07 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG T 27 TYR 0.029 0.002 TYR K 59 PHE 0.015 0.002 PHE G 258 TRP 0.021 0.002 TRP T 127 HIS 0.008 0.001 HIS T 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (20288) covalent geometry : angle 0.69107 / 0.35 (27716) SS BOND : bond 0.00494 / 0.26 ( 4) SS BOND : angle 2.79186 / 1.34 ( 8) hydrogen bonds : bond 0.07681 / 5.13 ( 938) hydrogen bonds : angle 4.49658 / 3.15 ( 2652) Misc. bond : bond 0.00453 / 0.32 ( 2) link_BETA1-4 : bond 0.00144 / 0.10 ( 1) link_BETA1-4 : angle 2.73406 / 1.99 ( 3) link_NAG-ASN : bond 0.00147 / 0.10 ( 3) link_NAG-ASN : angle 2.73462 / 1.35 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 0.771 Fit side-chains TARDY: cannot create tardy model for: "GLU U 125 " (corrupted residue). Skipping it. REVERT: G 9 ARG cc_start: 0.3774 (OUTLIER) cc_final: 0.3382 (mtm180) REVERT: G 62 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: G 82 LYS cc_start: 0.7316 (tttm) cc_final: 0.6589 (ttmt) REVERT: G 297 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: G 394 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7253 (mtt) REVERT: G 439 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.6903 (mm) REVERT: K 49 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8722 (mt) REVERT: K 122 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7597 (mmm160) REVERT: K 139 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7650 (pp) REVERT: K 248 ARG cc_start: 0.7652 (mmp-170) cc_final: 0.7217 (mmp80) REVERT: K 356 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7290 (m-70) REVERT: K 384 LYS cc_start: 0.5899 (OUTLIER) cc_final: 0.4943 (tttt) REVERT: S 89 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6769 (mm-30) REVERT: S 184 ARG cc_start: 0.6225 (mpp80) cc_final: 0.5714 (mpt90) REVERT: S 185 ARG cc_start: 0.5960 (OUTLIER) cc_final: 0.5381 (ttm110) REVERT: T 33 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7910 (pt0) REVERT: T 49 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.9167 (mt0) REVERT: T 262 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7429 (ttt180) REVERT: T 270 GLU cc_start: 0.7929 (pm20) cc_final: 0.7490 (pm20) REVERT: U 30 GLU cc_start: 0.8056 (pt0) cc_final: 0.7359 (pp20) REVERT: U 110 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7266 (tm-30) REVERT: U 132 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: U 302 ILE cc_start: 0.8541 (mm) cc_final: 0.8302 (mm) outliers start: 66 outliers final: 28 residues processed: 238 average time/residue: 0.6575 time to fit residues: 176.3731 Evaluate side-chains 233 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 ARG Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 394 MET Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 122 ARG Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 264 SER Chi-restraints excluded: chain K residue 269 ASN Chi-restraints excluded: chain K residue 306 SER Chi-restraints excluded: chain K residue 356 HIS Chi-restraints excluded: chain K residue 384 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain S residue 185 ARG Chi-restraints excluded: chain S residue 189 VAL Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 463 SER Chi-restraints excluded: chain S residue 523 ILE Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain T residue 49 GLN Chi-restraints excluded: chain T residue 277 GLU Chi-restraints excluded: chain T residue 302 THR Chi-restraints excluded: chain T residue 306 ASP Chi-restraints excluded: chain T residue 326 ILE Chi-restraints excluded: chain T residue 336 LEU Chi-restraints excluded: chain T residue 355 GLN Chi-restraints excluded: chain T residue 511 GLU Chi-restraints excluded: chain U residue 110 GLN Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 357 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 139 optimal weight: 8.9990 chunk 168 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 151 optimal weight: 0.0000 chunk 57 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 323 ASN S 283 ASN S 454 ASN T 164 ASN U 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.151299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111221 restraints weight = 20925.824| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.93 r_work: 0.3116 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20298 Z= 0.125 Angle : 0.596 9.916 27736 Z= 0.299 Chirality : 0.043 0.354 3234 Planarity : 0.005 0.050 3329 Dihedral : 14.398 143.560 3160 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.69 % Favored : 97.27 % Rotamer: Outliers : 2.32 % Allowed : 13.57 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.17), residues: 2377 helix: 1.97 (0.17), residues: 1008 sheet: 1.09 (0.24), residues: 418 loop : -0.99 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG T 27 TYR 0.027 0.001 TYR T 169 PHE 0.013 0.001 PHE T 48 TRP 0.018 0.001 TRP T 127 HIS 0.006 0.001 HIS T 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (20288) covalent geometry : angle 0.59192 / 0.30 (27716) SS BOND : bond 0.00944 / 0.52 ( 4) SS BOND : angle 2.52681 / 1.28 ( 8) hydrogen bonds : bond 0.05955 / 4.00 ( 938) hydrogen bonds : angle 4.29665 / 3.02 ( 2652) Misc. bond : bond 0.00428 / 0.31 ( 2) link_BETA1-4 : bond 0.00297 / 0.20 ( 1) link_BETA1-4 : angle 2.29110 / 1.64 ( 3) link_NAG-ASN : bond 0.00158 / 0.11 ( 3) link_NAG-ASN : angle 2.60199 / 1.10 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: G 9 ARG cc_start: 0.3824 (OUTLIER) cc_final: 0.3369 (mtm180) REVERT: G 82 LYS cc_start: 0.7164 (tttm) cc_final: 0.6470 (ttmt) REVERT: G 116 ASP cc_start: 0.6238 (t0) cc_final: 0.5942 (t0) REVERT: G 297 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: G 355 GLN cc_start: 0.8129 (tt0) cc_final: 0.7925 (tt0) REVERT: G 394 MET cc_start: 0.7471 (ttm) cc_final: 0.7170 (mtt) REVERT: G 439 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.6805 (mm) REVERT: G 602 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7751 (tt) REVERT: K 49 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8607 (mt) REVERT: K 139 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7574 (pp) REVERT: K 248 ARG cc_start: 0.7472 (mmp-170) cc_final: 0.7084 (mmp80) REVERT: K 356 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.7281 (m-70) REVERT: K 384 LYS cc_start: 0.5854 (OUTLIER) cc_final: 0.4833 (tttt) REVERT: S 89 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6683 (mm-30) REVERT: S 109 ARG cc_start: 0.6553 (ppt170) cc_final: 0.6259 (ppt170) REVERT: S 184 ARG cc_start: 0.6259 (mpp80) cc_final: 0.5735 (mpt90) REVERT: S 197 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6165 (pm20) REVERT: S 198 ASP cc_start: 0.7004 (p0) cc_final: 0.6791 (p0) REVERT: S 271 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8089 (t0) REVERT: T 33 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7886 (pt0) REVERT: T 262 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7318 (ttt180) REVERT: T 270 GLU cc_start: 0.7842 (pm20) cc_final: 0.7376 (pm20) REVERT: U 30 GLU cc_start: 0.8058 (pt0) cc_final: 0.7339 (pp20) REVERT: U 132 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6730 (tm-30) REVERT: U 134 ARG cc_start: 0.7816 (ttp-170) cc_final: 0.7347 (ttm-80) outliers start: 46 outliers final: 18 residues processed: 228 average time/residue: 0.6492 time to fit residues: 167.1634 Evaluate side-chains 223 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 ARG Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain G residue 602 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 264 SER Chi-restraints excluded: chain K residue 306 SER Chi-restraints excluded: chain K residue 356 HIS Chi-restraints excluded: chain K residue 384 LYS Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 197 GLU Chi-restraints excluded: chain S residue 271 ASP Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 478 GLU Chi-restraints excluded: chain S residue 523 ILE Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain T residue 302 THR Chi-restraints excluded: chain T residue 326 ILE Chi-restraints excluded: chain T residue 336 LEU Chi-restraints excluded: chain U residue 111 LYS Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain U residue 131 MET Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 357 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 94 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 196 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 29 optimal weight: 0.4980 chunk 87 optimal weight: 0.4980 chunk 171 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 202 optimal weight: 8.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 323 ASN S 283 ASN S 298 HIS S 392 GLN S 454 ASN T 164 ASN U 110 GLN U 163 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.155751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116444 restraints weight = 21133.112| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.83 r_work: 0.3188 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20298 Z= 0.103 Angle : 0.537 10.569 27736 Z= 0.267 Chirality : 0.041 0.358 3234 Planarity : 0.005 0.051 3329 Dihedral : 13.494 152.326 3160 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.52 % Favored : 97.43 % Rotamer: Outliers : 1.97 % Allowed : 14.02 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.17), residues: 2377 helix: 2.23 (0.17), residues: 1005 sheet: 1.12 (0.24), residues: 428 loop : -0.81 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG T 27 TYR 0.028 0.001 TYR T 169 PHE 0.009 0.001 PHE T 48 TRP 0.015 0.001 TRP S 428 HIS 0.006 0.001 HIS T 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (20288) covalent geometry : angle 0.53463 / 0.27 (27716) SS BOND : bond 0.00264 / 0.13 ( 4) SS BOND : angle 1.92052 / 0.95 ( 8) hydrogen bonds : bond 0.04431 / 2.97 ( 938) hydrogen bonds : angle 4.05226 / 2.85 ( 2652) Misc. bond : bond 0.00407 / 0.29 ( 2) link_BETA1-4 : bond 0.00382 / 0.25 ( 1) link_BETA1-4 : angle 1.82380 / 1.31 ( 3) link_NAG-ASN : bond 0.00183 / 0.12 ( 3) link_NAG-ASN : angle 1.89817 / 0.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: G 9 ARG cc_start: 0.3777 (OUTLIER) cc_final: 0.3356 (mtm180) REVERT: G 297 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: G 323 ASN cc_start: 0.7737 (t0) cc_final: 0.7479 (t0) REVERT: G 394 MET cc_start: 0.7216 (ttm) cc_final: 0.6926 (mtt) REVERT: G 439 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.6873 (mm) REVERT: G 476 LEU cc_start: 0.7313 (mt) cc_final: 0.6970 (mm) REVERT: K 139 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7483 (pp) REVERT: K 248 ARG cc_start: 0.7461 (mmp-170) cc_final: 0.7093 (mmp80) REVERT: K 311 GLU cc_start: 0.7672 (tt0) cc_final: 0.7271 (tp30) REVERT: K 356 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7242 (m-70) REVERT: K 384 LYS cc_start: 0.5795 (OUTLIER) cc_final: 0.4734 (tptp) REVERT: S 12 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: S 89 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6645 (mm-30) REVERT: S 184 ARG cc_start: 0.6308 (mpp80) cc_final: 0.5864 (mmm-85) REVERT: S 197 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6026 (pm20) REVERT: S 271 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8075 (t0) REVERT: T 262 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7408 (ttt180) REVERT: T 270 GLU cc_start: 0.7654 (pm20) cc_final: 0.7135 (pm20) REVERT: T 305 GLN cc_start: 0.8315 (tt0) cc_final: 0.8035 (tt0) REVERT: T 322 ASP cc_start: 0.7820 (m-30) cc_final: 0.7582 (m-30) REVERT: U 30 GLU cc_start: 0.8077 (pt0) cc_final: 0.7378 (pp20) REVERT: U 110 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6727 (tt0) REVERT: U 132 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6743 (tm-30) REVERT: U 134 ARG cc_start: 0.7844 (ttp-170) cc_final: 0.7369 (ttm-80) REVERT: U 346 ASN cc_start: 0.8290 (m-40) cc_final: 0.7953 (m110) outliers start: 39 outliers final: 13 residues processed: 235 average time/residue: 0.6296 time to fit residues: 167.3362 Evaluate side-chains 215 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 ARG Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 264 SER Chi-restraints excluded: chain K residue 306 SER Chi-restraints excluded: chain K residue 356 HIS Chi-restraints excluded: chain K residue 384 LYS Chi-restraints excluded: chain S residue 12 GLU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 197 GLU Chi-restraints excluded: chain S residue 271 ASP Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 523 ILE Chi-restraints excluded: chain T residue 336 LEU Chi-restraints excluded: chain U residue 110 GLN Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain U residue 131 MET Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 357 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 167 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 283 ASN S 454 ASN T 164 ASN U 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.151532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112403 restraints weight = 20890.933| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.98 r_work: 0.3124 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20298 Z= 0.134 Angle : 0.605 10.776 27736 Z= 0.303 Chirality : 0.043 0.352 3234 Planarity : 0.005 0.057 3329 Dihedral : 13.375 153.325 3160 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.73 % Favored : 97.22 % Rotamer: Outliers : 1.71 % Allowed : 14.67 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.17), residues: 2377 helix: 2.18 (0.17), residues: 1009 sheet: 1.10 (0.24), residues: 432 loop : -0.82 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG T 27 TYR 0.027 0.001 TYR T 169 PHE 0.013 0.002 PHE T 48 TRP 0.017 0.001 TRP T 127 HIS 0.006 0.001 HIS T 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (20288) covalent geometry : angle 0.60114 / 0.30 (27716) SS BOND : bond 0.00384 / 0.19 ( 4) SS BOND : angle 2.98118 / 1.46 ( 8) hydrogen bonds : bond 0.05911 / 3.94 ( 938) hydrogen bonds : angle 4.15760 / 2.93 ( 2652) Misc. bond : bond 0.00396 / 0.28 ( 2) link_BETA1-4 : bond 0.00234 / 0.16 ( 1) link_BETA1-4 : angle 2.17193 / 1.55 ( 3) link_NAG-ASN : bond 0.00194 / 0.13 ( 3) link_NAG-ASN : angle 2.04760 / 0.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: G 9 ARG cc_start: 0.3762 (OUTLIER) cc_final: 0.3291 (mtm180) REVERT: G 62 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: G 82 LYS cc_start: 0.7163 (tttm) cc_final: 0.6554 (ttmt) REVERT: G 297 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: G 323 ASN cc_start: 0.7789 (t0) cc_final: 0.7541 (t0) REVERT: G 394 MET cc_start: 0.7517 (ttm) cc_final: 0.7124 (mtt) REVERT: G 439 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.6959 (mm) REVERT: G 476 LEU cc_start: 0.7464 (mt) cc_final: 0.7074 (mm) REVERT: K 139 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7591 (pp) REVERT: K 248 ARG cc_start: 0.7557 (mmp-170) cc_final: 0.7155 (mmp80) REVERT: K 356 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7259 (m-70) REVERT: K 384 LYS cc_start: 0.5788 (OUTLIER) cc_final: 0.4506 (tptt) REVERT: S 12 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: S 89 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6670 (mm-30) REVERT: S 184 ARG cc_start: 0.6336 (mpp80) cc_final: 0.5780 (mpt90) REVERT: S 197 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6076 (pm20) REVERT: S 198 ASP cc_start: 0.7102 (p0) cc_final: 0.6896 (p0) REVERT: S 271 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8114 (t0) REVERT: T 33 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7873 (pt0) REVERT: T 262 ARG cc_start: 0.7989 (mtt90) cc_final: 0.7326 (ttt180) REVERT: T 270 GLU cc_start: 0.7717 (pm20) cc_final: 0.7244 (pm20) REVERT: T 305 GLN cc_start: 0.8308 (tt0) cc_final: 0.8027 (tt0) REVERT: T 322 ASP cc_start: 0.7868 (m-30) cc_final: 0.7666 (m-30) REVERT: U 30 GLU cc_start: 0.8057 (pt0) cc_final: 0.7340 (pp20) REVERT: U 132 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6775 (tm-30) REVERT: U 134 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7390 (ttm-80) outliers start: 34 outliers final: 13 residues processed: 219 average time/residue: 0.6818 time to fit residues: 168.0413 Evaluate side-chains 218 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 ARG Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 264 SER Chi-restraints excluded: chain K residue 269 ASN Chi-restraints excluded: chain K residue 306 SER Chi-restraints excluded: chain K residue 356 HIS Chi-restraints excluded: chain K residue 384 LYS Chi-restraints excluded: chain S residue 12 GLU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 197 GLU Chi-restraints excluded: chain S residue 271 ASP Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 523 ILE Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain T residue 336 LEU Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain U residue 131 MET Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 357 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 33 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 222 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 225 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 283 ASN S 454 ASN T 164 ASN ** U 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.151886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112225 restraints weight = 20755.946| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.88 r_work: 0.3126 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20298 Z= 0.127 Angle : 0.588 10.318 27736 Z= 0.295 Chirality : 0.042 0.354 3234 Planarity : 0.005 0.056 3329 Dihedral : 13.010 155.100 3156 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.73 % Favored : 97.22 % Rotamer: Outliers : 1.77 % Allowed : 14.52 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.17), residues: 2377 helix: 2.13 (0.17), residues: 1009 sheet: 1.09 (0.24), residues: 432 loop : -0.79 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG T 27 TYR 0.028 0.001 TYR T 169 PHE 0.014 0.001 PHE S 286 TRP 0.017 0.001 TRP T 127 HIS 0.006 0.001 HIS T 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (20288) covalent geometry : angle 0.58491 / 0.29 (27716) SS BOND : bond 0.00330 / 0.16 ( 4) SS BOND : angle 2.71460 / 1.39 ( 8) hydrogen bonds : bond 0.05757 / 3.85 ( 938) hydrogen bonds : angle 4.16082 / 2.93 ( 2652) Misc. bond : bond 0.00407 / 0.29 ( 2) link_BETA1-4 : bond 0.00187 / 0.12 ( 1) link_BETA1-4 : angle 2.15453 / 1.55 ( 3) link_NAG-ASN : bond 0.00171 / 0.11 ( 3) link_NAG-ASN : angle 1.98430 / 0.95 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.773 Fit side-chains REVERT: G 9 ARG cc_start: 0.3749 (OUTLIER) cc_final: 0.3311 (mtm180) REVERT: G 82 LYS cc_start: 0.7123 (tttm) cc_final: 0.6525 (ttmt) REVERT: G 297 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7967 (tt0) REVERT: G 323 ASN cc_start: 0.7645 (t0) cc_final: 0.7421 (t0) REVERT: G 394 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7162 (mtt) REVERT: G 439 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.6889 (mm) REVERT: G 476 LEU cc_start: 0.7458 (mt) cc_final: 0.7083 (mm) REVERT: K 139 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7601 (pp) REVERT: K 248 ARG cc_start: 0.7539 (mmp-170) cc_final: 0.7136 (mmp80) REVERT: K 356 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.7251 (m-70) REVERT: K 384 LYS cc_start: 0.5831 (OUTLIER) cc_final: 0.4525 (tptt) REVERT: S 12 GLU cc_start: 0.6671 (mp0) cc_final: 0.6400 (mp0) REVERT: S 89 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6683 (mm-30) REVERT: S 184 ARG cc_start: 0.6374 (mpp80) cc_final: 0.5806 (mpt90) REVERT: S 197 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6026 (pm20) REVERT: S 198 ASP cc_start: 0.7067 (p0) cc_final: 0.6857 (p0) REVERT: S 271 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8106 (t0) REVERT: T 262 ARG cc_start: 0.7990 (mtt90) cc_final: 0.7325 (ttt180) REVERT: T 270 GLU cc_start: 0.7687 (pm20) cc_final: 0.7211 (pm20) REVERT: T 305 GLN cc_start: 0.8313 (tt0) cc_final: 0.8031 (tt0) REVERT: U 30 GLU cc_start: 0.8022 (pt0) cc_final: 0.7323 (pp20) REVERT: U 132 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: U 134 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7381 (ttm-80) outliers start: 35 outliers final: 17 residues processed: 221 average time/residue: 0.6656 time to fit residues: 165.9670 Evaluate side-chains 225 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 ARG Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 394 MET Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 264 SER Chi-restraints excluded: chain K residue 269 ASN Chi-restraints excluded: chain K residue 306 SER Chi-restraints excluded: chain K residue 356 HIS Chi-restraints excluded: chain K residue 384 LYS Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 197 GLU Chi-restraints excluded: chain S residue 271 ASP Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 523 ILE Chi-restraints excluded: chain T residue 296 VAL Chi-restraints excluded: chain T residue 326 ILE Chi-restraints excluded: chain T residue 336 LEU Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain U residue 131 MET Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 357 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 86 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 201 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 283 ASN S 454 ASN T 164 ASN U 110 GLN U 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.149948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110692 restraints weight = 20840.165| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.97 r_work: 0.3098 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20298 Z= 0.152 Angle : 0.639 10.597 27736 Z= 0.322 Chirality : 0.044 0.350 3234 Planarity : 0.005 0.063 3329 Dihedral : 12.904 153.845 3156 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.10 % Rotamer: Outliers : 1.71 % Allowed : 14.57 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.17), residues: 2377 helix: 2.08 (0.17), residues: 1000 sheet: 1.16 (0.24), residues: 414 loop : -0.87 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG T 27 TYR 0.028 0.002 TYR T 169 PHE 0.014 0.002 PHE T 48 TRP 0.018 0.002 TRP T 127 HIS 0.007 0.001 HIS T 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (20288) covalent geometry : angle 0.63423 / 0.32 (27716) SS BOND : bond 0.00392 / 0.20 ( 4) SS BOND : angle 3.39936 / 1.71 ( 8) hydrogen bonds : bond 0.06720 / 4.49 ( 938) hydrogen bonds : angle 4.27453 / 3.01 ( 2652) Misc. bond : bond 0.00412 / 0.29 ( 2) link_BETA1-4 : bond 0.00209 / 0.14 ( 1) link_BETA1-4 : angle 2.42306 / 1.75 ( 3) link_NAG-ASN : bond 0.00142 / 0.10 ( 3) link_NAG-ASN : angle 2.87397 / 1.23 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4754 Ramachandran restraints generated. 2377 Oldfield, 0 Emsley, 2377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.757 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU U 125 " (corrupted residue). Skipping it. REVERT: G 9 ARG cc_start: 0.3795 (OUTLIER) cc_final: 0.3316 (mtm180) REVERT: G 62 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: G 82 LYS cc_start: 0.7180 (tttm) cc_final: 0.6572 (ttmt) REVERT: G 297 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: G 323 ASN cc_start: 0.7778 (t0) cc_final: 0.7562 (t0) REVERT: G 394 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7158 (mtt) REVERT: G 439 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.6928 (mm) REVERT: K 49 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8650 (mt) REVERT: K 139 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7651 (pp) REVERT: K 248 ARG cc_start: 0.7614 (mmp-170) cc_final: 0.7192 (mmp80) REVERT: K 356 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7224 (m-70) REVERT: K 384 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.4772 (tttt) REVERT: S 12 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6464 (mp0) REVERT: S 88 HIS cc_start: 0.7388 (t70) cc_final: 0.6990 (t-90) REVERT: S 89 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6799 (mm-30) REVERT: S 184 ARG cc_start: 0.6332 (mpp80) cc_final: 0.5781 (mpt90) REVERT: S 197 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6099 (pm20) REVERT: S 271 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8107 (t0) REVERT: T 165 ASP cc_start: 0.7130 (t0) cc_final: 0.6831 (p0) REVERT: T 262 ARG cc_start: 0.8008 (mtt90) cc_final: 0.7350 (ttt180) REVERT: T 270 GLU cc_start: 0.7793 (pm20) cc_final: 0.7315 (pm20) REVERT: T 305 GLN cc_start: 0.8319 (tt0) cc_final: 0.8070 (tt0) REVERT: U 30 GLU cc_start: 0.8056 (pt0) cc_final: 0.7320 (pp20) REVERT: U 110 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6464 (tt0) REVERT: U 132 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6807 (tm-30) REVERT: U 134 ARG cc_start: 0.7853 (ttp-170) cc_final: 0.7402 (ttm-80) outliers start: 34 outliers final: 16 residues processed: 227 average time/residue: 0.6439 time to fit residues: 164.7873 Evaluate side-chains 231 residues out of total 2074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 ARG Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 394 MET Chi-restraints excluded: chain G residue 439 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 264 SER Chi-restraints excluded: chain K residue 269 ASN Chi-restraints excluded: chain K residue 306 SER Chi-restraints excluded: chain K residue 356 HIS Chi-restraints excluded: chain K residue 384 LYS Chi-restraints excluded: chain S residue 12 GLU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 197 GLU Chi-restraints excluded: chain S residue 271 ASP Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 523 ILE Chi-restraints excluded: chain T residue 326 ILE Chi-restraints excluded: chain T residue 336 LEU Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain U residue 110 GLN Chi-restraints excluded: chain U residue 129 THR Chi-restraints excluded: chain U residue 131 MET Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 357 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 182 optimal weight: 0.0050 chunk 206 optimal weight: 0.3980 chunk 122 optimal weight: 9.9990 chunk 108 optimal weight: 40.0000 chunk 112 optimal weight: 0.2980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 283 ASN S 454 ASN T 164 ASN U 110 GLN U 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110975 restraints weight = 20822.294| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.96 r_work: 0.3101 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.220 20298 Z= 0.188 Angle : 0.794 59.140 27736 Z= 0.430 Chirality : 0.051 1.494 3234 Planarity : 0.005 0.060 3329 Dihedral : 12.900 153.879 3156 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.90 % Favored : 97.06 % Rotamer: Outliers : 1.66 % Allowed : 14.67 % Favored : 83.66 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.17), residues: 2377 helix: 2.06 (0.17), residues: 1000 sheet: 1.15 (0.24), residues: 414 loop : -0.88 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG T 27 TYR 0.027 0.001 TYR T 169 PHE 0.014 0.002 PHE T 48 TRP 0.019 0.001 TRP T 127 HIS 0.007 0.001 HIS T 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 (20288) covalent geometry : angle 0.78899 / 0.43 (27716) SS BOND : bond 0.00345 / 0.17 ( 4) SS BOND : angle 3.89112 / 1.81 ( 8) hydrogen bonds : bond 0.06569 / 4.39 ( 938) hydrogen bonds : angle 4.27684 / 3.01 ( 2652) Misc. bond : bond 0.00418 / 0.30 ( 2) link_BETA1-4 : bond 0.00197 / 0.13 ( 1) link_BETA1-4 : angle 2.40866 / 1.74 ( 3) link_NAG-ASN : bond 0.00208 / 0.13 ( 3) link_NAG-ASN : angle 2.90586 / 1.24 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8193.07 seconds wall clock time: 140 minutes 0.09 seconds (8400.09 seconds total)