Starting phenix.real_space_refine on Tue Sep 15 11:04:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r72_24290/09_2026/7r72_24290.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r72_24290/09_2026/7r72_24290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7r72_24290/09_2026/7r72_24290.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r72_24290/09_2026/7r72_24290.cif" model { file = "/net/cci-nas-00/data/ceres_data/7r72_24290/09_2026/7r72_24290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r72_24290/09_2026/7r72_24290.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r72_24290/09_2026/7r72_24290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r72_24290/09_2026/7r72_24290.map" } resolution = 3.07 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= 0.000 sd= 0.002 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 Zn 1 6.06 5 P 700 5.49 5 S 79 5.16 5 C 22178 2.51 5 N 7150 2.21 5 O 9335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39443 Number of models: 1 Model: "" Number of chains: 25 Chain: "1" Number of atoms: 13716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 13716 Classifications: {'RNAv2': 641} Modifications used: {'rna2p_pur': 63, 'rna2p_pyr': 48, 'rna3p_pur': 290, 'rna3p_pyr': 240} Link IDs: {'rna2p': 111, 'rna3p': 529} Chain breaks: 12 Chain: "2" Number of atoms: 1255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1255 Classifications: {'RNAv2': 59} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 24, 'rna3p_pyr': 24} Link IDs: {'rna2p': 11, 'rna3p': 47} Chain breaks: 3 Chain: "8" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 480 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "G" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 175 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "I" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2675 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "P" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain breaks: 4 Chain: "R" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "U" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "X" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "b" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 431 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "d" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 593 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain breaks: 2 Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "j" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 212 Classifications: {'peptide': 27} Link IDs: {'PCIS': 1, 'TRANS': 25} Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "m" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3302 Classifications: {'peptide': 412} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 385} Chain breaks: 3 Chain: "n" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 861 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain breaks: 1 Chain: "p" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2629 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 10, 'TRANS': 326} Chain breaks: 2 Chain: "t" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 221 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "u" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 481 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 1 Chain: "w" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1562 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain breaks: 6 Chain: "x" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4340 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 22, 'TRANS': 516} Chain breaks: 3 Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24691 SG CYS g 44 98.529 84.835 124.691 1.00 16.44 S ATOM 24709 SG CYS g 47 96.450 82.797 122.332 1.00 18.06 S ATOM 24963 SG CYS g 81 94.739 85.362 124.581 1.00 15.15 S ATOM 24982 SG CYS g 84 96.016 82.289 126.142 1.00 14.24 S Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ILE m 445 " occ=0.74 ... (6 atoms not shown) pdb=" CD1 ILE m 445 " occ=0.74 residue: pdb=" N ILE m 466 " occ=0.64 ... (6 atoms not shown) pdb=" CD1 ILE m 466 " occ=0.64 residue: pdb=" N PRO m 484 " occ=0.79 ... (5 atoms not shown) pdb=" CD PRO m 484 " occ=0.79 residue: pdb=" N ASP m 485 " occ=0.85 ... (6 atoms not shown) pdb=" OD2 ASP m 485 " occ=0.85 residue: pdb=" N LYS m 529 " occ=0.59 ... (7 atoms not shown) pdb=" NZ LYS m 529 " occ=0.59 residue: pdb=" N ARG m 720 " occ=0.60 ... (9 atoms not shown) pdb=" NH2 ARG m 720 " occ=0.60 Time building chain proxies: 6.75, per 1000 atoms: 0.17 Number of scatterers: 39443 At special positions: 0 Unit cell: (180.36, 174.96, 183.6, 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) Zn 1 29.99 S 79 16.00 P 700 15.00 O 9335 8.00 N 7150 7.00 C 22178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 962.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 81 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 47 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 84 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 44 " Number of angles added : 6 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 28 sheets defined 43.3% alpha, 15.8% beta 213 base pairs and 345 stacking pairs defined. Time for finding SS restraints: 4.91 Creating SS restraints... Processing helix chain '8' and resid 5 through 15 Processing helix chain '8' and resid 15 through 35 removed outlier: 4.040A pdb=" N GLY 8 35 " --> pdb=" O LYS 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 41 through 50 Processing helix chain '8' and resid 51 through 60 Processing helix chain 'G' and resid 47 through 52 removed outlier: 4.174A pdb=" N VAL G 50 " --> pdb=" O SER G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 62 Processing helix chain 'I' and resid 131 through 150 removed outlier: 4.246A pdb=" N GLU I 150 " --> pdb=" O THR I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 165 Processing helix chain 'I' and resid 170 through 189 removed outlier: 3.913A pdb=" N VAL I 182 " --> pdb=" O MET I 178 " (cutoff:3.500A) Proline residue: I 183 - end of helix Processing helix chain 'I' and resid 198 through 203 removed outlier: 4.128A pdb=" N LYS I 202 " --> pdb=" O THR I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 236 removed outlier: 3.504A pdb=" N LYS I 236 " --> pdb=" O GLN I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 261 removed outlier: 3.890A pdb=" N SER I 261 " --> pdb=" O LYS I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 281 removed outlier: 3.794A pdb=" N ILE I 272 " --> pdb=" O PHE I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 304 Processing helix chain 'I' and resid 308 through 325 removed outlier: 3.538A pdb=" N ILE I 317 " --> pdb=" O GLU I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 335 Processing helix chain 'I' and resid 336 through 344 removed outlier: 6.271A pdb=" N ASP I 341 " --> pdb=" O LEU I 338 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL I 342 " --> pdb=" O SER I 339 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 366 removed outlier: 3.679A pdb=" N ARG I 366 " --> pdb=" O LYS I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 370 through 421 removed outlier: 3.812A pdb=" N GLU I 400 " --> pdb=" O ALA I 396 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG I 401 " --> pdb=" O GLU I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 437 Processing helix chain 'I' and resid 438 through 440 No H-bonds generated for 'chain 'I' and resid 438 through 440' Processing helix chain 'P' and resid 25 through 32 Processing helix chain 'P' and resid 84 through 90 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 34 removed outlier: 3.803A pdb=" N GLN R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 47 Processing helix chain 'R' and resid 90 through 112 Processing helix chain 'R' and resid 116 through 129 Processing helix chain 'R' and resid 134 through 162 removed outlier: 5.442A pdb=" N LYS R 153 " --> pdb=" O ALA R 149 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ALA R 154 " --> pdb=" O GLN R 150 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN R 156 " --> pdb=" O GLU R 152 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU R 157 " --> pdb=" O LYS R 153 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 25 removed outlier: 3.816A pdb=" N ASN U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 41 Processing helix chain 'U' and resid 42 through 46 removed outlier: 3.770A pdb=" N GLY U 45 " --> pdb=" O LYS U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 87 Processing helix chain 'X' and resid 58 through 62 Processing helix chain 'X' and resid 69 through 80 removed outlier: 3.790A pdb=" N ASN X 80 " --> pdb=" O VAL X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 104 Processing helix chain 'X' and resid 131 through 138 Processing helix chain 'Z' and resid 59 through 66 Processing helix chain 'Z' and resid 99 through 102 Processing helix chain 'Z' and resid 103 through 124 Processing helix chain 'b' and resid 490 through 511 Processing helix chain 'b' and resid 527 through 539 removed outlier: 4.052A pdb=" N MET b 531 " --> pdb=" O SER b 527 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 21 Processing helix chain 'c' and resid 26 through 36 Processing helix chain 'c' and resid 49 through 64 Processing helix chain 'c' and resid 73 through 82 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 27 through 44 Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'g' and resid 58 through 65 removed outlier: 3.787A pdb=" N TYR g 62 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA g 63 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL g 65 " --> pdb=" O TYR g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 70 Processing helix chain 'g' and resid 81 through 111 Processing helix chain 'k' and resid 7 through 16 Processing helix chain 'k' and resid 58 through 68 Processing helix chain 'm' and resid 393 through 397 Processing helix chain 'm' and resid 408 through 413 Processing helix chain 'm' and resid 418 through 422 Processing helix chain 'm' and resid 519 through 532 removed outlier: 4.149A pdb=" N ASN m 525 " --> pdb=" O ASP m 521 " (cutoff:3.500A) Processing helix chain 'm' and resid 533 through 538 removed outlier: 3.655A pdb=" N THR m 538 " --> pdb=" O GLY m 535 " (cutoff:3.500A) Processing helix chain 'm' and resid 579 through 584 removed outlier: 3.548A pdb=" N GLU m 584 " --> pdb=" O GLN m 580 " (cutoff:3.500A) Processing helix chain 'm' and resid 616 through 619 removed outlier: 3.673A pdb=" N THR m 619 " --> pdb=" O SER m 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 616 through 619' Processing helix chain 'n' and resid 10 through 15 Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 48 through 53 Processing helix chain 'n' and resid 64 through 69 removed outlier: 3.629A pdb=" N ILE n 68 " --> pdb=" O TYR n 64 " (cutoff:3.500A) Processing helix chain 'n' and resid 551 through 556 Processing helix chain 'n' and resid 557 through 559 No H-bonds generated for 'chain 'n' and resid 557 through 559' Processing helix chain 'n' and resid 560 through 583 Processing helix chain 'p' and resid 237 through 241 removed outlier: 3.597A pdb=" N MET p 241 " --> pdb=" O TYR p 238 " (cutoff:3.500A) Processing helix chain 'p' and resid 245 through 252 removed outlier: 4.020A pdb=" N ASP p 249 " --> pdb=" O ASP p 245 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE p 250 " --> pdb=" O PRO p 246 " (cutoff:3.500A) Processing helix chain 'p' and resid 258 through 267 Processing helix chain 't' and resid 25 through 37 Processing helix chain 'u' and resid 52 through 58 Processing helix chain 'u' and resid 105 through 112 Processing helix chain 'u' and resid 114 through 129 Processing helix chain 'u' and resid 130 through 138 Processing helix chain 'w' and resid 348 through 388 removed outlier: 4.097A pdb=" N ILE w 352 " --> pdb=" O GLU w 348 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN w 388 " --> pdb=" O ARG w 384 " (cutoff:3.500A) Processing helix chain 'w' and resid 409 through 416 removed outlier: 3.814A pdb=" N THR w 416 " --> pdb=" O THR w 412 " (cutoff:3.500A) Processing helix chain 'w' and resid 418 through 424 removed outlier: 3.896A pdb=" N LEU w 422 " --> pdb=" O ILE w 418 " (cutoff:3.500A) Processing helix chain 'w' and resid 455 through 479 removed outlier: 4.182A pdb=" N ALA w 459 " --> pdb=" O SER w 455 " (cutoff:3.500A) Processing helix chain 'w' and resid 481 through 490 removed outlier: 3.759A pdb=" N ARG w 485 " --> pdb=" O ASP w 481 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG w 490 " --> pdb=" O ALA w 486 " (cutoff:3.500A) Processing helix chain 'w' and resid 552 through 560 Processing helix chain 'w' and resid 638 through 652 Processing helix chain 'w' and resid 696 through 701 Processing helix chain 'x' and resid 15 through 26 Processing helix chain 'x' and resid 31 through 42 removed outlier: 3.528A pdb=" N ILE x 38 " --> pdb=" O GLN x 34 " (cutoff:3.500A) Proline residue: x 39 - end of helix Processing helix chain 'x' and resid 56 through 72 Proline residue: x 64 - end of helix Processing helix chain 'x' and resid 92 through 108 Processing helix chain 'x' and resid 129 through 141 Processing helix chain 'x' and resid 148 through 158 Processing helix chain 'x' and resid 173 through 178 Processing helix chain 'x' and resid 182 through 193 removed outlier: 3.584A pdb=" N LYS x 188 " --> pdb=" O LYS x 184 " (cutoff:3.500A) Processing helix chain 'x' and resid 211 through 217 removed outlier: 3.700A pdb=" N PHE x 214 " --> pdb=" O SER x 211 " (cutoff:3.500A) Processing helix chain 'x' and resid 244 through 246 No H-bonds generated for 'chain 'x' and resid 244 through 246' Processing helix chain 'x' and resid 247 through 257 Processing helix chain 'x' and resid 270 through 287 Processing helix chain 'x' and resid 304 through 317 Processing helix chain 'x' and resid 353 through 358 Processing helix chain 'x' and resid 359 through 361 No H-bonds generated for 'chain 'x' and resid 359 through 361' Processing helix chain 'x' and resid 362 through 366 Processing helix chain 'x' and resid 378 through 389 removed outlier: 4.139A pdb=" N PHE x 382 " --> pdb=" O ARG x 378 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE x 383 " --> pdb=" O GLU x 379 " (cutoff:3.500A) Proline residue: x 384 - end of helix Processing helix chain 'x' and resid 406 through 416 Processing helix chain 'x' and resid 418 through 438 Processing helix chain 'x' and resid 451 through 459 Processing helix chain 'x' and resid 467 through 474 Processing helix chain 'x' and resid 502 through 515 removed outlier: 3.721A pdb=" N LYS x 507 " --> pdb=" O LYS x 503 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU x 508 " --> pdb=" O LYS x 504 " (cutoff:3.500A) Processing helix chain 'x' and resid 515 through 533 Processing helix chain 'x' and resid 536 through 558 removed outlier: 3.814A pdb=" N LYS x 556 " --> pdb=" O LYS x 552 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 127 through 128 Processing sheet with id=AA2, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AA3, first strand: chain 'U' and resid 54 through 58 removed outlier: 8.191A pdb=" N TYR U 103 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR U 16 " --> pdb=" O TYR U 103 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU U 105 " --> pdb=" O THR U 16 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP U 18 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N PHE U 107 " --> pdb=" O ASP U 18 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 23 through 24 Processing sheet with id=AA5, first strand: chain 'X' and resid 63 through 66 removed outlier: 3.826A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.642A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N HIS Z 40 " --> pdb=" O PRO Z 28 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS Z 22 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.971A pdb=" N THR c 24 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE c 92 " --> pdb=" O THR c 24 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 12 through 15 Processing sheet with id=AA9, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.494A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'j' and resid 16 through 18 removed outlier: 3.616A pdb=" N THR j 33 " --> pdb=" O HIS j 28 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'k' and resid 3 through 5 removed outlier: 4.390A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ARG k 46 " --> pdb=" O THR k 22 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA k 23 " --> pdb=" O ASN k 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 399 through 405 Processing sheet with id=AB4, first strand: chain 'm' and resid 428 through 434 removed outlier: 5.215A pdb=" N CYS m 429 " --> pdb=" O THR m 806 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N THR m 806 " --> pdb=" O CYS m 429 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR m 431 " --> pdb=" O LEU m 804 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR m 801 " --> pdb=" O GLY m 797 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'm' and resid 440 through 445 removed outlier: 3.638A pdb=" N THR m 442 " --> pdb=" O GLY m 455 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR m 460 " --> pdb=" O SER m 456 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU m 465 " --> pdb=" O GLU m 471 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU m 471 " --> pdb=" O GLU m 465 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 488 through 493 removed outlier: 3.979A pdb=" N ILE m 589 " --> pdb=" O LEU m 512 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'm' and resid 599 through 602 Processing sheet with id=AB8, first strand: chain 'm' and resid 642 through 647 removed outlier: 5.943A pdb=" N VAL m 662 " --> pdb=" O LYS m 675 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS m 675 " --> pdb=" O VAL m 662 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE m 664 " --> pdb=" O VAL m 673 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'm' and resid 683 through 688 removed outlier: 6.584A pdb=" N SER m 698 " --> pdb=" O SER m 684 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE m 686 " --> pdb=" O ILE m 696 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE m 696 " --> pdb=" O ILE m 686 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE m 688 " --> pdb=" O ASN m 694 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN m 694 " --> pdb=" O ILE m 688 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'm' and resid 726 through 731 removed outlier: 3.515A pdb=" N SER m 728 " --> pdb=" O ALA m 741 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE m 747 " --> pdb=" O LYS m 769 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS m 769 " --> pdb=" O ILE m 747 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL m 749 " --> pdb=" O LEU m 767 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'p' and resid 96 through 100 removed outlier: 3.670A pdb=" N ASN p 98 " --> pdb=" O ILE p 451 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'p' and resid 106 through 110 removed outlier: 3.510A pdb=" N SER p 108 " --> pdb=" O GLY p 121 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL p 127 " --> pdb=" O GLN p 139 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN p 139 " --> pdb=" O VAL p 127 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR p 129 " --> pdb=" O GLN p 137 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN p 137 " --> pdb=" O GLU p 196 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'p' and resid 147 through 154 removed outlier: 6.811A pdb=" N ALA p 161 " --> pdb=" O ARG p 148 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL p 150 " --> pdb=" O VAL p 159 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL p 159 " --> pdb=" O VAL p 150 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR p 152 " --> pdb=" O ARG p 157 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ARG p 157 " --> pdb=" O TYR p 152 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY p 162 " --> pdb=" O THR p 166 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N THR p 166 " --> pdb=" O GLY p 162 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS p 171 " --> pdb=" O THR p 200 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N THR p 200 " --> pdb=" O LYS p 171 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'p' and resid 211 through 216 removed outlier: 6.553A pdb=" N ALA p 225 " --> pdb=" O VAL p 212 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE p 214 " --> pdb=" O LEU p 223 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU p 223 " --> pdb=" O ILE p 214 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL p 216 " --> pdb=" O ARG p 221 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG p 221 " --> pdb=" O VAL p 216 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER p 226 " --> pdb=" O SER p 230 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER p 230 " --> pdb=" O SER p 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'p' and resid 290 through 293 removed outlier: 3.519A pdb=" N SER p 307 " --> pdb=" O THR p 311 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR p 311 " --> pdb=" O SER p 307 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE p 312 " --> pdb=" O THR p 325 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR p 325 " --> pdb=" O ILE p 312 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR p 314 " --> pdb=" O ILE p 323 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'p' and resid 332 through 338 removed outlier: 4.161A pdb=" N HIS p 352 " --> pdb=" O SER p 348 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'p' and resid 378 through 383 removed outlier: 3.619A pdb=" N SER p 395 " --> pdb=" O THR p 399 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR p 399 " --> pdb=" O SER p 395 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR p 412 " --> pdb=" O VAL p 402 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'x' and resid 119 through 122 removed outlier: 6.162A pdb=" N GLN x 120 " --> pdb=" O ILE x 146 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER x 86 " --> pdb=" O LEU x 145 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY x 147 " --> pdb=" O SER x 86 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE x 88 " --> pdb=" O GLY x 147 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU x 87 " --> pdb=" O VAL x 170 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASP x 172 " --> pdb=" O LEU x 87 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE x 89 " --> pdb=" O ASP x 172 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL x 47 " --> pdb=" O LEU x 201 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N SER x 203 " --> pdb=" O VAL x 47 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL x 49 " --> pdb=" O SER x 203 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP x 46 " --> pdb=" O VAL x 222 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE x 224 " --> pdb=" O ASP x 46 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL x 48 " --> pdb=" O ILE x 224 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'x' and resid 294 through 299 removed outlier: 6.365A pdb=" N LYS x 263 " --> pdb=" O LEU x 341 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE x 343 " --> pdb=" O LYS x 263 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE x 265 " --> pdb=" O ILE x 343 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N GLU x 394 " --> pdb=" O LEU x 236 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU x 238 " --> pdb=" O GLU x 394 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 3186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 538 hydrogen bonds 878 hydrogen bond angles 0 basepair planarities 213 basepair parallelities 345 stacking parallelities Total time for adding SS restraints: 11.96 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8763 1.33 - 1.45: 12294 1.45 - 1.57: 19026 1.57 - 1.70: 1383 1.70 - 1.82: 131 Bond restraints: 41597 Sorted by residual: bond pdb=" N9 G 11794 " pdb=" C4 G 11794 " ideal model delta sigma weight residual 1.375 1.401 -0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" CA ARG P 135 " pdb=" C ARG P 135 " ideal model delta sigma weight residual 1.523 1.538 -0.016 1.23e-02 6.61e+03 1.65e+00 bond pdb=" N9 G 11953 " pdb=" C4 G 11953 " ideal model delta sigma weight residual 1.375 1.400 -0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" CA ASN m 550 " pdb=" CB ASN m 550 " ideal model delta sigma weight residual 1.526 1.545 -0.019 1.51e-02 4.39e+03 1.59e+00 bond pdb=" CB VAL I 184 " pdb=" CG2 VAL I 184 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.41e+00 ... (remaining 41592 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 56954 2.10 - 4.20: 2194 4.20 - 6.30: 265 6.30 - 8.40: 9 8.40 - 10.50: 2 Bond angle restraints: 59424 Sorted by residual: angle pdb=" N ARG P 135 " pdb=" CA ARG P 135 " pdb=" C ARG P 135 " ideal model delta sigma weight residual 110.42 117.92 -7.50 1.46e+00 4.69e-01 2.64e+01 angle pdb=" N GLY P 134 " pdb=" CA GLY P 134 " pdb=" C GLY P 134 " ideal model delta sigma weight residual 112.73 117.72 -4.99 1.20e+00 6.94e-01 1.73e+01 angle pdb=" C ARG m 423 " pdb=" N PRO m 424 " pdb=" CA PRO m 424 " ideal model delta sigma weight residual 127.00 136.57 -9.57 2.40e+00 1.74e-01 1.59e+01 angle pdb=" C HIS P 133 " pdb=" CA HIS P 133 " pdb=" CB HIS P 133 " ideal model delta sigma weight residual 116.63 112.09 4.54 1.16e+00 7.43e-01 1.53e+01 angle pdb=" C3' G 11954 " pdb=" O3' G 11954 " pdb=" P U 11955 " ideal model delta sigma weight residual 119.70 124.30 -4.60 1.20e+00 6.94e-01 1.47e+01 ... (remaining 59419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.73: 21913 30.73 - 61.45: 1696 61.45 - 92.18: 190 92.18 - 122.91: 1 122.91 - 153.63: 2 Dihedral angle restraints: 23802 sinusoidal: 14911 harmonic: 8891 Sorted by residual: dihedral pdb=" C4' G 11935 " pdb=" C3' G 11935 " pdb=" C2' G 11935 " pdb=" C1' G 11935 " ideal model delta sinusoidal sigma weight residual 36.34 -38.09 74.44 1 3.10e+00 1.04e-01 7.31e+02 dihedral pdb=" C4' A 11446 " pdb=" C3' A 11446 " pdb=" C2' A 11446 " pdb=" C1' A 11446 " ideal model delta sinusoidal sigma weight residual 36.34 -37.78 74.13 1 3.10e+00 1.04e-01 7.26e+02 dihedral pdb=" C4' U 11522 " pdb=" C3' U 11522 " pdb=" C2' U 11522 " pdb=" C1' U 11522 " ideal model delta sinusoidal sigma weight residual 36.35 -37.72 74.06 1 3.10e+00 1.04e-01 7.25e+02 ... (remaining 23799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 5772 0.067 - 0.135: 505 0.135 - 0.202: 86 0.202 - 0.270: 778 0.270 - 0.337: 118 Chirality restraints: 7259 Sorted by residual: chirality pdb=" P C 11965 " pdb=" OP1 C 11965 " pdb=" OP2 C 11965 " pdb=" O5' C 11965 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C3' G 11935 " pdb=" C4' G 11935 " pdb=" O3' G 11935 " pdb=" C2' G 11935 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" P A 11575 " pdb=" OP1 A 11575 " pdb=" OP2 A 11575 " pdb=" O5' A 11575 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 7256 not shown) Planarity restraints: 4902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 2 127 " 0.032 2.00e-02 2.50e+03 1.63e-02 5.95e+00 pdb=" N1 U 2 127 " -0.035 2.00e-02 2.50e+03 pdb=" C2 U 2 127 " -0.004 2.00e-02 2.50e+03 pdb=" O2 U 2 127 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U 2 127 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U 2 127 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U 2 127 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U 2 127 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U 2 127 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11602 " -0.030 2.00e-02 2.50e+03 1.38e-02 5.27e+00 pdb=" N9 A 11602 " 0.033 2.00e-02 2.50e+03 pdb=" C8 A 11602 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A 11602 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 11602 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A 11602 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A 11602 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A 11602 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 11602 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 11602 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A 11602 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 11807 " -0.031 2.00e-02 2.50e+03 1.28e-02 4.88e+00 pdb=" N9 G 11807 " 0.029 2.00e-02 2.50e+03 pdb=" C8 G 11807 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 11807 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G 11807 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G 11807 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G 11807 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G 11807 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 11807 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G 11807 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G 11807 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G 11807 " 0.006 2.00e-02 2.50e+03 ... (remaining 4899 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 306 2.59 - 3.16: 30331 3.16 - 3.74: 66555 3.74 - 4.32: 94794 4.32 - 4.90: 139966 Nonbonded interactions: 331952 Sorted by model distance: nonbonded pdb=" OP1 U 11924 " pdb=" NH2 ARG R 136 " model vdw 2.007 3.120 nonbonded pdb=" OG SER I 332 " pdb=" O LEU I 524 " model vdw 2.092 3.040 nonbonded pdb=" OG SER p 307 " pdb=" OD1 ASP p 309 " model vdw 2.110 3.040 nonbonded pdb=" OG SER p 395 " pdb=" OD1 ASP p 397 " model vdw 2.120 3.040 nonbonded pdb=" OP2 G 2 103 " pdb=" O2' A 2 105 " model vdw 2.124 3.040 ... (remaining 331947 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=0.17 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: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 42.240 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41601 Z= 0.159 Angle : 0.797 10.496 59430 Z= 0.352 Chirality : 0.093 0.337 7259 Planarity : 0.004 0.047 4902 Dihedral : 18.694 153.633 17996 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 0.41 % Allowed : 1.29 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2946 helix: 1.68 (0.15), residues: 1214 sheet: 0.25 (0.23), residues: 532 loop : -0.35 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG p 168 TYR 0.018 0.001 TYR U 75 PHE 0.024 0.002 PHE x 61 TRP 0.023 0.001 TRP m 464 HIS 0.003 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (41597) covalent geometry : angle 0.79619 / 0.35 (59424) hydrogen bonds : bond 0.12394 / 6.30 ( 1648) hydrogen bonds : angle 5.25106 / 2.07 ( 4064) metal coordination : bond 0.00397 / 0.20 ( 4) metal coordination : angle 2.82048 / 0.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 398 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 49 TYR cc_start: 0.8666 (p90) cc_final: 0.8428 (p90) REVERT: P 138 LYS cc_start: 0.7450 (ttpt) cc_final: 0.7001 (tptt) REVERT: U 104 ARG cc_start: 0.7773 (ptt180) cc_final: 0.7555 (ptt180) REVERT: k 36 LYS cc_start: 0.8179 (ttpp) cc_final: 0.7946 (ttpt) REVERT: p 370 GLN cc_start: 0.7824 (pt0) cc_final: 0.7590 (mt0) REVERT: w 552 SER cc_start: 0.7862 (p) cc_final: 0.7631 (p) REVERT: x 241 CYS cc_start: 0.6151 (m) cc_final: 0.5835 (m) REVERT: x 345 LEU cc_start: 0.8017 (tp) cc_final: 0.7736 (mp) outliers start: 11 outliers final: 3 residues processed: 406 average time/residue: 0.2670 time to fit residues: 169.5962 Evaluate side-chains 302 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 299 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 292 ASN Chi-restraints excluded: chain x residue 435 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 ASN X 137 ASN b 500 GLN j 30 GLN p 342 ASN ** p 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097137 restraints weight = 62578.243| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.30 r_work: 0.2988 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 41601 Z= 0.207 Angle : 1.216 21.072 59430 Z= 0.493 Chirality : 0.110 1.272 7259 Planarity : 0.004 0.053 4902 Dihedral : 17.684 158.523 11656 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.37 % Rotamer: Outliers : 1.11 % Allowed : 6.44 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.00 (0.16), residues: 2946 helix: 1.86 (0.15), residues: 1224 sheet: 0.26 (0.23), residues: 541 loop : -0.36 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG x 357 TYR 0.012 0.001 TYR x 276 PHE 0.024 0.001 PHE x 61 TRP 0.022 0.002 TRP m 464 HIS 0.005 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (41597) covalent geometry : angle 1.21608 / 0.49 (59424) hydrogen bonds : bond 0.05008 / 2.56 ( 1648) hydrogen bonds : angle 4.06762 / 1.61 ( 4064) metal coordination : bond 0.00477 / 0.24 ( 4) metal coordination : angle 2.98644 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 319 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 138 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7119 (tptt) REVERT: U 49 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7231 (t0) REVERT: k 36 LYS cc_start: 0.8146 (ttpp) cc_final: 0.7898 (ttpt) REVERT: p 370 GLN cc_start: 0.8330 (pt0) cc_final: 0.7895 (mt0) REVERT: u 122 ARG cc_start: 0.7265 (mmp80) cc_final: 0.6948 (mmm-85) REVERT: w 552 SER cc_start: 0.7837 (p) cc_final: 0.7615 (p) REVERT: x 241 CYS cc_start: 0.6430 (m) cc_final: 0.6226 (m) REVERT: x 345 LEU cc_start: 0.7553 (tp) cc_final: 0.7262 (mp) REVERT: x 487 TRP cc_start: 0.7041 (m100) cc_final: 0.6651 (m100) REVERT: x 523 LYS cc_start: 0.6910 (mtmm) cc_final: 0.6614 (tttt) outliers start: 30 outliers final: 21 residues processed: 332 average time/residue: 0.2583 time to fit residues: 133.5636 Evaluate side-chains 318 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 296 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 49 ASN Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain w residue 452 ASP Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 292 ASN Chi-restraints excluded: chain x residue 381 ASP Chi-restraints excluded: chain x residue 538 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 305 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 180 optimal weight: 0.2980 chunk 7 optimal weight: 4.9990 chunk 263 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 319 ASN Z 106 GLN c 71 GLN g 108 GLN p 255 ASN p 396 HIS t 25 ASN x 439 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.127214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091032 restraints weight = 62608.538| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.36 r_work: 0.2863 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 41601 Z= 0.355 Angle : 1.148 22.409 59430 Z= 0.480 Chirality : 0.099 1.403 7259 Planarity : 0.005 0.054 4902 Dihedral : 18.054 174.803 11654 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 1.92 % Allowed : 8.81 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.64 (0.16), residues: 2946 helix: 1.62 (0.15), residues: 1221 sheet: 0.00 (0.23), residues: 540 loop : -0.58 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG x 466 TYR 0.015 0.002 TYR n 572 PHE 0.029 0.003 PHE x 61 TRP 0.023 0.002 TRP m 464 HIS 0.007 0.002 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00776 / 0.36 (41597) covalent geometry : angle 1.14776 / 0.48 (59424) hydrogen bonds : bond 0.06227 / 3.19 ( 1648) hydrogen bonds : angle 4.15772 / 1.64 ( 4064) metal coordination : bond 0.01103 / 0.55 ( 4) metal coordination : angle 3.03639 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 302 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 45 LYS cc_start: 0.7720 (mtmt) cc_final: 0.7308 (ptpp) REVERT: 8 53 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7868 (tt0) REVERT: I 296 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: P 138 LYS cc_start: 0.7891 (ttpt) cc_final: 0.7138 (tptt) REVERT: U 49 ASN cc_start: 0.7848 (t0) cc_final: 0.7531 (t0) REVERT: k 13 GLU cc_start: 0.8904 (tt0) cc_final: 0.8434 (tp30) REVERT: p 370 GLN cc_start: 0.8278 (pt0) cc_final: 0.7833 (mt0) REVERT: p 427 ASP cc_start: 0.7784 (t0) cc_final: 0.7476 (t0) REVERT: u 122 ARG cc_start: 0.7415 (mmp80) cc_final: 0.6929 (mmm-85) REVERT: w 451 LYS cc_start: 0.3439 (tttp) cc_final: 0.2480 (tttp) REVERT: x 487 TRP cc_start: 0.7352 (m100) cc_final: 0.6982 (m100) REVERT: x 498 TYR cc_start: 0.5374 (OUTLIER) cc_final: 0.4250 (t80) outliers start: 52 outliers final: 36 residues processed: 330 average time/residue: 0.2642 time to fit residues: 135.7039 Evaluate side-chains 329 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 291 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 265 HIS Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 550 ASN Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 272 VAL Chi-restraints excluded: chain x residue 349 THR Chi-restraints excluded: chain x residue 381 ASP Chi-restraints excluded: chain x residue 439 HIS Chi-restraints excluded: chain x residue 494 ASN Chi-restraints excluded: chain x residue 498 TYR Chi-restraints excluded: chain x residue 538 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 174 optimal weight: 0.5980 chunk 358 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 312 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN g 108 GLN j 30 GLN t 25 ASN w 545 GLN ** x 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.127648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091559 restraints weight = 62630.664| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.28 r_work: 0.2872 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 41601 Z= 0.253 Angle : 1.006 16.055 59430 Z= 0.420 Chirality : 0.086 1.044 7259 Planarity : 0.004 0.055 4902 Dihedral : 18.142 175.685 11652 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.11 % Allowed : 10.80 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.64 (0.16), residues: 2946 helix: 1.68 (0.15), residues: 1224 sheet: -0.00 (0.22), residues: 535 loop : -0.65 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG g 74 TYR 0.011 0.001 TYR x 276 PHE 0.024 0.002 PHE x 61 TRP 0.019 0.002 TRP m 464 HIS 0.026 0.001 HIS x 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.25 (41597) covalent geometry : angle 1.00603 / 0.42 (59424) hydrogen bonds : bond 0.05526 / 2.84 ( 1648) hydrogen bonds : angle 4.01318 / 1.59 ( 4064) metal coordination : bond 0.00765 / 0.38 ( 4) metal coordination : angle 2.90415 / 0.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 298 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 44 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: I 288 ASP cc_start: 0.7538 (t0) cc_final: 0.7307 (t0) REVERT: I 296 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7578 (mt0) REVERT: P 138 LYS cc_start: 0.7887 (ttpt) cc_final: 0.7181 (tptt) REVERT: R 144 GLN cc_start: 0.8091 (tp40) cc_final: 0.7854 (tp-100) REVERT: d 11 GLU cc_start: 0.5612 (pm20) cc_final: 0.5283 (pm20) REVERT: p 370 GLN cc_start: 0.8308 (pt0) cc_final: 0.7829 (mt0) REVERT: u 122 ARG cc_start: 0.7351 (mmp80) cc_final: 0.6980 (mmm-85) REVERT: w 370 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7144 (mt-10) REVERT: w 451 LYS cc_start: 0.3211 (tttp) cc_final: 0.2230 (tttp) REVERT: x 108 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7679 (mt-10) REVERT: x 487 TRP cc_start: 0.7404 (m100) cc_final: 0.7162 (m100) REVERT: x 498 TYR cc_start: 0.5312 (OUTLIER) cc_final: 0.4167 (t80) outliers start: 57 outliers final: 38 residues processed: 330 average time/residue: 0.2849 time to fit residues: 147.7355 Evaluate side-chains 330 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 289 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 44 GLU Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 550 ASN Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 683 LEU Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 464 SER Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 697 ASP Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 439 HIS Chi-restraints excluded: chain x residue 447 LEU Chi-restraints excluded: chain x residue 498 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 116 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 320 optimal weight: 3.9990 chunk 279 optimal weight: 0.0070 chunk 214 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 chunk 339 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 203 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 108 GLN j 30 GLN p 368 GLN t 25 ASN ** x 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 292 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.127326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.091071 restraints weight = 62525.703| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.31 r_work: 0.2870 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 41601 Z= 0.250 Angle : 0.988 16.142 59430 Z= 0.413 Chirality : 0.084 1.043 7259 Planarity : 0.004 0.054 4902 Dihedral : 18.136 177.961 11652 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.44 % Allowed : 11.76 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.62 (0.16), residues: 2946 helix: 1.70 (0.15), residues: 1222 sheet: -0.09 (0.22), residues: 539 loop : -0.67 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG g 74 TYR 0.010 0.001 TYR x 276 PHE 0.025 0.002 PHE x 61 TRP 0.019 0.002 TRP m 464 HIS 0.010 0.001 HIS x 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.25 (41597) covalent geometry : angle 0.98760 / 0.41 (59424) hydrogen bonds : bond 0.05567 / 2.87 ( 1648) hydrogen bonds : angle 3.97618 / 1.57 ( 4064) metal coordination : bond 0.00721 / 0.36 ( 4) metal coordination : angle 2.97894 / 0.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 304 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: 8 52 ARG cc_start: 0.8044 (mtp85) cc_final: 0.7437 (mtp85) REVERT: 8 53 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7937 (tt0) REVERT: I 288 ASP cc_start: 0.7576 (t0) cc_final: 0.7297 (t0) REVERT: I 296 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7590 (mt0) REVERT: I 534 LYS cc_start: 0.8328 (tptm) cc_final: 0.7675 (pttt) REVERT: P 138 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7272 (tptt) REVERT: d 11 GLU cc_start: 0.5673 (pm20) cc_final: 0.5217 (pm20) REVERT: p 370 GLN cc_start: 0.8371 (pt0) cc_final: 0.7874 (mt0) REVERT: u 104 GLU cc_start: 0.4059 (OUTLIER) cc_final: 0.3539 (mp0) REVERT: u 122 ARG cc_start: 0.7330 (mmp80) cc_final: 0.6934 (mmm-85) REVERT: w 451 LYS cc_start: 0.3298 (tttp) cc_final: 0.2678 (tttp) REVERT: x 108 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7786 (mt-10) REVERT: x 487 TRP cc_start: 0.7311 (m100) cc_final: 0.7088 (m100) REVERT: x 498 TYR cc_start: 0.5406 (OUTLIER) cc_final: 0.4260 (t80) outliers start: 66 outliers final: 47 residues processed: 343 average time/residue: 0.2752 time to fit residues: 148.6708 Evaluate side-chains 337 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 287 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 265 HIS Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 539 PHE Chi-restraints excluded: chain m residue 550 ASN Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 683 LEU Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 452 ASP Chi-restraints excluded: chain w residue 464 SER Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain x residue 25 MET Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 272 VAL Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 447 LEU Chi-restraints excluded: chain x residue 498 TYR Chi-restraints excluded: chain x residue 538 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 221 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 295 optimal weight: 0.7980 chunk 303 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 360 optimal weight: 1.9990 chunk 333 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 299 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 108 GLN j 30 GLN p 368 GLN p 426 ASN t 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.128717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.092301 restraints weight = 62604.367| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.30 r_work: 0.2909 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 41601 Z= 0.195 Angle : 0.924 14.842 59430 Z= 0.385 Chirality : 0.079 0.879 7259 Planarity : 0.004 0.055 4902 Dihedral : 18.094 176.662 11652 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.37 % Allowed : 12.25 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.72 (0.16), residues: 2946 helix: 1.82 (0.15), residues: 1221 sheet: -0.03 (0.22), residues: 551 loop : -0.67 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG x 466 TYR 0.009 0.001 TYR p 152 PHE 0.023 0.002 PHE x 61 TRP 0.017 0.001 TRP m 464 HIS 0.005 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (41597) covalent geometry : angle 0.92349 / 0.39 (59424) hydrogen bonds : bond 0.05238 / 2.71 ( 1648) hydrogen bonds : angle 3.87359 / 1.53 ( 4064) metal coordination : bond 0.00553 / 0.28 ( 4) metal coordination : angle 3.05417 / 1.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 295 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 52 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7418 (mtp85) REVERT: 8 53 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7933 (tt0) REVERT: I 288 ASP cc_start: 0.7526 (t0) cc_final: 0.7189 (t0) REVERT: I 296 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: I 379 GLU cc_start: 0.8365 (tt0) cc_final: 0.8002 (tp30) REVERT: I 534 LYS cc_start: 0.8281 (tptm) cc_final: 0.7620 (pttt) REVERT: P 138 LYS cc_start: 0.8051 (ttpt) cc_final: 0.7222 (tptt) REVERT: R 152 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6447 (tt0) REVERT: p 370 GLN cc_start: 0.8372 (pt0) cc_final: 0.7912 (mt0) REVERT: u 104 GLU cc_start: 0.3906 (OUTLIER) cc_final: 0.3462 (mp0) REVERT: u 122 ARG cc_start: 0.7314 (mmp80) cc_final: 0.7022 (mmm-85) REVERT: w 451 LYS cc_start: 0.2424 (tttp) cc_final: 0.1909 (tttp) REVERT: x 108 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7740 (mt-10) REVERT: x 487 TRP cc_start: 0.7264 (m100) cc_final: 0.6903 (m100) REVERT: x 498 TYR cc_start: 0.5288 (OUTLIER) cc_final: 0.4149 (t80) outliers start: 64 outliers final: 46 residues processed: 335 average time/residue: 0.2745 time to fit residues: 144.8293 Evaluate side-chains 334 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 284 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 550 ASN Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 683 LEU Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain m residue 714 THR Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 464 SER Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 697 ASP Chi-restraints excluded: chain x residue 25 MET Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 69 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 272 VAL Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 447 LEU Chi-restraints excluded: chain x residue 498 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 256 optimal weight: 0.9990 chunk 293 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 267 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 198 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 47 ASN g 108 GLN j 30 GLN p 368 GLN p 426 ASN t 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.128093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.092209 restraints weight = 62552.776| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.33 r_work: 0.2887 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 41601 Z= 0.214 Angle : 0.938 14.561 59430 Z= 0.392 Chirality : 0.079 0.896 7259 Planarity : 0.004 0.057 4902 Dihedral : 18.097 178.086 11652 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.96 % Allowed : 12.17 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.68 (0.16), residues: 2946 helix: 1.81 (0.15), residues: 1216 sheet: -0.05 (0.22), residues: 537 loop : -0.70 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG g 74 TYR 0.009 0.001 TYR X 103 PHE 0.024 0.002 PHE x 61 TRP 0.017 0.001 TRP m 464 HIS 0.005 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (41597) covalent geometry : angle 0.93730 / 0.39 (59424) hydrogen bonds : bond 0.05360 / 2.79 ( 1648) hydrogen bonds : angle 3.90378 / 1.54 ( 4064) metal coordination : bond 0.00602 / 0.30 ( 4) metal coordination : angle 3.00196 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 289 time to evaluate : 1.178 Fit side-chains REVERT: 8 52 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7427 (mtp85) REVERT: 8 53 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7890 (tt0) REVERT: I 288 ASP cc_start: 0.7521 (t0) cc_final: 0.7180 (t0) REVERT: I 296 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7588 (mt0) REVERT: I 439 MET cc_start: 0.8989 (mmp) cc_final: 0.8440 (mmp) REVERT: I 534 LYS cc_start: 0.8280 (tptm) cc_final: 0.7637 (pttt) REVERT: P 138 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7293 (tptt) REVERT: R 152 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6472 (tt0) REVERT: X 21 LYS cc_start: 0.7036 (mtpt) cc_final: 0.5263 (pptt) REVERT: c 41 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9054 (tp) REVERT: m 548 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: p 370 GLN cc_start: 0.8383 (pt0) cc_final: 0.7947 (mt0) REVERT: u 104 GLU cc_start: 0.3976 (OUTLIER) cc_final: 0.3524 (mp0) REVERT: u 122 ARG cc_start: 0.7319 (mmp80) cc_final: 0.7059 (mmm-85) REVERT: w 451 LYS cc_start: 0.2786 (tttp) cc_final: 0.1748 (tttp) REVERT: x 108 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7741 (mt-10) REVERT: x 363 ARG cc_start: 0.5014 (mmt-90) cc_final: 0.4525 (mmt90) REVERT: x 487 TRP cc_start: 0.7293 (m100) cc_final: 0.7069 (m100) REVERT: x 498 TYR cc_start: 0.5331 (OUTLIER) cc_final: 0.4204 (t80) outliers start: 80 outliers final: 54 residues processed: 340 average time/residue: 0.2540 time to fit residues: 137.6312 Evaluate side-chains 340 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 280 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 120 GLU Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 47 ASN Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 538 THR Chi-restraints excluded: chain m residue 548 GLU Chi-restraints excluded: chain m residue 550 ASN Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 683 LEU Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain m residue 714 THR Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain w residue 416 THR Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 452 ASP Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 697 ASP Chi-restraints excluded: chain x residue 25 MET Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 69 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 272 VAL Chi-restraints excluded: chain x residue 329 VAL Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 447 LEU Chi-restraints excluded: chain x residue 498 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 199 optimal weight: 3.9990 chunk 327 optimal weight: 4.9990 chunk 182 optimal weight: 0.6980 chunk 321 optimal weight: 1.9990 chunk 297 optimal weight: 0.1980 chunk 157 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 229 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 30 GLN p 426 ASN t 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094944 restraints weight = 62274.429| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.27 r_work: 0.2970 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41601 Z= 0.135 Angle : 0.863 11.884 59430 Z= 0.360 Chirality : 0.072 0.738 7259 Planarity : 0.004 0.057 4902 Dihedral : 18.090 176.798 11652 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.00 % Allowed : 13.43 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.89 (0.16), residues: 2946 helix: 2.02 (0.15), residues: 1209 sheet: 0.01 (0.22), residues: 545 loop : -0.60 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG x 549 TYR 0.012 0.001 TYR p 304 PHE 0.022 0.001 PHE x 61 TRP 0.018 0.001 TRP m 464 HIS 0.003 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (41597) covalent geometry : angle 0.86239 / 0.36 (59424) hydrogen bonds : bond 0.04990 / 2.59 ( 1648) hydrogen bonds : angle 3.78408 / 1.49 ( 4064) metal coordination : bond 0.00291 / 0.15 ( 4) metal coordination : angle 3.07612 / 1.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 305 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 53 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7799 (tt0) REVERT: I 288 ASP cc_start: 0.7438 (t0) cc_final: 0.7079 (t0) REVERT: I 296 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7463 (mt0) REVERT: I 379 GLU cc_start: 0.8310 (tt0) cc_final: 0.8029 (tp30) REVERT: I 439 MET cc_start: 0.8952 (mmp) cc_final: 0.8437 (mmp) REVERT: P 138 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7245 (tptt) REVERT: R 152 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6438 (tt0) REVERT: X 73 MET cc_start: 0.8667 (mmm) cc_final: 0.8430 (mmm) REVERT: c 41 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9029 (tp) REVERT: p 370 GLN cc_start: 0.8375 (pt0) cc_final: 0.7944 (mt0) REVERT: u 122 ARG cc_start: 0.7358 (mmp80) cc_final: 0.7091 (mmm-85) REVERT: w 387 MET cc_start: 0.3536 (mmp) cc_final: 0.3051 (mtt) REVERT: w 451 LYS cc_start: 0.2089 (tttp) cc_final: 0.1374 (tttp) REVERT: x 108 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7711 (mt-10) REVERT: x 363 ARG cc_start: 0.5019 (mmt-90) cc_final: 0.4588 (mmt90) REVERT: x 487 TRP cc_start: 0.7257 (m100) cc_final: 0.7035 (m100) REVERT: x 498 TYR cc_start: 0.5213 (OUTLIER) cc_final: 0.4062 (t80) outliers start: 54 outliers final: 38 residues processed: 340 average time/residue: 0.2570 time to fit residues: 138.5470 Evaluate side-chains 333 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 291 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 550 ASN Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 452 ASP Chi-restraints excluded: chain w residue 464 SER Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain w residue 697 ASP Chi-restraints excluded: chain x residue 25 MET Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 329 VAL Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 447 LEU Chi-restraints excluded: chain x residue 498 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 0.9990 chunk 90 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 188 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 240 optimal weight: 2.9990 chunk 241 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 ASN p 368 GLN p 426 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.096894 restraints weight = 62574.811| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.28 r_work: 0.2983 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41601 Z= 0.132 Angle : 0.833 11.812 59430 Z= 0.347 Chirality : 0.070 0.720 7259 Planarity : 0.004 0.055 4902 Dihedral : 17.969 176.416 11652 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.89 % Allowed : 13.65 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.99 (0.16), residues: 2946 helix: 2.12 (0.15), residues: 1210 sheet: 0.10 (0.22), residues: 549 loop : -0.57 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG x 378 TYR 0.012 0.001 TYR I 227 PHE 0.022 0.001 PHE x 61 TRP 0.016 0.001 TRP m 464 HIS 0.004 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (41597) covalent geometry : angle 0.83286 / 0.35 (59424) hydrogen bonds : bond 0.04932 / 2.56 ( 1648) hydrogen bonds : angle 3.70387 / 1.46 ( 4064) metal coordination : bond 0.00280 / 0.14 ( 4) metal coordination : angle 3.00428 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 309 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 53 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7788 (tt0) REVERT: I 280 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8330 (tt) REVERT: I 288 ASP cc_start: 0.7471 (t0) cc_final: 0.7078 (t0) REVERT: I 296 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7456 (mt0) REVERT: I 439 MET cc_start: 0.8951 (mmp) cc_final: 0.8415 (mmp) REVERT: P 138 LYS cc_start: 0.8078 (ttpt) cc_final: 0.7274 (tptt) REVERT: R 152 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6475 (tt0) REVERT: X 73 MET cc_start: 0.8724 (mmm) cc_final: 0.8519 (mmm) REVERT: Z 109 GLU cc_start: 0.8552 (tp30) cc_final: 0.7892 (pt0) REVERT: c 41 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9003 (tp) REVERT: p 370 GLN cc_start: 0.8386 (pt0) cc_final: 0.8033 (mt0) REVERT: u 122 ARG cc_start: 0.7344 (mmp80) cc_final: 0.7120 (mmm-85) REVERT: w 451 LYS cc_start: 0.2438 (tttp) cc_final: 0.1615 (tttt) REVERT: x 363 ARG cc_start: 0.5078 (mmt-90) cc_final: 0.4670 (mmt90) REVERT: x 498 TYR cc_start: 0.5338 (OUTLIER) cc_final: 0.4219 (t80) outliers start: 51 outliers final: 37 residues processed: 341 average time/residue: 0.2640 time to fit residues: 142.8710 Evaluate side-chains 337 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 295 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 538 THR Chi-restraints excluded: chain m residue 550 ASN Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain m residue 714 THR Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain p residue 207 HIS Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain w residue 359 LEU Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 452 ASP Chi-restraints excluded: chain w residue 464 SER Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain x residue 25 MET Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 329 VAL Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 447 LEU Chi-restraints excluded: chain x residue 498 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 154 optimal weight: 2.9990 chunk 269 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 339 optimal weight: 5.9990 chunk 325 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 221 optimal weight: 0.3980 chunk 67 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 ASN c 71 GLN g 108 GLN j 20 ASN p 368 GLN p 426 ASN t 25 ASN u 110 ASN w 545 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.129245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.093786 restraints weight = 62032.230| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.26 r_work: 0.2911 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 41601 Z= 0.203 Angle : 0.902 14.291 59430 Z= 0.377 Chirality : 0.075 0.807 7259 Planarity : 0.004 0.056 4902 Dihedral : 17.990 178.404 11652 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.07 % Allowed : 13.65 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.16), residues: 2946 helix: 1.96 (0.15), residues: 1216 sheet: 0.08 (0.22), residues: 538 loop : -0.59 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG u 113 TYR 0.010 0.001 TYR R 124 PHE 0.025 0.002 PHE x 61 TRP 0.016 0.001 TRP m 464 HIS 0.006 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (41597) covalent geometry : angle 0.90185 / 0.38 (59424) hydrogen bonds : bond 0.05266 / 2.75 ( 1648) hydrogen bonds : angle 3.82008 / 1.51 ( 4064) metal coordination : bond 0.00608 / 0.30 ( 4) metal coordination : angle 2.99661 / 1.00 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 292 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 52 ARG cc_start: 0.8198 (mtp85) cc_final: 0.7683 (mtp85) REVERT: 8 53 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7744 (tt0) REVERT: I 288 ASP cc_start: 0.7475 (t0) cc_final: 0.7151 (t0) REVERT: I 296 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7573 (mt0) REVERT: P 138 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7269 (tptt) REVERT: R 152 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6496 (tt0) REVERT: X 21 LYS cc_start: 0.7008 (mtpt) cc_final: 0.5189 (pptt) REVERT: X 73 MET cc_start: 0.8782 (mmm) cc_final: 0.8550 (mmm) REVERT: b 518 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6666 (mt) REVERT: c 41 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9027 (tp) REVERT: c 76 GLU cc_start: 0.7753 (mp0) cc_final: 0.7541 (mp0) REVERT: d 27 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8541 (mtmm) REVERT: p 370 GLN cc_start: 0.8340 (pt0) cc_final: 0.7991 (mt0) REVERT: u 122 ARG cc_start: 0.7312 (mmp80) cc_final: 0.7050 (mmm-85) REVERT: w 451 LYS cc_start: 0.2559 (tttp) cc_final: 0.1827 (tttp) REVERT: x 363 ARG cc_start: 0.4960 (mmt-90) cc_final: 0.4542 (mmt90) REVERT: x 498 TYR cc_start: 0.5269 (OUTLIER) cc_final: 0.4104 (t80) outliers start: 56 outliers final: 43 residues processed: 327 average time/residue: 0.2630 time to fit residues: 137.5376 Evaluate side-chains 335 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 287 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain R residue 152 GLU Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 75 ASN Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 538 THR Chi-restraints excluded: chain m residue 550 ASN Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain m residue 714 THR Chi-restraints excluded: chain p residue 244 VAL Chi-restraints excluded: chain p residue 434 TRP Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 452 ASP Chi-restraints excluded: chain w residue 464 SER Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain x residue 25 MET Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 69 VAL Chi-restraints excluded: chain x residue 105 SER Chi-restraints excluded: chain x residue 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 272 VAL Chi-restraints excluded: chain x residue 329 VAL Chi-restraints excluded: chain x residue 400 VAL Chi-restraints excluded: chain x residue 447 LEU Chi-restraints excluded: chain x residue 498 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 182 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 349 optimal weight: 20.0000 chunk 119 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 226 ASN U 49 ASN ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 ASN p 426 ASN t 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.130028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.094842 restraints weight = 62204.605| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.26 r_work: 0.2936 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 41601 Z= 0.161 Angle : 0.876 13.249 59430 Z= 0.367 Chirality : 0.073 0.785 7259 Planarity : 0.004 0.056 4902 Dihedral : 18.024 178.202 11652 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.00 % Allowed : 13.80 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.16), residues: 2946 helix: 1.99 (0.15), residues: 1216 sheet: -0.01 (0.22), residues: 535 loop : -0.58 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG u 113 TYR 0.026 0.001 TYR m 486 PHE 0.023 0.001 PHE x 61 TRP 0.016 0.001 TRP m 464 HIS 0.004 0.001 HIS 8 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (41597) covalent geometry : angle 0.87564 / 0.37 (59424) hydrogen bonds : bond 0.05084 / 2.65 ( 1648) hydrogen bonds : angle 3.78789 / 1.49 ( 4064) metal coordination : bond 0.00466 / 0.23 ( 4) metal coordination : angle 3.04003 / 1.01 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12344.50 seconds wall clock time: 211 minutes 15.40 seconds (12675.40 seconds total)