Starting phenix.real_space_refine on Fri Feb 23 17:58:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r72_24290/02_2024/7r72_24290.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r72_24290/02_2024/7r72_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r72_24290/02_2024/7r72_24290.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r72_24290/02_2024/7r72_24290.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r72_24290/02_2024/7r72_24290.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r72_24290/02_2024/7r72_24290.pdb" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "m PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'RNA': 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: {'RNA': 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: 20.75, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 18.18 Conformation dependent library (CDL) restraints added in 4.3 seconds 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: 15.36 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: 25.92 Time building geometry restraints manager: 19.21 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=" O5' C 11941 " pdb=" C5' C 11941 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.71e+00 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=" O5' C 12050 " pdb=" C5' C 12050 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.71e+00 bond pdb=" O5' U 11942 " pdb=" C5' U 11942 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.65e+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 ... (remaining 41592 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.58: 4623 106.58 - 114.08: 25443 114.08 - 121.58: 19702 121.58 - 129.07: 8938 129.07 - 136.57: 718 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=" N LYS I 208 " pdb=" CA LYS I 208 " pdb=" C LYS I 208 " ideal model delta sigma weight residual 114.56 109.75 4.81 1.27e+00 6.20e-01 1.43e+01 ... (remaining 59419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 24390 35.72 - 71.44: 1730 71.44 - 107.16: 190 107.16 - 142.88: 3 142.88 - 178.60: 3 Dihedral angle restraints: 26316 sinusoidal: 17425 harmonic: 8891 Sorted by residual: dihedral pdb=" O4' U 11764 " pdb=" C1' U 11764 " pdb=" N1 U 11764 " pdb=" C2 U 11764 " ideal model delta sinusoidal sigma weight residual 232.00 53.40 178.60 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C 11631 " pdb=" C1' C 11631 " pdb=" N1 C 11631 " pdb=" C2 C 11631 " ideal model delta sinusoidal sigma weight residual -160.00 -76.08 -83.92 1 1.50e+01 4.44e-03 3.81e+01 dihedral pdb=" CA GLY d 66 " pdb=" C GLY d 66 " pdb=" N VAL d 67 " pdb=" CA VAL d 67 " ideal model delta harmonic sigma weight residual 180.00 -151.94 -28.06 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 26313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 6064 0.046 - 0.093: 912 0.093 - 0.139: 247 0.139 - 0.185: 30 0.185 - 0.231: 6 Chirality restraints: 7259 Sorted by residual: chirality pdb=" C1' G 11560 " pdb=" O4' G 11560 " pdb=" C2' G 11560 " pdb=" N9 G 11560 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C1' G 11525 " pdb=" O4' G 11525 " pdb=" C2' G 11525 " pdb=" N9 G 11525 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ARG P 135 " pdb=" N ARG P 135 " pdb=" C ARG P 135 " pdb=" CB ARG P 135 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+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 2.520 nonbonded pdb=" OG SER I 332 " pdb=" O LEU I 524 " model vdw 2.092 2.440 nonbonded pdb=" OG SER p 307 " pdb=" OD1 ASP p 309 " model vdw 2.110 2.440 nonbonded pdb=" OG SER p 395 " pdb=" OD1 ASP p 397 " model vdw 2.120 2.440 nonbonded pdb=" OP2 G 2 103 " pdb=" O2' A 2 105 " model vdw 2.124 2.440 ... (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 ========== 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 17.750 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 126.980 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.140 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 41597 Z= 0.185 Angle : 0.531 10.496 59424 Z= 0.287 Chirality : 0.037 0.231 7259 Planarity : 0.004 0.047 4902 Dihedral : 20.032 178.602 20510 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (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 TRP 0.023 0.001 TRP m 464 HIS 0.003 0.001 HIS 8 18 PHE 0.024 0.002 PHE x 61 TYR 0.018 0.001 TYR U 75 ARG 0.006 0.000 ARG p 168 *********************** 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 fitting. rotamer outliers: 11 poor density : 398 time to evaluate : 3.189 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: 0.7004 (tptt) REVERT: U 104 ARG cc_start: 0.7773 (ptt180) cc_final: 0.7554 (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: 0.5836 (m) REVERT: x 345 LEU cc_start: 0.8016 (tp) cc_final: 0.7735 (mp) outliers start: 11 outliers final: 4 residues processed: 406 average time/residue: 0.6095 time to fit residues: 385.1075 Evaluate side-chains 303 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 299 time to evaluate : 3.414 ------------------------------------------------------------------------------- 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 403 ILE 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 304 optimal weight: 8.9990 chunk 273 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 146 optimal weight: 0.0270 chunk 282 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 327 optimal weight: 4.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 ASN U 49 ASN X 137 ASN b 500 GLN ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 30 GLN ** p 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41597 Z= 0.176 Angle : 0.508 8.749 59424 Z= 0.265 Chirality : 0.036 0.232 7259 Planarity : 0.004 0.050 4902 Dihedral : 21.183 178.690 14172 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.40 % Rotamer: Outliers : 1.11 % Allowed : 6.66 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.16), residues: 2946 helix: 1.91 (0.15), residues: 1225 sheet: 0.30 (0.23), residues: 539 loop : -0.33 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP m 464 HIS 0.005 0.001 HIS R 134 PHE 0.024 0.001 PHE x 61 TYR 0.012 0.001 TYR x 276 ARG 0.013 0.000 ARG x 357 *********************** 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 348 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 318 time to evaluate : 3.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 138 LYS cc_start: 0.7574 (ttpt) cc_final: 0.7033 (tptt) REVERT: U 104 ARG cc_start: 0.7790 (ptt180) cc_final: 0.7586 (ptt180) REVERT: k 36 LYS cc_start: 0.8217 (ttpp) cc_final: 0.7991 (ttpt) REVERT: p 370 GLN cc_start: 0.7896 (pt0) cc_final: 0.7676 (mt0) REVERT: w 552 SER cc_start: 0.8212 (p) cc_final: 0.7920 (p) REVERT: x 241 CYS cc_start: 0.6326 (m) cc_final: 0.6106 (m) outliers start: 30 outliers final: 20 residues processed: 332 average time/residue: 0.5982 time to fit residues: 310.3116 Evaluate side-chains 316 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 296 time to evaluate : 3.672 ------------------------------------------------------------------------------- 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 55 THR Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 70 GLU Chi-restraints excluded: chain Z residue 66 THR 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 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 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 381 ASP Chi-restraints excluded: chain x residue 494 ASN 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 182 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 328 optimal weight: 9.9990 chunk 354 optimal weight: 7.9990 chunk 292 optimal weight: 6.9990 chunk 325 optimal weight: 0.0470 chunk 111 optimal weight: 4.9990 chunk 263 optimal weight: 20.0000 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 319 ASN I 326 ASN U 49 ASN Z 106 GLN ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 71 GLN g 108 GLN p 255 ASN p 342 ASN p 396 HIS t 25 ASN x 439 HIS ** x 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 41597 Z= 0.441 Angle : 0.662 9.575 59424 Z= 0.344 Chirality : 0.045 0.345 7259 Planarity : 0.005 0.050 4902 Dihedral : 21.157 173.864 14166 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.00 % Allowed : 8.88 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.16), residues: 2946 helix: 1.58 (0.15), residues: 1228 sheet: 0.00 (0.23), residues: 534 loop : -0.57 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP m 464 HIS 0.007 0.002 HIS 8 18 PHE 0.030 0.003 PHE x 61 TYR 0.015 0.002 TYR n 572 ARG 0.006 0.001 ARG 8 52 *********************** 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 360 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 306 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 296 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: P 138 LYS cc_start: 0.7586 (ttpt) cc_final: 0.7047 (tptt) REVERT: U 104 ARG cc_start: 0.7933 (ptt180) cc_final: 0.7673 (ptt180) REVERT: X 106 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8109 (t0) REVERT: p 370 GLN cc_start: 0.7905 (pt0) cc_final: 0.7621 (mt0) REVERT: u 118 LYS cc_start: 0.7147 (mttp) cc_final: 0.6858 (mtmt) REVERT: w 387 MET cc_start: 0.3441 (mmp) cc_final: 0.2839 (mtt) REVERT: w 451 LYS cc_start: 0.2568 (tttp) cc_final: 0.2202 (tttp) REVERT: x 498 TYR cc_start: 0.5004 (OUTLIER) cc_final: 0.4261 (t80) outliers start: 54 outliers final: 38 residues processed: 337 average time/residue: 0.5915 time to fit residues: 315.0177 Evaluate side-chains 330 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 289 time to evaluate : 3.571 ------------------------------------------------------------------------------- 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 296 GLN Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain U residue 21 SER 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 X residue 106 ASP Chi-restraints excluded: chain Z residue 66 THR 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 m residue 776 ILE 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 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 326 THR 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 324 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 329 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 chunk 172 optimal weight: 0.9980 chunk 312 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 ASN ** R 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 ASN Z 106 GLN c 47 ASN j 30 GLN t 25 ASN w 545 GLN x 292 ASN x 439 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41597 Z= 0.211 Angle : 0.526 8.266 59424 Z= 0.275 Chirality : 0.038 0.297 7259 Planarity : 0.004 0.051 4902 Dihedral : 21.122 175.741 14166 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.92 % Allowed : 10.80 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.16), residues: 2946 helix: 1.88 (0.15), residues: 1218 sheet: 0.08 (0.23), residues: 534 loop : -0.52 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP x 487 HIS 0.014 0.001 HIS x 439 PHE 0.023 0.002 PHE x 61 TYR 0.009 0.001 TYR x 276 ARG 0.006 0.000 ARG u 122 *********************** 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 349 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 297 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 296 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: P 138 LYS cc_start: 0.7584 (ttpt) cc_final: 0.7085 (tptt) REVERT: X 106 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8098 (t0) REVERT: p 370 GLN cc_start: 0.7885 (pt0) cc_final: 0.7609 (mt0) REVERT: w 451 LYS cc_start: 0.2530 (tttp) cc_final: 0.2127 (tttt) REVERT: x 498 TYR cc_start: 0.4989 (OUTLIER) cc_final: 0.4205 (t80) REVERT: x 523 LYS cc_start: 0.6427 (mtmm) cc_final: 0.6208 (tptp) outliers start: 52 outliers final: 41 residues processed: 326 average time/residue: 0.5663 time to fit residues: 291.8439 Evaluate side-chains 325 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 281 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 137 LEU 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 58 HIS Chi-restraints excluded: chain U residue 21 SER 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 X residue 106 ASP Chi-restraints excluded: chain Z residue 66 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 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 683 LEU Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain m residue 710 ASP 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 416 THR Chi-restraints excluded: chain w residue 450 ILE 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 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 381 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 290 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 297 optimal weight: 0.0050 chunk 241 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 178 optimal weight: 0.0770 chunk 313 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.5352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 55 GLN G 59 GLN I 326 ASN ** R 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 71 GLN j 30 GLN m 613 GLN p 368 GLN t 25 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 41597 Z= 0.118 Angle : 0.470 9.150 59424 Z= 0.247 Chirality : 0.035 0.253 7259 Planarity : 0.003 0.053 4902 Dihedral : 21.078 179.024 14166 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.89 % Allowed : 11.76 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.16), residues: 2946 helix: 2.14 (0.15), residues: 1216 sheet: 0.24 (0.22), residues: 546 loop : -0.47 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP m 464 HIS 0.004 0.001 HIS x 439 PHE 0.023 0.001 PHE x 61 TYR 0.010 0.001 TYR p 304 ARG 0.003 0.000 ARG 8 52 *********************** 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 356 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 305 time to evaluate : 3.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 296 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: P 138 LYS cc_start: 0.7570 (ttpt) cc_final: 0.7106 (tptt) REVERT: p 370 GLN cc_start: 0.7926 (pt0) cc_final: 0.7692 (mt0) REVERT: w 451 LYS cc_start: 0.1785 (tttp) cc_final: 0.1358 (tttm) REVERT: x 498 TYR cc_start: 0.4917 (OUTLIER) cc_final: 0.4183 (t80) outliers start: 51 outliers final: 34 residues processed: 336 average time/residue: 0.5788 time to fit residues: 307.2278 Evaluate side-chains 326 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 290 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 137 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 P residue 53 ASP Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain b residue 519 MET 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 710 ASP 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 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 x residue 47 VAL 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 381 ASP Chi-restraints excluded: chain x residue 494 ASN Chi-restraints excluded: chain x residue 498 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 5.9990 chunk 314 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 349 optimal weight: 9.9990 chunk 289 optimal weight: 0.7980 chunk 161 optimal weight: 0.0020 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 GLN I 326 ASN ** R 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 613 GLN p 356 HIS p 368 GLN t 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41597 Z= 0.175 Angle : 0.483 8.072 59424 Z= 0.252 Chirality : 0.036 0.258 7259 Planarity : 0.004 0.052 4902 Dihedral : 21.028 178.879 14166 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.07 % Allowed : 12.80 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.16), residues: 2946 helix: 2.13 (0.15), residues: 1223 sheet: 0.23 (0.23), residues: 544 loop : -0.48 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP m 464 HIS 0.005 0.001 HIS R 118 PHE 0.024 0.001 PHE x 61 TYR 0.009 0.001 TYR R 124 ARG 0.005 0.000 ARG 8 52 *********************** 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 362 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 306 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 52 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7599 (mtp85) REVERT: I 296 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: P 138 LYS cc_start: 0.7626 (ttpt) cc_final: 0.7106 (tptt) REVERT: p 370 GLN cc_start: 0.7990 (pt0) cc_final: 0.7776 (mt0) REVERT: w 451 LYS cc_start: 0.1684 (tttp) cc_final: 0.1450 (tttp) REVERT: x 251 LEU cc_start: 0.7871 (mp) cc_final: 0.7616 (mp) REVERT: x 498 TYR cc_start: 0.5169 (OUTLIER) cc_final: 0.4389 (t80) outliers start: 56 outliers final: 44 residues processed: 339 average time/residue: 0.5807 time to fit residues: 310.7912 Evaluate side-chains 344 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 298 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 137 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 336 MET Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain U residue 21 SER 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 Z residue 66 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 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 699 SER Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain m residue 710 ASP 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 416 THR Chi-restraints excluded: chain w residue 450 ILE 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 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 381 ASP Chi-restraints excluded: chain x residue 494 ASN 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 336 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 294 optimal weight: 0.9990 chunk 195 optimal weight: 0.0770 chunk 347 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 212 optimal weight: 0.0010 chunk 160 optimal weight: 10.0000 overall best weight: 0.9748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 71 GLN m 613 GLN p 356 HIS p 368 GLN p 426 ASN t 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 41597 Z= 0.150 Angle : 0.477 8.211 59424 Z= 0.250 Chirality : 0.035 0.255 7259 Planarity : 0.003 0.051 4902 Dihedral : 21.035 179.041 14165 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.15 % Allowed : 12.62 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.16), residues: 2946 helix: 2.17 (0.15), residues: 1217 sheet: 0.23 (0.23), residues: 544 loop : -0.47 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP m 464 HIS 0.004 0.001 HIS 8 18 PHE 0.023 0.001 PHE x 61 TYR 0.009 0.001 TYR R 124 ARG 0.004 0.000 ARG R 151 *********************** 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 361 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 303 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 52 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7574 (mtp85) REVERT: I 296 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7416 (mt0) REVERT: P 138 LYS cc_start: 0.7616 (ttpt) cc_final: 0.7098 (tptt) REVERT: p 237 ILE cc_start: 0.7502 (mp) cc_final: 0.7267 (mm) REVERT: p 370 GLN cc_start: 0.7952 (pt0) cc_final: 0.7745 (mt0) REVERT: w 451 LYS cc_start: 0.1861 (tttp) cc_final: 0.1372 (tttp) REVERT: x 251 LEU cc_start: 0.7841 (mp) cc_final: 0.7562 (mp) REVERT: x 498 TYR cc_start: 0.5195 (OUTLIER) cc_final: 0.4400 (t80) outliers start: 58 outliers final: 48 residues processed: 335 average time/residue: 0.5542 time to fit residues: 293.9721 Evaluate side-chains 349 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 299 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 137 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 336 MET Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain U residue 21 SER 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 Z residue 66 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 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 699 SER Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain m residue 710 ASP 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 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 557 MET Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain x residue 25 MET 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 381 ASP Chi-restraints excluded: chain x residue 494 ASN 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 215 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 237 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 273 optimal weight: 0.0670 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 56 GLN ** R 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 613 GLN p 356 HIS p 426 ASN t 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 41597 Z= 0.146 Angle : 0.472 8.327 59424 Z= 0.247 Chirality : 0.035 0.253 7259 Planarity : 0.003 0.052 4902 Dihedral : 21.030 179.205 14165 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.26 % Allowed : 12.62 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.16), residues: 2946 helix: 2.20 (0.15), residues: 1217 sheet: 0.24 (0.23), residues: 544 loop : -0.46 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP m 464 HIS 0.004 0.001 HIS 8 18 PHE 0.023 0.001 PHE x 61 TYR 0.009 0.001 TYR R 124 ARG 0.006 0.000 ARG R 151 *********************** 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 360 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 299 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 52 ARG cc_start: 0.7821 (mtp85) cc_final: 0.7527 (mtp85) REVERT: I 296 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7412 (mt0) REVERT: P 138 LYS cc_start: 0.7575 (ttpt) cc_final: 0.7070 (tptt) REVERT: p 237 ILE cc_start: 0.7574 (mp) cc_final: 0.7308 (mm) REVERT: w 451 LYS cc_start: 0.1918 (tttp) cc_final: 0.1420 (tttp) REVERT: x 251 LEU cc_start: 0.7828 (mp) cc_final: 0.7546 (mp) REVERT: x 498 TYR cc_start: 0.5266 (OUTLIER) cc_final: 0.4364 (t80) outliers start: 61 outliers final: 52 residues processed: 332 average time/residue: 0.5699 time to fit residues: 300.3169 Evaluate side-chains 350 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 296 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 137 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 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 56 THR Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain U residue 21 SER 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 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 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 699 SER Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain m residue 710 ASP 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 416 THR 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 553 SER Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain x residue 25 MET 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 326 THR Chi-restraints excluded: chain x residue 329 VAL Chi-restraints excluded: chain x residue 381 ASP Chi-restraints excluded: chain x residue 494 ASN 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 316 optimal weight: 6.9990 chunk 333 optimal weight: 4.9990 chunk 304 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 254 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 292 optimal weight: 6.9990 chunk 306 optimal weight: 0.8980 chunk 323 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 56 GLN ** R 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 85 GLN Z 123 GLN m 613 GLN p 356 HIS p 426 ASN t 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 41597 Z= 0.243 Angle : 0.523 8.296 59424 Z= 0.273 Chirality : 0.038 0.282 7259 Planarity : 0.004 0.053 4902 Dihedral : 21.020 177.428 14165 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.26 % Allowed : 13.06 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.16), residues: 2946 helix: 2.05 (0.15), residues: 1224 sheet: 0.07 (0.23), residues: 548 loop : -0.50 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP m 464 HIS 0.006 0.001 HIS 8 18 PHE 0.025 0.002 PHE x 61 TYR 0.010 0.001 TYR R 124 ARG 0.005 0.000 ARG R 151 *********************** 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 353 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 292 time to evaluate : 3.453 Fit side-chains revert: symmetry clash REVERT: 8 52 ARG cc_start: 0.7849 (mtp85) cc_final: 0.7519 (mtp85) REVERT: I 296 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7500 (mt0) REVERT: P 138 LYS cc_start: 0.7665 (ttpt) cc_final: 0.7109 (tptt) REVERT: w 451 LYS cc_start: 0.1960 (tttp) cc_final: 0.1560 (tttp) REVERT: x 251 LEU cc_start: 0.7894 (mp) cc_final: 0.7603 (mp) REVERT: x 498 TYR cc_start: 0.5320 (OUTLIER) cc_final: 0.4571 (t80) outliers start: 61 outliers final: 49 residues processed: 330 average time/residue: 0.5714 time to fit residues: 299.5671 Evaluate side-chains 339 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 288 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 137 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 430 LEU Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain U residue 21 SER 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 Z residue 66 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 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 699 SER Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain m residue 710 ASP 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 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 553 SER 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 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 272 VAL Chi-restraints excluded: chain x residue 326 THR Chi-restraints excluded: chain x residue 381 ASP Chi-restraints excluded: chain x residue 494 ASN 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 212 optimal weight: 0.0870 chunk 342 optimal weight: 0.0270 chunk 209 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 359 optimal weight: 8.9990 chunk 331 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 221 optimal weight: 0.6980 chunk 175 optimal weight: 7.9990 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 56 GLN ** R 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 GLN ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 ASN m 613 GLN p 356 HIS p 426 ASN t 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 41597 Z= 0.171 Angle : 0.496 7.995 59424 Z= 0.260 Chirality : 0.036 0.273 7259 Planarity : 0.004 0.057 4902 Dihedral : 21.028 177.921 14165 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.96 % Allowed : 13.39 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.16), residues: 2946 helix: 2.08 (0.15), residues: 1223 sheet: 0.07 (0.23), residues: 543 loop : -0.47 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP m 464 HIS 0.004 0.001 HIS 8 18 PHE 0.023 0.001 PHE x 61 TYR 0.009 0.001 TYR R 124 ARG 0.005 0.000 ARG R 151 ********************** 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 350 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 297 time to evaluate : 3.289 Fit side-chains revert: symmetry clash REVERT: 8 52 ARG cc_start: 0.7838 (mtp85) cc_final: 0.7555 (mtp85) REVERT: I 296 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7484 (mt0) REVERT: P 138 LYS cc_start: 0.7669 (ttpt) cc_final: 0.7111 (tptt) REVERT: w 451 LYS cc_start: 0.1894 (tttp) cc_final: 0.1425 (tttp) REVERT: x 498 TYR cc_start: 0.5298 (OUTLIER) cc_final: 0.4553 (t80) outliers start: 53 outliers final: 46 residues processed: 328 average time/residue: 0.6097 time to fit residues: 319.1206 Evaluate side-chains 337 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 289 time to evaluate : 3.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 137 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 P residue 53 ASP Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 58 HIS Chi-restraints excluded: chain U residue 21 SER 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 b residue 518 ILE Chi-restraints excluded: chain b residue 519 MET 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 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 699 SER Chi-restraints excluded: chain m residue 705 LEU Chi-restraints excluded: chain m residue 710 ASP 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 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 553 SER 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 225 THR Chi-restraints excluded: chain x residue 236 LEU Chi-restraints excluded: chain x residue 272 VAL Chi-restraints excluded: chain x residue 326 THR Chi-restraints excluded: chain x residue 381 ASP Chi-restraints excluded: chain x residue 494 ASN 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 227 optimal weight: 0.0470 chunk 305 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 264 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 56 GLN ** R 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 GLN j 20 ASN m 613 GLN p 426 ASN t 25 ASN ** x 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.090806 restraints weight = 61888.769| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.35 r_work: 0.2858 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41597 Z= 0.199 Angle : 0.499 8.091 59424 Z= 0.262 Chirality : 0.036 0.273 7259 Planarity : 0.004 0.061 4902 Dihedral : 21.013 177.953 14165 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.92 % Allowed : 13.47 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.16), residues: 2946 helix: 2.08 (0.15), residues: 1218 sheet: 0.07 (0.23), residues: 540 loop : -0.51 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP m 464 HIS 0.005 0.001 HIS 8 18 PHE 0.024 0.001 PHE x 61 TYR 0.009 0.001 TYR R 124 ARG 0.004 0.000 ARG u 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8233.87 seconds wall clock time: 153 minutes 25.60 seconds (9205.60 seconds total)