Starting phenix.real_space_refine on Sat Mar 7 11:07:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nad_24270/03_2026/7nad_24270.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nad_24270/03_2026/7nad_24270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nad_24270/03_2026/7nad_24270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nad_24270/03_2026/7nad_24270.map" model { file = "/net/cci-nas-00/data/ceres_data/7nad_24270/03_2026/7nad_24270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nad_24270/03_2026/7nad_24270.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 62 atoms to isotropic. 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 756 5.49 5 S 85 5.16 5 C 24289 2.51 5 N 7816 2.21 5 O 10176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43123 Number of models: 1 Model: "" Number of chains: 27 Chain: "1" Number of atoms: 14914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 14914 Classifications: {'RNA': 697} Modifications used: {'rna2p_pur': 69, 'rna2p_pyr': 49, 'rna3p_pur': 315, 'rna3p_pyr': 264} Link IDs: {'rna2p': 118, 'rna3p': 578} Chain breaks: 13 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: "5" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1061 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 2 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: "V" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 277 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain breaks: 3 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: "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: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2628 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: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2707 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 11, 'TRANS': 316} Chain breaks: 11 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: "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 27227 SG CYS g 44 98.783 85.978 120.304 1.00 6.36 S ATOM 27245 SG CYS g 47 96.771 83.954 117.842 1.00 5.81 S ATOM 27499 SG CYS g 81 94.964 86.469 120.063 1.00 6.44 S ATOM 27518 SG CYS g 84 96.252 83.432 121.654 1.00 5.43 S Residues with excluded nonbonded symmetry interactions: 8 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 residue: pdb=" N SER w 29 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER w 29 " occ=0.50 residue: pdb=" N LEU w 138 " occ=0.50 ... (6 atoms not shown) pdb=" CD2 LEU w 138 " occ=0.50 Time building chain proxies: 7.54, per 1000 atoms: 0.17 Number of scatterers: 43123 At special positions: 0 Unit cell: (180.36, 177.12, 179.28, 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 85 16.00 P 756 15.00 O 10176 8.00 N 7816 7.00 C 24289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.3 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 84 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 47 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 44 " Number of angles added : 6 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6378 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 30 sheets defined 44.5% alpha, 15.2% beta 227 base pairs and 370 stacking pairs defined. Time for finding SS restraints: 5.79 Creating SS restraints... Processing helix chain '5' and resid 32 through 42 removed outlier: 3.537A pdb=" N ARG 5 36 " --> pdb=" O ASP 5 32 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY 5 42 " --> pdb=" O ASP 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 93 removed outlier: 3.519A pdb=" N GLU 5 90 " --> pdb=" O LYS 5 86 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER 5 91 " --> pdb=" O THR 5 87 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN 5 93 " --> pdb=" O LYS 5 89 " (cutoff:3.500A) Processing helix chain '5' and resid 164 through 180 Processing helix chain '5' and resid 217 through 230 Processing helix chain '8' and resid 5 through 15 Processing helix chain '8' and resid 15 through 35 removed outlier: 4.329A 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: 3.979A 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: 3.874A pdb=" N GLU I 150 " --> pdb=" O THR I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 167 removed outlier: 3.512A pdb=" N LEU I 159 " --> pdb=" O ASN I 155 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL I 166 " --> pdb=" O LEU I 162 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU I 167 " --> pdb=" O CYS I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 189 removed outlier: 3.953A 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: 4.082A pdb=" N LYS I 202 " --> pdb=" O THR I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 236 Processing helix chain 'I' and resid 242 through 260 Processing helix chain 'I' and resid 261 through 266 removed outlier: 5.372A pdb=" N SER I 264 " --> pdb=" O SER I 261 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N HIS I 265 " --> pdb=" O THR I 262 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE I 266 " --> pdb=" O ALA I 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 261 through 266' Processing helix chain 'I' and resid 268 through 281 removed outlier: 3.867A pdb=" N ILE I 272 " --> pdb=" O PHE I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 305 Processing helix chain 'I' and resid 308 through 325 removed outlier: 3.621A pdb=" N ILE I 317 " --> pdb=" O GLU I 313 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR I 324 " --> pdb=" O LYS I 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 335 Processing helix chain 'I' and resid 336 through 340 removed outlier: 3.531A pdb=" N LEU I 340 " --> pdb=" O LEU I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 366 removed outlier: 3.580A pdb=" N ARG I 366 " --> pdb=" O LYS I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 370 through 421 removed outlier: 3.620A pdb=" N GLU I 386 " --> pdb=" O GLN I 382 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU I 400 " --> pdb=" O ALA I 396 " (cutoff:3.500A) removed outlier: 3.904A 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 'I' and resid 519 through 523 removed outlier: 3.657A pdb=" N ARG I 523 " --> pdb=" O ARG I 520 " (cutoff:3.500A) 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: 3.732A 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: 5.002A pdb=" N LYS R 153 " --> pdb=" O ALA R 149 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALA R 154 " --> pdb=" O GLN R 150 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN R 156 " --> pdb=" O GLU R 152 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU R 157 " --> pdb=" O LYS R 153 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG R 162 " --> pdb=" O GLU R 158 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 25 Processing helix chain 'U' and resid 29 through 40 Processing helix chain 'U' and resid 42 through 46 removed outlier: 3.637A 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: 3.733A 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 58 through 66 Processing helix chain 'Z' and resid 89 through 93 removed outlier: 3.918A pdb=" N LYS Z 93 " --> pdb=" O GLU Z 90 " (cutoff:3.500A) Processing helix chain 'Z' and resid 98 through 102 removed outlier: 3.588A pdb=" N PHE Z 101 " --> pdb=" O THR Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 125 Processing helix chain 'b' and resid 490 through 511 removed outlier: 3.558A pdb=" N ALA b 494 " --> pdb=" O LYS b 490 " (cutoff:3.500A) Processing helix chain 'b' and resid 527 through 539 removed outlier: 3.963A 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 37 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 24 through 26 No H-bonds generated for 'chain 'd' and resid 24 through 26' Processing helix chain 'd' and resid 27 through 44 Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'd' and resid 61 through 63 No H-bonds generated for 'chain 'd' and resid 61 through 63' Processing helix chain 'g' and resid 58 through 65 removed outlier: 3.836A pdb=" N TYR g 62 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA g 63 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR g 64 " --> pdb=" O GLN g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 70 Processing helix chain 'g' and resid 81 through 110 Processing helix chain 'k' and resid 7 through 16 Processing helix chain 'k' and resid 58 through 69 Processing helix chain 'm' and resid 393 through 397 removed outlier: 3.502A pdb=" N ALA m 397 " --> pdb=" O ASP m 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 393 through 397' Processing helix chain 'm' and resid 408 through 413 Processing helix chain 'm' and resid 418 through 423 removed outlier: 4.229A pdb=" N ARG m 423 " --> pdb=" O LYS m 420 " (cutoff:3.500A) Processing helix chain 'm' and resid 519 through 532 removed outlier: 4.015A pdb=" N ASN m 525 " --> pdb=" O ASP m 521 " (cutoff:3.500A) Processing helix chain 'm' and resid 533 through 538 removed outlier: 3.539A pdb=" N THR m 538 " --> pdb=" O GLY m 535 " (cutoff:3.500A) Processing helix chain 'm' and resid 579 through 584 Processing helix chain 'm' and resid 616 through 619 removed outlier: 3.620A 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 removed outlier: 3.517A pdb=" N ASN n 14 " --> pdb=" O GLY n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 39 Processing helix chain 'n' and resid 48 through 53 Processing helix chain 'n' and resid 64 through 70 removed outlier: 3.690A 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 582 Processing helix chain 'p' and resid 237 through 241 Processing helix chain 'p' and resid 245 through 252 removed outlier: 4.101A pdb=" N ASP p 249 " --> pdb=" O ASP p 245 " (cutoff:3.500A) removed outlier: 4.254A 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 'p' and resid 268 through 270 No H-bonds generated for 'chain 'p' and resid 268 through 270' 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 28 through 40 removed outlier: 3.978A pdb=" N LYS w 32 " --> pdb=" O ARG w 28 " (cutoff:3.500A) Processing helix chain 'w' and resid 129 through 144 removed outlier: 3.933A pdb=" N PHE w 133 " --> pdb=" O VAL w 129 " (cutoff:3.500A) Processing helix chain 'w' and resid 165 through 176 removed outlier: 4.228A pdb=" N LEU w 169 " --> pdb=" O ASP w 165 " (cutoff:3.500A) Processing helix chain 'w' and resid 209 through 213 Processing helix chain 'w' and resid 214 through 219 removed outlier: 3.701A pdb=" N PHE w 219 " --> pdb=" O PRO w 215 " (cutoff:3.500A) Processing helix chain 'w' and resid 348 through 388 removed outlier: 4.098A pdb=" N ILE w 352 " --> pdb=" O GLU w 348 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN w 388 " --> pdb=" O ARG w 384 " (cutoff:3.500A) Processing helix chain 'w' and resid 409 through 416 removed outlier: 3.504A pdb=" N THR w 416 " --> pdb=" O THR w 412 " (cutoff:3.500A) Processing helix chain 'w' and resid 419 through 425 Processing helix chain 'w' and resid 456 through 479 Processing helix chain 'w' and resid 481 through 491 removed outlier: 3.819A pdb=" N ARG w 485 " --> pdb=" O ASP w 481 " (cutoff:3.500A) removed outlier: 3.609A 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: 3.583A 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: 4.154A 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: 3.723A pdb=" N LYS x 507 " --> pdb=" O LYS x 503 " (cutoff:3.500A) removed outlier: 3.896A 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 '5' and resid 145 through 148 removed outlier: 6.840A pdb=" N ASP x 46 " --> pdb=" O VAL x 222 " (cutoff:3.500A) removed outlier: 7.699A 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) removed outlier: 7.718A pdb=" N VAL x 226 " --> pdb=" O VAL x 48 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP x 50 " --> pdb=" O VAL x 226 " (cutoff:3.500A) removed outlier: 6.226A 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: 6.393A pdb=" N LEU x 87 " --> pdb=" O VAL x 170 " (cutoff:3.500A) removed outlier: 7.691A 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: 6.519A pdb=" N SER x 86 " --> pdb=" O LEU x 145 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N GLY x 147 " --> pdb=" O SER x 86 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE x 88 " --> pdb=" O GLY x 147 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN x 120 " --> pdb=" O ILE x 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 127 through 129 Processing sheet with id=AA3, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AA4, first strand: chain 'U' and resid 54 through 58 removed outlier: 7.977A pdb=" N TYR U 103 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR U 16 " --> pdb=" O TYR U 103 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU U 105 " --> pdb=" O THR U 16 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP U 18 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N PHE U 107 " --> pdb=" O ASP U 18 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'V' and resid 22 through 24 Processing sheet with id=AA6, first strand: chain 'X' and resid 23 through 24 Processing sheet with id=AA7, first strand: chain 'X' and resid 63 through 66 removed outlier: 3.812A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.669A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N HIS Z 40 " --> pdb=" O PRO Z 28 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LYS Z 22 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 22 through 25 removed outlier: 7.090A pdb=" N THR c 24 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ILE c 92 " --> pdb=" O THR c 24 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE c 42 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'd' and resid 12 through 15 Processing sheet with id=AB2, first strand: chain 'g' and resid 20 through 24 Processing sheet with id=AB3, first strand: chain 'k' and resid 3 through 4 removed outlier: 4.868A pdb=" N ARG k 46 " --> pdb=" O THR k 22 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 399 through 405 Processing sheet with id=AB5, first strand: chain 'm' and resid 428 through 433 removed outlier: 5.292A pdb=" N CYS m 429 " --> pdb=" O THR m 806 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR m 806 " --> pdb=" O CYS m 429 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR m 431 " --> pdb=" O LEU m 804 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 440 through 445 removed outlier: 3.587A pdb=" N THR m 442 " --> pdb=" O GLY m 455 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR m 460 " --> pdb=" O SER m 456 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU m 465 " --> pdb=" O GLU m 471 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU m 471 " --> pdb=" O GLU m 465 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'm' and resid 488 through 493 removed outlier: 3.925A pdb=" N ILE m 589 " --> pdb=" O LEU m 512 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'm' and resid 599 through 602 Processing sheet with id=AB9, first strand: chain 'm' and resid 642 through 647 removed outlier: 5.850A pdb=" N VAL m 662 " --> pdb=" O LYS m 675 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS m 675 " --> pdb=" O VAL m 662 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE m 664 " --> pdb=" O VAL m 673 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'm' and resid 683 through 688 Processing sheet with id=AC2, first strand: chain 'm' and resid 726 through 731 removed outlier: 3.546A pdb=" N SER m 728 " --> pdb=" O ALA m 741 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE m 747 " --> pdb=" O LYS m 769 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS m 769 " --> pdb=" O ILE m 747 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL m 749 " --> pdb=" O LEU m 767 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'p' and resid 96 through 100 removed outlier: 7.021A pdb=" N ILE p 451 " --> pdb=" O LEU p 97 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER p 99 " --> pdb=" O ILE p 449 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE p 449 " --> pdb=" O SER p 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'p' and resid 106 through 110 removed outlier: 3.556A pdb=" N SER p 108 " --> pdb=" O GLY p 121 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL p 127 " --> pdb=" O GLN p 139 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN p 139 " --> pdb=" O VAL p 127 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR p 129 " --> pdb=" O GLN p 137 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN p 137 " --> pdb=" O GLU p 196 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'p' and resid 147 through 154 removed outlier: 6.814A pdb=" N ALA p 161 " --> pdb=" O ARG p 148 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL p 150 " --> pdb=" O VAL p 159 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL p 159 " --> pdb=" O VAL p 150 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TYR p 152 " --> pdb=" O ARG p 157 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ARG p 157 " --> pdb=" O TYR p 152 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY p 162 " --> pdb=" O THR p 166 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR p 166 " --> pdb=" O GLY p 162 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LYS p 171 " --> pdb=" O THR p 200 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR p 200 " --> pdb=" O LYS p 171 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'p' and resid 211 through 216 Processing sheet with id=AC7, first strand: chain 'p' and resid 290 through 293 removed outlier: 3.558A pdb=" N SER p 307 " --> pdb=" O THR p 311 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR p 311 " --> pdb=" O SER p 307 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE p 312 " --> pdb=" O THR p 325 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR p 325 " --> pdb=" O ILE p 312 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR p 314 " --> pdb=" O ILE p 323 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'p' and resid 332 through 338 removed outlier: 4.176A pdb=" N HIS p 352 " --> pdb=" O SER p 348 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'p' and resid 378 through 383 removed outlier: 6.230A pdb=" N VAL p 400 " --> pdb=" O THR p 413 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR p 413 " --> pdb=" O VAL p 400 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL p 402 " --> pdb=" O MET p 411 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'w' and resid 156 through 161 removed outlier: 6.495A pdb=" N PHE w 202 " --> pdb=" O PHE w 177 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE w 177 " --> pdb=" O PHE w 202 " (cutoff:3.500A) Processing sheet with id=AD2, 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=AD3, first strand: chain 'x' and resid 294 through 299 removed outlier: 6.364A 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: 8.913A 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) 1235 hydrogen bonds defined for protein. 3543 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 572 hydrogen bonds 938 hydrogen bond angles 0 basepair planarities 227 basepair parallelities 370 stacking parallelities Total time for adding SS restraints: 16.47 Time building geometry restraints manager: 4.58 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: 9344 1.33 - 1.45: 13311 1.45 - 1.57: 21160 1.57 - 1.69: 1494 1.69 - 1.81: 141 Bond restraints: 45450 Sorted by residual: bond pdb=" O3' G 12121 " pdb=" P G 12122 " ideal model delta sigma weight residual 1.607 1.644 -0.037 1.50e-02 4.44e+03 6.07e+00 bond pdb=" O5' G 12123 " pdb=" C5' G 12123 " ideal model delta sigma weight residual 1.420 1.444 -0.024 1.50e-02 4.44e+03 2.57e+00 bond pdb=" CB PRO u 131 " pdb=" CG PRO u 131 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.51e+00 bond pdb=" CB GLU R 152 " pdb=" CG GLU R 152 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" O5' G 12122 " pdb=" C5' G 12122 " ideal model delta sigma weight residual 1.420 1.441 -0.021 1.50e-02 4.44e+03 2.03e+00 ... (remaining 45445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 64228 2.14 - 4.29: 557 4.29 - 6.43: 62 6.43 - 8.57: 6 8.57 - 10.72: 3 Bond angle restraints: 64856 Sorted by residual: angle pdb=" N ASN x 406 " pdb=" CA ASN x 406 " pdb=" C ASN x 406 " ideal model delta sigma weight residual 112.86 123.58 -10.72 1.22e+00 6.72e-01 7.72e+01 angle pdb=" N SER p 101 " pdb=" CA SER p 101 " pdb=" C SER p 101 " ideal model delta sigma weight residual 110.41 117.58 -7.17 1.23e+00 6.61e-01 3.40e+01 angle pdb=" N ARG P 131 " pdb=" CA ARG P 131 " pdb=" C ARG P 131 " ideal model delta sigma weight residual 108.19 114.39 -6.20 1.29e+00 6.01e-01 2.31e+01 angle pdb=" N LYS d 65 " pdb=" CA LYS d 65 " pdb=" C LYS d 65 " ideal model delta sigma weight residual 111.28 116.45 -5.17 1.09e+00 8.42e-01 2.25e+01 angle pdb=" N THR p 311 " pdb=" CA THR p 311 " pdb=" C THR p 311 " ideal model delta sigma weight residual 109.50 116.40 -6.90 1.58e+00 4.01e-01 1.91e+01 ... (remaining 64851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 26755 35.98 - 71.96: 1781 71.96 - 107.94: 210 107.94 - 143.91: 2 143.91 - 179.89: 4 Dihedral angle restraints: 28752 sinusoidal: 18993 harmonic: 9759 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 -128.00 51.89 -179.89 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 12318 " pdb=" C1' U 12318 " pdb=" N1 U 12318 " pdb=" C2 U 12318 " ideal model delta sinusoidal sigma weight residual -128.00 27.66 -155.66 1 1.70e+01 3.46e-03 6.35e+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 -74.21 -85.79 1 1.50e+01 4.44e-03 3.95e+01 ... (remaining 28749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 7445 0.080 - 0.159: 424 0.159 - 0.239: 27 0.239 - 0.318: 1 0.318 - 0.398: 2 Chirality restraints: 7899 Sorted by residual: chirality pdb=" CA ASN x 406 " pdb=" N ASN x 406 " pdb=" C ASN x 406 " pdb=" CB ASN x 406 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CG LEU R 155 " pdb=" CB LEU R 155 " pdb=" CD1 LEU R 155 " pdb=" CD2 LEU R 155 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA THR p 311 " pdb=" N THR p 311 " pdb=" C THR p 311 " pdb=" CB THR p 311 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 7896 not shown) Planarity restraints: 5385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU I 330 " 0.023 2.00e-02 2.50e+03 4.50e-02 2.02e+01 pdb=" C GLU I 330 " -0.078 2.00e-02 2.50e+03 pdb=" O GLU I 330 " 0.029 2.00e-02 2.50e+03 pdb=" N GLU I 331 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN u 130 " -0.068 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO u 131 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO u 131 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO u 131 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G 11646 " -0.032 2.00e-02 2.50e+03 1.43e-02 6.14e+00 pdb=" N9 G 11646 " 0.036 2.00e-02 2.50e+03 pdb=" C8 G 11646 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G 11646 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G 11646 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G 11646 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G 11646 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G 11646 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G 11646 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G 11646 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G 11646 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G 11646 " 0.004 2.00e-02 2.50e+03 ... (remaining 5382 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 2163 2.71 - 3.26: 39223 3.26 - 3.80: 75280 3.80 - 4.35: 99717 4.35 - 4.90: 146210 Nonbonded interactions: 362593 Sorted by model distance: nonbonded pdb=" O2' G 11560 " pdb=" O4' G 11561 " model vdw 2.159 3.040 nonbonded pdb=" OP2 G 1 894 " pdb=" N2 G 1 894 " model vdw 2.166 3.120 nonbonded pdb=" OG SER p 217 " pdb=" OD1 ASN p 219 " model vdw 2.203 3.040 nonbonded pdb=" O2' C 11657 " pdb=" O2' G 11796 " model vdw 2.203 3.040 nonbonded pdb=" OG SER p 122 " pdb=" OD1 ASP p 124 " model vdw 2.210 3.040 ... (remaining 362588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.17 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 50.410 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.002 0.079 45454 Z= 0.122 Angle : 0.518 10.716 64862 Z= 0.283 Chirality : 0.038 0.398 7899 Planarity : 0.004 0.101 5385 Dihedral : 19.893 179.893 22374 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.34 % Allowed : 1.24 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.15), residues: 3220 helix: 1.77 (0.15), residues: 1347 sheet: 0.37 (0.22), residues: 571 loop : -0.40 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 5 74 TYR 0.014 0.001 TYR c 23 PHE 0.024 0.001 PHE x 61 TRP 0.021 0.001 TRP m 464 HIS 0.003 0.001 HIS 8 18 Details of bonding type rmsd covalent geometry : bond 0.00239 (45450) covalent geometry : angle 0.51726 (64856) hydrogen bonds : bond 0.11833 ( 1807) hydrogen bonds : angle 4.94523 ( 4481) metal coordination : bond 0.00168 ( 4) metal coordination : angle 3.00650 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 349 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: b 503 MET cc_start: 0.7416 (mtt) cc_final: 0.7069 (mtt) REVERT: b 521 ARG cc_start: 0.8463 (mtt90) cc_final: 0.8038 (mtt90) REVERT: j 28 HIS cc_start: 0.7745 (t-90) cc_final: 0.7442 (t-170) REVERT: x 500 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.5502 (t80) outliers start: 10 outliers final: 4 residues processed: 359 average time/residue: 0.2997 time to fit residues: 168.5550 Evaluate side-chains 286 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 281 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 435 TYR Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 165 ASN I 382 GLN V 98 ASN Z 40 HIS p 342 ASN w 137 GLN x 292 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.149200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129123 restraints weight = 56201.921| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.28 r_work: 0.3171 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 45454 Z= 0.261 Angle : 0.608 9.109 64862 Z= 0.315 Chirality : 0.042 0.287 7899 Planarity : 0.005 0.058 5385 Dihedral : 21.169 177.915 15359 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.21 % Allowed : 6.53 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.15), residues: 3220 helix: 1.72 (0.14), residues: 1359 sheet: 0.10 (0.21), residues: 604 loop : -0.45 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG u 135 TYR 0.016 0.002 TYR m 608 PHE 0.027 0.002 PHE p 100 TRP 0.023 0.002 TRP m 464 HIS 0.010 0.001 HIS p 310 Details of bonding type rmsd covalent geometry : bond 0.00563 (45450) covalent geometry : angle 0.60669 (64856) hydrogen bonds : bond 0.05439 ( 1807) hydrogen bonds : angle 4.10408 ( 4481) metal coordination : bond 0.00741 ( 4) metal coordination : angle 3.86507 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: I 345 ASP cc_start: 0.8100 (m-30) cc_final: 0.7878 (m-30) REVERT: I 419 LYS cc_start: 0.6985 (mptt) cc_final: 0.6784 (mptt) REVERT: U 49 ASN cc_start: 0.7462 (t0) cc_final: 0.7114 (t0) REVERT: b 503 MET cc_start: 0.7993 (mtt) cc_final: 0.7793 (mtt) REVERT: n 27 VAL cc_start: 0.7867 (OUTLIER) cc_final: 0.7550 (m) REVERT: u 113 ARG cc_start: 0.7449 (ptt90) cc_final: 0.7161 (ptt90) REVERT: x 500 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.5543 (t80) outliers start: 36 outliers final: 17 residues processed: 308 average time/residue: 0.2719 time to fit residues: 133.9358 Evaluate side-chains 290 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 271 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain m residue 407 ILE Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain u residue 136 ILE Chi-restraints excluded: chain w residue 542 LEU Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 292 ASN Chi-restraints excluded: chain x residue 435 TYR Chi-restraints excluded: chain x residue 500 TYR Chi-restraints excluded: chain x residue 532 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 311 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 315 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 262 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 369 optimal weight: 6.9990 chunk 250 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 36 ASN Z 106 GLN c 47 ASN d 57 GLN ** p 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 16 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.152291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132294 restraints weight = 56341.262| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.26 r_work: 0.3214 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 45454 Z= 0.116 Angle : 0.494 9.673 64862 Z= 0.258 Chirality : 0.036 0.219 7899 Planarity : 0.004 0.047 5385 Dihedral : 21.101 179.136 15359 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.08 % Allowed : 8.58 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.15), residues: 3220 helix: 1.95 (0.14), residues: 1365 sheet: 0.27 (0.22), residues: 591 loop : -0.43 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG u 135 TYR 0.021 0.001 TYR p 238 PHE 0.023 0.001 PHE x 61 TRP 0.017 0.001 TRP m 464 HIS 0.004 0.001 HIS 8 18 Details of bonding type rmsd covalent geometry : bond 0.00236 (45450) covalent geometry : angle 0.49262 (64856) hydrogen bonds : bond 0.04344 ( 1807) hydrogen bonds : angle 3.80577 ( 4481) metal coordination : bond 0.00355 ( 4) metal coordination : angle 3.38796 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: b 503 MET cc_start: 0.7983 (mtt) cc_final: 0.7751 (mtt) REVERT: n 27 VAL cc_start: 0.7910 (OUTLIER) cc_final: 0.7650 (m) REVERT: u 122 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6233 (ttp-170) REVERT: x 500 TYR cc_start: 0.6754 (OUTLIER) cc_final: 0.5551 (t80) outliers start: 32 outliers final: 21 residues processed: 294 average time/residue: 0.2723 time to fit residues: 127.8267 Evaluate side-chains 288 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain u residue 136 ILE Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 728 MET Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 3 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 chunk 345 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 308 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 376 optimal weight: 10.0000 chunk 378 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 49 ASN p 342 ASN j 16 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.151660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131769 restraints weight = 56144.678| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.25 r_work: 0.3211 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 45454 Z= 0.135 Angle : 0.494 8.780 64862 Z= 0.259 Chirality : 0.036 0.209 7899 Planarity : 0.004 0.045 5385 Dihedral : 21.038 179.158 15356 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.55 % Allowed : 10.16 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.15), residues: 3220 helix: 2.02 (0.14), residues: 1365 sheet: 0.24 (0.22), residues: 599 loop : -0.39 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG u 135 TYR 0.024 0.001 TYR p 96 PHE 0.024 0.001 PHE x 61 TRP 0.015 0.001 TRP m 464 HIS 0.006 0.001 HIS 8 18 Details of bonding type rmsd covalent geometry : bond 0.00283 (45450) covalent geometry : angle 0.49329 (64856) hydrogen bonds : bond 0.04315 ( 1807) hydrogen bonds : angle 3.72263 ( 4481) metal coordination : bond 0.00441 ( 4) metal coordination : angle 3.36179 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 274 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: 5 77 ARG cc_start: 0.6325 (mtm-85) cc_final: 0.6112 (mtm-85) REVERT: b 503 MET cc_start: 0.7984 (mtt) cc_final: 0.7725 (mtt) REVERT: u 122 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6284 (ttp-170) REVERT: x 498 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.5181 (t80) REVERT: x 500 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.5486 (t80) REVERT: x 514 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7536 (ttpt) outliers start: 46 outliers final: 27 residues processed: 303 average time/residue: 0.2687 time to fit residues: 131.2828 Evaluate side-chains 300 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 269 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain I residue 379 GLU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain m residue 407 ILE Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 777 ASN Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 498 TYR Chi-restraints excluded: chain x residue 500 TYR Chi-restraints excluded: chain x residue 514 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 45 optimal weight: 5.9990 chunk 349 optimal weight: 0.0570 chunk 374 optimal weight: 0.0170 chunk 283 optimal weight: 9.9990 chunk 381 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 316 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 308 optimal weight: 7.9990 overall best weight: 2.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 49 ASN ** p 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.148436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128852 restraints weight = 55996.584| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.21 r_work: 0.3173 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 45454 Z= 0.239 Angle : 0.584 8.217 64862 Z= 0.303 Chirality : 0.041 0.255 7899 Planarity : 0.004 0.046 5385 Dihedral : 21.073 177.260 15355 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.78 % Allowed : 11.20 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.15), residues: 3220 helix: 1.80 (0.14), residues: 1363 sheet: 0.08 (0.21), residues: 588 loop : -0.51 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG u 135 TYR 0.027 0.002 TYR p 238 PHE 0.025 0.002 PHE x 61 TRP 0.016 0.002 TRP m 464 HIS 0.009 0.001 HIS 8 18 Details of bonding type rmsd covalent geometry : bond 0.00514 (45450) covalent geometry : angle 0.58299 (64856) hydrogen bonds : bond 0.05143 ( 1807) hydrogen bonds : angle 3.90178 ( 4481) metal coordination : bond 0.00756 ( 4) metal coordination : angle 3.57809 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: b 503 MET cc_start: 0.8027 (mtt) cc_final: 0.7724 (mtt) REVERT: b 514 LYS cc_start: 0.6843 (ptpt) cc_final: 0.6639 (ptpt) REVERT: x 498 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.5451 (t80) REVERT: x 500 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.5610 (t80) outliers start: 53 outliers final: 36 residues processed: 302 average time/residue: 0.2707 time to fit residues: 130.0587 Evaluate side-chains 300 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 262 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 67 ILE Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain I residue 379 GLU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 424 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 777 ASN Chi-restraints excluded: chain m residue 779 LEU Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain p residue 438 VAL Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 467 MET Chi-restraints excluded: chain x residue 498 TYR Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 51 optimal weight: 8.9990 chunk 377 optimal weight: 0.0020 chunk 361 optimal weight: 2.9990 chunk 317 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 314 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 363 optimal weight: 3.9990 chunk 382 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 313 optimal weight: 0.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 47 ASN p 342 ASN x 244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.150592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130416 restraints weight = 56248.290| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.26 r_work: 0.3183 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 45454 Z= 0.139 Angle : 0.510 8.164 64862 Z= 0.268 Chirality : 0.037 0.218 7899 Planarity : 0.004 0.049 5385 Dihedral : 21.061 178.085 15355 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.45 % Allowed : 12.45 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.15), residues: 3220 helix: 1.94 (0.14), residues: 1361 sheet: 0.13 (0.22), residues: 586 loop : -0.45 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG u 135 TYR 0.025 0.001 TYR p 96 PHE 0.022 0.001 PHE x 61 TRP 0.016 0.001 TRP m 464 HIS 0.006 0.001 HIS 8 18 Details of bonding type rmsd covalent geometry : bond 0.00291 (45450) covalent geometry : angle 0.50894 (64856) hydrogen bonds : bond 0.04442 ( 1807) hydrogen bonds : angle 3.76148 ( 4481) metal coordination : bond 0.00434 ( 4) metal coordination : angle 3.44279 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 264 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: b 503 MET cc_start: 0.8003 (mtt) cc_final: 0.7719 (mtt) REVERT: x 498 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.5451 (t80) REVERT: x 500 TYR cc_start: 0.6887 (OUTLIER) cc_final: 0.5712 (t80) outliers start: 43 outliers final: 33 residues processed: 290 average time/residue: 0.2672 time to fit residues: 124.1895 Evaluate side-chains 300 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 265 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 379 GLU Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 777 ASN Chi-restraints excluded: chain p residue 165 ARG Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 438 VAL Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 289 ILE Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 498 TYR Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 54 optimal weight: 20.0000 chunk 181 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 320 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 334 optimal weight: 5.9990 chunk 307 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 240 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 49 ASN ** p 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.149928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130726 restraints weight = 55949.045| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.16 r_work: 0.3200 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 45454 Z= 0.171 Angle : 0.525 8.354 64862 Z= 0.274 Chirality : 0.038 0.216 7899 Planarity : 0.004 0.051 5385 Dihedral : 21.033 178.041 15355 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.75 % Allowed : 12.78 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.15), residues: 3220 helix: 1.92 (0.14), residues: 1363 sheet: 0.03 (0.21), residues: 594 loop : -0.48 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG u 135 TYR 0.025 0.001 TYR p 238 PHE 0.024 0.002 PHE x 61 TRP 0.015 0.001 TRP m 464 HIS 0.007 0.001 HIS p 310 Details of bonding type rmsd covalent geometry : bond 0.00365 (45450) covalent geometry : angle 0.52367 (64856) hydrogen bonds : bond 0.04569 ( 1807) hydrogen bonds : angle 3.75617 ( 4481) metal coordination : bond 0.00555 ( 4) metal coordination : angle 3.55216 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 265 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: U 49 ASN cc_start: 0.7287 (t160) cc_final: 0.6805 (t0) REVERT: b 503 MET cc_start: 0.8000 (mtt) cc_final: 0.7705 (mtt) REVERT: x 498 TYR cc_start: 0.7135 (OUTLIER) cc_final: 0.5492 (t80) REVERT: x 500 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.5756 (t80) outliers start: 52 outliers final: 43 residues processed: 299 average time/residue: 0.2755 time to fit residues: 131.6450 Evaluate side-chains 303 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 379 GLU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 777 ASN Chi-restraints excluded: chain m residue 779 LEU Chi-restraints excluded: chain p residue 165 ARG Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain p residue 310 HIS Chi-restraints excluded: chain p residue 388 GLU Chi-restraints excluded: chain p residue 438 VAL Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain w residue 176 LEU Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 289 ILE Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 467 MET Chi-restraints excluded: chain x residue 474 LEU Chi-restraints excluded: chain x residue 498 TYR Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 377 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 362 optimal weight: 9.9990 chunk 382 optimal weight: 9.9990 chunk 277 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 384 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 49 ASN p 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.147855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128466 restraints weight = 56194.456| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.20 r_work: 0.3162 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 45454 Z= 0.254 Angle : 0.598 7.736 64862 Z= 0.311 Chirality : 0.042 0.243 7899 Planarity : 0.005 0.050 5385 Dihedral : 21.091 176.407 15355 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.82 % Allowed : 13.12 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.15), residues: 3220 helix: 1.73 (0.14), residues: 1362 sheet: -0.07 (0.21), residues: 587 loop : -0.59 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG u 135 TYR 0.026 0.002 TYR p 238 PHE 0.026 0.002 PHE x 61 TRP 0.015 0.002 TRP m 464 HIS 0.009 0.001 HIS p 310 Details of bonding type rmsd covalent geometry : bond 0.00546 (45450) covalent geometry : angle 0.59735 (64856) hydrogen bonds : bond 0.05250 ( 1807) hydrogen bonds : angle 3.91315 ( 4481) metal coordination : bond 0.00773 ( 4) metal coordination : angle 3.63827 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 1.080 Fit side-chains REVERT: b 503 MET cc_start: 0.8016 (mtt) cc_final: 0.7695 (mtt) REVERT: b 514 LYS cc_start: 0.6865 (ptpt) cc_final: 0.6633 (ptpt) REVERT: x 498 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.5506 (t80) REVERT: x 500 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.5791 (t80) outliers start: 54 outliers final: 47 residues processed: 306 average time/residue: 0.2697 time to fit residues: 131.9706 Evaluate side-chains 319 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 270 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 67 ILE Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 379 GLU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 424 THR Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 777 ASN Chi-restraints excluded: chain m residue 779 LEU Chi-restraints excluded: chain p residue 165 ARG Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain p residue 388 GLU Chi-restraints excluded: chain p residue 438 VAL Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain w residue 176 LEU Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 289 ILE Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 467 MET Chi-restraints excluded: chain x residue 474 LEU Chi-restraints excluded: chain x residue 498 TYR Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 134 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 379 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 383 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 321 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 392 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.148676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129311 restraints weight = 55866.453| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.17 r_work: 0.3183 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 45454 Z= 0.191 Angle : 0.557 7.861 64862 Z= 0.292 Chirality : 0.039 0.232 7899 Planarity : 0.004 0.060 5385 Dihedral : 21.096 176.627 15355 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.82 % Allowed : 13.49 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.15), residues: 3220 helix: 1.76 (0.14), residues: 1362 sheet: -0.06 (0.21), residues: 587 loop : -0.58 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG u 135 TYR 0.024 0.002 TYR p 238 PHE 0.024 0.002 PHE x 61 TRP 0.015 0.002 TRP m 464 HIS 0.007 0.001 HIS 8 18 Details of bonding type rmsd covalent geometry : bond 0.00406 (45450) covalent geometry : angle 0.55624 (64856) hydrogen bonds : bond 0.04902 ( 1807) hydrogen bonds : angle 3.86199 ( 4481) metal coordination : bond 0.00608 ( 4) metal coordination : angle 3.58836 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: b 503 MET cc_start: 0.7996 (mtt) cc_final: 0.7681 (mtt) REVERT: b 514 LYS cc_start: 0.6803 (ptpt) cc_final: 0.6564 (ptpt) REVERT: x 498 TYR cc_start: 0.7086 (OUTLIER) cc_final: 0.5505 (t80) REVERT: x 500 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.5788 (t80) outliers start: 54 outliers final: 50 residues processed: 299 average time/residue: 0.2694 time to fit residues: 128.3243 Evaluate side-chains 314 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 379 GLU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 424 THR Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 97 LEU Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain m residue 506 VAL Chi-restraints excluded: chain m residue 568 VAL Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 777 ASN Chi-restraints excluded: chain m residue 779 LEU Chi-restraints excluded: chain p residue 165 ARG Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain p residue 342 ASN Chi-restraints excluded: chain p residue 388 GLU Chi-restraints excluded: chain p residue 438 VAL Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain w residue 176 LEU Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 47 VAL Chi-restraints excluded: chain x residue 289 ILE Chi-restraints excluded: chain x residue 353 MET Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 467 MET Chi-restraints excluded: chain x residue 474 LEU Chi-restraints excluded: chain x residue 498 TYR Chi-restraints excluded: chain x residue 500 TYR Chi-restraints excluded: chain x residue 514 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 336 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 chunk 303 optimal weight: 0.7980 chunk 321 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 335 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 307 optimal weight: 0.0970 chunk 40 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.152373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.132559 restraints weight = 56444.736| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.27 r_work: 0.3213 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 45454 Z= 0.102 Angle : 0.489 9.284 64862 Z= 0.257 Chirality : 0.036 0.246 7899 Planarity : 0.004 0.063 5385 Dihedral : 21.037 178.523 15355 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.18 % Allowed : 13.99 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.15), residues: 3220 helix: 2.00 (0.14), residues: 1367 sheet: 0.04 (0.21), residues: 596 loop : -0.50 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG u 135 TYR 0.024 0.001 TYR p 96 PHE 0.022 0.001 PHE x 61 TRP 0.016 0.001 TRP m 464 HIS 0.004 0.001 HIS 8 18 Details of bonding type rmsd covalent geometry : bond 0.00204 (45450) covalent geometry : angle 0.48749 (64856) hydrogen bonds : bond 0.04102 ( 1807) hydrogen bonds : angle 3.65438 ( 4481) metal coordination : bond 0.00299 ( 4) metal coordination : angle 3.42463 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 272 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: I 244 ILE cc_start: 0.7395 (pt) cc_final: 0.7021 (mt) REVERT: b 503 MET cc_start: 0.7953 (mtt) cc_final: 0.7652 (mtt) REVERT: m 548 GLU cc_start: 0.7792 (mp0) cc_final: 0.7510 (mp0) REVERT: x 498 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.5491 (t80) REVERT: x 500 TYR cc_start: 0.6785 (OUTLIER) cc_final: 0.5819 (t80) outliers start: 35 outliers final: 28 residues processed: 295 average time/residue: 0.2743 time to fit residues: 128.7273 Evaluate side-chains 294 residues out of total 2973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 148 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain b residue 518 ILE Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 61 LYS Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 31 LEU Chi-restraints excluded: chain k residue 39 ARG Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain m residue 729 VAL Chi-restraints excluded: chain m residue 777 ASN Chi-restraints excluded: chain p residue 165 ARG Chi-restraints excluded: chain p residue 229 ASN Chi-restraints excluded: chain p residue 438 VAL Chi-restraints excluded: chain u residue 122 ARG Chi-restraints excluded: chain w residue 176 LEU Chi-restraints excluded: chain w residue 197 VAL Chi-restraints excluded: chain w residue 538 LEU Chi-restraints excluded: chain x residue 29 THR Chi-restraints excluded: chain x residue 367 VAL Chi-restraints excluded: chain x residue 498 TYR Chi-restraints excluded: chain x residue 500 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 64 optimal weight: 8.9990 chunk 297 optimal weight: 5.9990 chunk 265 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 298 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 277 optimal weight: 6.9990 chunk 390 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 ASN ** p 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130215 restraints weight = 56321.669| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.26 r_work: 0.3179 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 45454 Z= 0.154 Angle : 0.509 7.998 64862 Z= 0.267 Chirality : 0.037 0.208 7899 Planarity : 0.004 0.053 5385 Dihedral : 20.996 178.352 15355 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.38 % Allowed : 13.93 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.15), residues: 3220 helix: 1.98 (0.14), residues: 1362 sheet: -0.00 (0.21), residues: 596 loop : -0.51 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG u 113 TYR 0.022 0.001 TYR p 238 PHE 0.024 0.001 PHE x 61 TRP 0.015 0.001 TRP m 464 HIS 0.006 0.001 HIS p 310 Details of bonding type rmsd covalent geometry : bond 0.00326 (45450) covalent geometry : angle 0.50805 (64856) hydrogen bonds : bond 0.04391 ( 1807) hydrogen bonds : angle 3.69354 ( 4481) metal coordination : bond 0.00435 ( 4) metal coordination : angle 3.52423 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10536.91 seconds wall clock time: 181 minutes 14.55 seconds (10874.55 seconds total)