Starting phenix.real_space_refine on Tue Aug 26 19:27:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b3i_15829/08_2025/8b3i_15829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b3i_15829/08_2025/8b3i_15829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8b3i_15829/08_2025/8b3i_15829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b3i_15829/08_2025/8b3i_15829.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b3i_15829/08_2025/8b3i_15829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b3i_15829/08_2025/8b3i_15829.map" } resolution = 3.5 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= 0.137 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 S 118 5.16 5 C 12801 2.51 5 N 3480 2.21 5 O 3795 1.98 5 H 20180 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40377 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2290 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 15, 'TRANS': 130} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1237 Classifications: {'peptide': 76} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "R" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1284 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Chain: "U" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1207 Classifications: {'peptide': 76} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 5627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5627 Classifications: {'peptide': 365} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 355} Chain: "d" Number of atoms: 17196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 17196 Classifications: {'peptide': 1096} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1055} Chain breaks: 6 Chain: "e" Number of atoms: 11533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 11533 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 679} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3935 SG CYS R 42 65.760 82.049 142.272 1.00 51.27 S ATOM 3974 SG CYS R 45 67.643 80.995 140.268 1.00 47.50 S ATOM 4437 SG CYS R 83 68.813 84.450 140.531 1.00 53.62 S ATOM 4312 SG CYS R 75 57.082 89.042 151.310 1.00 64.78 S ATOM 4637 SG CYS R 94 58.570 88.624 147.211 1.00 58.83 S ATOM 4106 SG CYS R 53 72.027 83.527 139.811 1.00 64.90 S ATOM 4150 SG CYS R 56 75.951 83.499 140.927 1.00 66.80 S ATOM 4215 SG CYS R 68 74.085 82.511 143.351 1.00 65.16 S Time building chain proxies: 5.37, per 1000 atoms: 0.13 Number of scatterers: 40377 At special positions: 0 Unit cell: (103.95, 139.65, 187.95, 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 3 29.99 S 118 16.00 O 3795 8.00 N 3480 7.00 C 12801 6.00 H 20180 1.00 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: 3.54 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " Number of angles added : 6 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 44 sheets defined 28.8% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'D' and resid 2 through 16 removed outlier: 3.660A pdb=" N ILE D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 98 through 110 removed outlier: 3.515A pdb=" N LEU D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 130 removed outlier: 3.839A pdb=" N ILE D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 146 removed outlier: 3.612A pdb=" N TYR D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 35 removed outlier: 3.522A pdb=" N ILE N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'R' and resid 53 through 58 removed outlier: 4.205A pdb=" N ALA R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.050A pdb=" N ARG R 86 " --> pdb=" O HIS R 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 35 Processing helix chain 'U' and resid 55 through 60 removed outlier: 3.528A pdb=" N ASN U 60 " --> pdb=" O SER U 57 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 10 Processing helix chain 'a' and resid 14 through 29 removed outlier: 3.918A pdb=" N LEU a 18 " --> pdb=" O ASP a 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 255 Processing helix chain 'd' and resid 366 through 370 removed outlier: 4.121A pdb=" N GLN d 370 " --> pdb=" O LEU d 367 " (cutoff:3.500A) Processing helix chain 'd' and resid 755 through 759 Processing helix chain 'd' and resid 986 through 990 Processing helix chain 'd' and resid 1044 through 1062 Processing helix chain 'd' and resid 1069 through 1074 Processing helix chain 'd' and resid 1091 through 1096 Processing helix chain 'd' and resid 1101 through 1109 Processing helix chain 'd' and resid 1125 through 1138 Processing helix chain 'e' and resid 57 through 75 Processing helix chain 'e' and resid 82 through 96 Processing helix chain 'e' and resid 98 through 122 removed outlier: 3.506A pdb=" N ALA e 109 " --> pdb=" O GLN e 105 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN e 115 " --> pdb=" O GLU e 111 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA e 116 " --> pdb=" O ASP e 112 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU e 119 " --> pdb=" O GLN e 115 " (cutoff:3.500A) Proline residue: e 120 - end of helix Processing helix chain 'e' and resid 127 through 153 removed outlier: 3.585A pdb=" N LYS e 133 " --> pdb=" O VAL e 129 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS e 142 " --> pdb=" O CYS e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 153 through 159 Processing helix chain 'e' and resid 159 through 164 removed outlier: 3.947A pdb=" N GLN e 163 " --> pdb=" O THR e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 169 through 182 Processing helix chain 'e' and resid 185 through 205 Processing helix chain 'e' and resid 210 through 224 Processing helix chain 'e' and resid 226 through 252 removed outlier: 3.580A pdb=" N GLU e 232 " --> pdb=" O LYS e 228 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU e 233 " --> pdb=" O ASP e 229 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS e 234 " --> pdb=" O SER e 230 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN e 252 " --> pdb=" O GLN e 248 " (cutoff:3.500A) Processing helix chain 'e' and resid 255 through 277 removed outlier: 3.648A pdb=" N ASN e 261 " --> pdb=" O PRO e 257 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE e 275 " --> pdb=" O GLY e 271 " (cutoff:3.500A) Processing helix chain 'e' and resid 279 through 281 No H-bonds generated for 'chain 'e' and resid 279 through 281' Processing helix chain 'e' and resid 282 through 295 Processing helix chain 'e' and resid 298 through 314 removed outlier: 4.670A pdb=" N ASP e 308 " --> pdb=" O GLN e 304 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS e 309 " --> pdb=" O LYS e 305 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP e 312 " --> pdb=" O ASP e 308 " (cutoff:3.500A) Processing helix chain 'e' and resid 315 through 327 Processing helix chain 'e' and resid 331 through 353 removed outlier: 3.599A pdb=" N HIS e 339 " --> pdb=" O ALA e 335 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR e 349 " --> pdb=" O LYS e 345 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA e 350 " --> pdb=" O THR e 346 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE e 351 " --> pdb=" O PHE e 347 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL e 352 " --> pdb=" O GLY e 348 " (cutoff:3.500A) Processing helix chain 'e' and resid 354 through 358 Processing helix chain 'e' and resid 361 through 379 Processing helix chain 'e' and resid 383 through 399 removed outlier: 3.883A pdb=" N ASN e 399 " --> pdb=" O GLU e 395 " (cutoff:3.500A) Processing helix chain 'e' and resid 403 through 418 removed outlier: 3.629A pdb=" N GLU e 407 " --> pdb=" O ASN e 403 " (cutoff:3.500A) Processing helix chain 'e' and resid 425 through 441 removed outlier: 3.605A pdb=" N ARG e 431 " --> pdb=" O GLU e 427 " (cutoff:3.500A) Processing helix chain 'e' and resid 445 through 463 removed outlier: 3.537A pdb=" N PHE e 449 " --> pdb=" O GLY e 445 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA e 451 " --> pdb=" O ASP e 447 " (cutoff:3.500A) Processing helix chain 'e' and resid 468 through 488 removed outlier: 7.631A pdb=" N ALA e 485 " --> pdb=" O HIS e 481 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N ALA e 486 " --> pdb=" O GLU e 482 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE e 487 " --> pdb=" O CYS e 483 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR e 488 " --> pdb=" O GLY e 484 " (cutoff:3.500A) Processing helix chain 'e' and resid 488 through 515 removed outlier: 3.577A pdb=" N MET e 494 " --> pdb=" O LYS e 490 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE e 495 " --> pdb=" O LEU e 491 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP e 503 " --> pdb=" O GLU e 499 " (cutoff:3.500A) Processing helix chain 'e' and resid 544 through 562 removed outlier: 3.675A pdb=" N LYS e 549 " --> pdb=" O PRO e 545 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU e 550 " --> pdb=" O GLU e 546 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN e 551 " --> pdb=" O MET e 547 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU e 552 " --> pdb=" O ILE e 548 " (cutoff:3.500A) Processing helix chain 'e' and resid 593 through 600 Processing helix chain 'e' and resid 610 through 618 removed outlier: 3.793A pdb=" N ALA e 616 " --> pdb=" O GLU e 612 " (cutoff:3.500A) Processing helix chain 'e' and resid 620 through 633 Processing helix chain 'e' and resid 693 through 708 Processing helix chain 'e' and resid 712 through 723 removed outlier: 3.581A pdb=" N LEU e 719 " --> pdb=" O LEU e 715 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR e 720 " --> pdb=" O VAL e 716 " (cutoff:3.500A) Processing helix chain 'e' and resid 728 through 742 Processing sheet with id=AA1, first strand: chain 'D' and resid 21 through 25 Processing sheet with id=AA2, first strand: chain 'N' and resid 12 through 16 removed outlier: 7.824A pdb=" N LEU N 67 " --> pdb=" O LEU N 2 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU N 69 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N LEU N 71 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL N 70 " --> pdb=" O ARG N 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 522 through 529 removed outlier: 3.814A pdb=" N VAL e 577 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL R 30 " --> pdb=" O LEU e 573 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU e 573 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N LEU R 32 " --> pdb=" O THR e 571 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N THR e 571 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N ALA R 34 " --> pdb=" O TRP e 569 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N TRP e 569 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY e 585 " --> pdb=" O PHE e 582 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE e 582 " --> pdb=" O GLY e 585 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 522 through 529 removed outlier: 3.814A pdb=" N VAL e 577 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL R 30 " --> pdb=" O LEU e 573 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU e 573 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N LEU R 32 " --> pdb=" O THR e 571 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N THR e 571 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N ALA R 34 " --> pdb=" O TRP e 569 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N TRP e 569 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ILE e 667 " --> pdb=" O LYS e 586 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLU e 588 " --> pdb=" O ILE e 667 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 70 through 72 Processing sheet with id=AA6, first strand: chain 'U' and resid 13 through 16 Processing sheet with id=AA7, first strand: chain 'a' and resid 30 through 32 removed outlier: 3.501A pdb=" N LEU a 359 " --> pdb=" O SER a 351 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 37 through 38 removed outlier: 7.387A pdb=" N ASP a 37 " --> pdb=" O CYS a 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'a' and resid 46 through 51 removed outlier: 6.405A pdb=" N GLY a 62 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU a 49 " --> pdb=" O LEU a 60 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU a 60 " --> pdb=" O LEU a 49 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE a 51 " --> pdb=" O TYR a 58 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYR a 58 " --> pdb=" O ILE a 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET a 59 " --> pdb=" O TYR a 71 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE a 68 " --> pdb=" O ILE a 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS a 88 " --> pdb=" O LEU a 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 102 through 107 removed outlier: 3.762A pdb=" N THR a 104 " --> pdb=" O SER a 118 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU a 124 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL a 137 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL a 126 " --> pdb=" O ALA a 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 144 through 149 removed outlier: 3.707A pdb=" N SER a 146 " --> pdb=" O GLY a 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 191 through 194 removed outlier: 3.545A pdb=" N ILE a 224 " --> pdb=" O LEU a 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 248 through 253 removed outlier: 3.985A pdb=" N ARG a 268 " --> pdb=" O GLY a 264 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 298 through 299 removed outlier: 3.560A pdb=" N THR a 298 " --> pdb=" O PHE a 309 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE a 316 " --> pdb=" O MET a 329 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N MET a 329 " --> pdb=" O ILE a 316 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL a 318 " --> pdb=" O ILE a 327 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'd' and resid 1007 through 1009 removed outlier: 3.510A pdb=" N PHE d1030 " --> pdb=" O GLY d1038 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE d1037 " --> pdb=" O ALA d 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 15 through 21 removed outlier: 3.891A pdb=" N GLY d 17 " --> pdb=" O ALA d 34 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 38 through 41 removed outlier: 4.032A pdb=" N LYS d 53 " --> pdb=" O ILE d 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 61 through 67 removed outlier: 6.620A pdb=" N LEU d 80 " --> pdb=" O ALA d 62 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET d 64 " --> pdb=" O PHE d 78 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE d 78 " --> pdb=" O MET d 64 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU d 66 " --> pdb=" O LEU d 76 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU d 76 " --> pdb=" O LEU d 66 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN d 85 " --> pdb=" O THR d 81 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA d 104 " --> pdb=" O ILE d 88 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU d 90 " --> pdb=" O THR d 102 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR d 102 " --> pdb=" O GLU d 90 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS d 92 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE d 100 " --> pdb=" O LYS d 92 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER d 94 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE d 98 " --> pdb=" O SER d 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 121 through 124 removed outlier: 3.740A pdb=" N ILE d 121 " --> pdb=" O ARG d 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'd' and resid 164 through 169 removed outlier: 6.580A pdb=" N VAL d 181 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL d 167 " --> pdb=" O CYS d 179 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS d 179 " --> pdb=" O VAL d 167 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE d 169 " --> pdb=" O THR d 177 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR d 177 " --> pdb=" O PHE d 169 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 220 through 221 removed outlier: 3.572A pdb=" N ILE d 248 " --> pdb=" O ILE d 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 258 through 263 removed outlier: 3.580A pdb=" N LEU d 273 " --> pdb=" O PHE d 281 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG d 279 " --> pdb=" O ASP d 275 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU d 280 " --> pdb=" O LEU d 304 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU d 304 " --> pdb=" O LEU d 280 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N MET d 282 " --> pdb=" O VAL d 302 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL d 302 " --> pdb=" O MET d 282 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU d 284 " --> pdb=" O LEU d 300 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU d 300 " --> pdb=" O LEU d 284 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU d 286 " --> pdb=" O LYS d 298 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'd' and resid 313 through 318 removed outlier: 4.927A pdb=" N LEU d 314 " --> pdb=" O GLY d 325 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY d 325 " --> pdb=" O LEU d 314 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR d 316 " --> pdb=" O PHE d 323 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE d 323 " --> pdb=" O TYR d 316 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP d 318 " --> pdb=" O VAL d 321 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER d 331 " --> pdb=" O THR d 352 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N THR d 352 " --> pdb=" O SER d 331 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU d 333 " --> pdb=" O MET d 350 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'd' and resid 362 through 365 Processing sheet with id=AC7, first strand: chain 'd' and resid 386 through 387 Processing sheet with id=AC8, first strand: chain 'd' and resid 390 through 391 Processing sheet with id=AC9, first strand: chain 'd' and resid 396 through 403 removed outlier: 5.707A pdb=" N GLU d 398 " --> pdb=" O THR d 703 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR d 703 " --> pdb=" O GLU d 398 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 407 through 413 removed outlier: 4.443A pdb=" N VAL d 435 " --> pdb=" O THR d 446 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 470 through 471 removed outlier: 3.506A pdb=" N SER d 488 " --> pdb=" O LEU d 478 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N SER d 480 " --> pdb=" O LEU d 486 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU d 486 " --> pdb=" O SER d 480 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 500 through 503 removed outlier: 6.614A pdb=" N LEU d 516 " --> pdb=" O HIS d 531 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N HIS d 531 " --> pdb=" O LEU d 516 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N TYR d 518 " --> pdb=" O ILE d 529 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 538 through 542 removed outlier: 6.520A pdb=" N GLY d 559 " --> pdb=" O ALA d 539 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU d 541 " --> pdb=" O ALA d 557 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA d 557 " --> pdb=" O LEU d 541 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER d 565 " --> pdb=" O LEU d 560 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS d 578 " --> pdb=" O ILE d 568 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS d 570 " --> pdb=" O LEU d 576 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU d 576 " --> pdb=" O LYS d 570 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 588 through 596 removed outlier: 3.521A pdb=" N SER d 590 " --> pdb=" O ALA d 605 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE d 614 " --> pdb=" O LEU d 602 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA d 610 " --> pdb=" O LEU d 606 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU d 611 " --> pdb=" O LYS d 628 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS d 628 " --> pdb=" O LEU d 611 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR d 613 " --> pdb=" O ARG d 626 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG d 626 " --> pdb=" O TYR d 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 637 through 642 removed outlier: 8.466A pdb=" N THR d 647 " --> pdb=" O SER d 661 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER d 661 " --> pdb=" O THR d 647 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 681 through 682 Processing sheet with id=AD8, first strand: chain 'd' and resid 720 through 727 removed outlier: 6.176A pdb=" N SER d 738 " --> pdb=" O PRO d 721 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS d 723 " --> pdb=" O LEU d 736 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS d 732 " --> pdb=" O GLN d 727 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER d 737 " --> pdb=" O ASN d 790 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG d 739 " --> pdb=" O VAL d 788 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N HIS d 789 " --> pdb=" O GLN d 806 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN d 806 " --> pdb=" O HIS d 789 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU d 791 " --> pdb=" O ALA d 804 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA d 804 " --> pdb=" O LEU d 791 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE d 793 " --> pdb=" O LEU d 802 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER d 762 " --> pdb=" O ALA d 804 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLN d 806 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER d 764 " --> pdb=" O GLN d 806 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 811 through 819 removed outlier: 5.468A pdb=" N ALA d 813 " --> pdb=" O ALA d 834 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA d 834 " --> pdb=" O ALA d 813 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG d 847 " --> pdb=" O THR d 833 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL d 850 " --> pdb=" O VAL d 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 811 through 819 removed outlier: 5.468A pdb=" N ALA d 813 " --> pdb=" O ALA d 834 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA d 834 " --> pdb=" O ALA d 813 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG d 847 " --> pdb=" O THR d 833 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY d 846 " --> pdb=" O VAL d 866 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'd' and resid 874 through 876 Processing sheet with id=AE3, first strand: chain 'd' and resid 890 through 893 removed outlier: 6.792A pdb=" N LEU d 890 " --> pdb=" O GLU d 902 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 911 through 917 removed outlier: 3.731A pdb=" N ASN d 941 " --> pdb=" O LYS d 936 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'd' and resid 954 through 961 removed outlier: 6.489A pdb=" N ASN d 964 " --> pdb=" O LEU d 960 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU d 974 " --> pdb=" O LEU d 997 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU d 997 " --> pdb=" O LEU d 974 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL d 976 " --> pdb=" O VAL d 995 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'd' and resid 1076 through 1078 Processing sheet with id=AE7, first strand: chain 'e' and resid 607 through 609 removed outlier: 3.502A pdb=" N PHE e 654 " --> pdb=" O PHE e 608 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'e' and resid 709 through 711 815 hydrogen bonds defined for protein. 2274 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.11 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20135 1.03 - 1.23: 81 1.23 - 1.42: 8461 1.42 - 1.62: 11903 1.62 - 1.82: 180 Bond restraints: 40760 Sorted by residual: bond pdb=" CB PRO e 520 " pdb=" CG PRO e 520 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.33e+00 bond pdb=" C GLU d 40 " pdb=" N ILE d 41 " ideal model delta sigma weight residual 1.334 1.313 0.021 1.29e-02 6.01e+03 2.60e+00 bond pdb=" CD2 TYR a 145 " pdb=" CE2 TYR a 145 " ideal model delta sigma weight residual 1.382 1.337 0.045 3.00e-02 1.11e+03 2.23e+00 bond pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.20e-02 2.07e+03 1.86e+00 bond pdb=" CB MET d 954 " pdb=" CG MET d 954 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.78e+00 ... (remaining 40755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 72456 1.71 - 3.41: 1150 3.41 - 5.12: 123 5.12 - 6.83: 9 6.83 - 8.53: 4 Bond angle restraints: 73742 Sorted by residual: angle pdb=" CA PRO e 520 " pdb=" N PRO e 520 " pdb=" CD PRO e 520 " ideal model delta sigma weight residual 112.00 103.95 8.05 1.40e+00 5.10e-01 3.30e+01 angle pdb=" N SER d 929 " pdb=" CA SER d 929 " pdb=" C SER d 929 " ideal model delta sigma weight residual 110.80 119.33 -8.53 2.13e+00 2.20e-01 1.60e+01 angle pdb=" N ILE d 884 " pdb=" CA ILE d 884 " pdb=" C ILE d 884 " ideal model delta sigma weight residual 110.05 106.19 3.86 1.09e+00 8.42e-01 1.25e+01 angle pdb=" N ARG R 91 " pdb=" CA ARG R 91 " pdb=" C ARG R 91 " ideal model delta sigma weight residual 107.93 112.89 -4.96 1.65e+00 3.67e-01 9.05e+00 angle pdb=" N VAL a 237 " pdb=" CA VAL a 237 " pdb=" C VAL a 237 " ideal model delta sigma weight residual 106.21 109.40 -3.19 1.07e+00 8.73e-01 8.87e+00 ... (remaining 73737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 17018 17.59 - 35.18: 1591 35.18 - 52.77: 329 52.77 - 70.36: 88 70.36 - 87.94: 18 Dihedral angle restraints: 19044 sinusoidal: 10467 harmonic: 8577 Sorted by residual: dihedral pdb=" CA ILE d 884 " pdb=" C ILE d 884 " pdb=" N ASN d 885 " pdb=" CA ASN d 885 " ideal model delta harmonic sigma weight residual -180.00 -151.06 -28.94 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ASN e 57 " pdb=" C ASN e 57 " pdb=" N TYR e 58 " pdb=" CA TYR e 58 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ARG e 51 " pdb=" C ARG e 51 " pdb=" N PRO e 52 " pdb=" CA PRO e 52 " ideal model delta harmonic sigma weight residual 180.00 -155.41 -24.59 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 19041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1993 0.034 - 0.068: 778 0.068 - 0.102: 227 0.102 - 0.136: 128 0.136 - 0.170: 8 Chirality restraints: 3134 Sorted by residual: chirality pdb=" CB VAL d 930 " pdb=" CA VAL d 930 " pdb=" CG1 VAL d 930 " pdb=" CG2 VAL d 930 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CA SER d 929 " pdb=" N SER d 929 " pdb=" C SER d 929 " pdb=" CB SER d 929 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CG LEU d1129 " pdb=" CB LEU d1129 " pdb=" CD1 LEU d1129 " pdb=" CD2 LEU d1129 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 3131 not shown) Planarity restraints: 6003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY e 519 " 0.090 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO e 520 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO e 520 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO e 520 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 272 " -0.012 2.00e-02 2.50e+03 1.46e-02 8.55e+00 pdb=" CG TRP a 272 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP a 272 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP a 272 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP a 272 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP a 272 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP a 272 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 272 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 272 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP a 272 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP a 272 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TRP a 272 " 0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP a 272 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP a 272 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP a 272 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP a 272 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER d 929 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C SER d 929 " 0.040 2.00e-02 2.50e+03 pdb=" O SER d 929 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL d 930 " -0.014 2.00e-02 2.50e+03 ... (remaining 6000 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.94: 229 1.94 - 2.60: 47794 2.60 - 3.27: 123451 3.27 - 3.93: 158732 3.93 - 4.60: 251484 Nonbonded interactions: 581690 Sorted by model distance: nonbonded pdb=" SG CYS R 75 " pdb=" OD2 ASP R 97 " model vdw 1.270 3.200 nonbonded pdb="HG23 ILE D 37 " pdb=" SG CYS D 107 " model vdw 1.535 3.020 nonbonded pdb=" OE2 GLU d 537 " pdb=" H GLU e 84 " model vdw 1.611 2.450 nonbonded pdb=" H ASP R 36 " pdb=" O GLY e 564 " model vdw 1.622 2.450 nonbonded pdb=" H ALA d 869 " pdb=" OD1 ASN d 885 " model vdw 1.625 2.450 ... (remaining 581685 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.220 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 40.810 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.006 0.251 20591 Z= 0.244 Angle : 0.693 30.444 27812 Z= 0.350 Chirality : 0.044 0.170 3134 Planarity : 0.004 0.132 3570 Dihedral : 13.764 87.945 7706 Min Nonbonded Distance : 1.270 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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 aren not related in a simple way. whole: -2.21 (0.16), residues: 2507 helix: 0.09 (0.21), residues: 646 sheet: -2.42 (0.19), residues: 665 loop : -1.68 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 702 TYR 0.018 0.001 TYR a 145 PHE 0.032 0.002 PHE e 48 TRP 0.046 0.002 TRP a 272 HIS 0.009 0.001 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00502 (20580) covalent geometry : angle 0.63583 (27806) hydrogen bonds : bond 0.24942 ( 792) hydrogen bonds : angle 9.65000 ( 2274) metal coordination : bond 0.12290 ( 11) metal coordination : angle 18.75287 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2711 time to fit residues: 75.7605 Evaluate side-chains 128 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 0.0370 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN ** d 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 GLN e 145 GLN e 164 ASN e 338 GLN e 399 ASN e 722 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.097686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.076854 restraints weight = 134364.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.080928 restraints weight = 53831.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.083451 restraints weight = 30612.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.085033 restraints weight = 20997.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.086023 restraints weight = 16090.961| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20591 Z= 0.193 Angle : 0.602 15.343 27812 Z= 0.324 Chirality : 0.044 0.163 3134 Planarity : 0.004 0.072 3570 Dihedral : 5.271 73.754 2731 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.40 % Allowed : 3.87 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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 aren not related in a simple way. whole: -2.01 (0.16), residues: 2507 helix: 0.50 (0.20), residues: 669 sheet: -2.41 (0.19), residues: 663 loop : -1.70 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 91 TYR 0.018 0.001 TYR a 312 PHE 0.019 0.001 PHE e 397 TRP 0.016 0.001 TRP e 63 HIS 0.005 0.001 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00416 (20580) covalent geometry : angle 0.59109 (27806) hydrogen bonds : bond 0.06165 ( 792) hydrogen bonds : angle 6.67940 ( 2274) metal coordination : bond 0.02084 ( 11) metal coordination : angle 7.96070 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 TYR cc_start: 0.8662 (t80) cc_final: 0.8400 (t80) REVERT: e 623 GLU cc_start: 0.8048 (mp0) cc_final: 0.7536 (mp0) outliers start: 9 outliers final: 8 residues processed: 138 average time/residue: 0.2567 time to fit residues: 58.5155 Evaluate side-chains 128 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain R residue 103 PHE Chi-restraints excluded: chain a residue 37 ASP Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 581 MET Chi-restraints excluded: chain d residue 698 THR Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 256 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 79 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 116 optimal weight: 0.0370 chunk 157 optimal weight: 0.5980 chunk 196 optimal weight: 0.9980 chunk 208 optimal weight: 0.7980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 481 GLN d 522 HIS ** d 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 309 HIS ** e 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.100656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.079181 restraints weight = 135966.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.083334 restraints weight = 55091.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.085892 restraints weight = 31487.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.087509 restraints weight = 21647.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.088533 restraints weight = 16656.723| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20591 Z= 0.117 Angle : 0.527 14.272 27812 Z= 0.278 Chirality : 0.042 0.155 3134 Planarity : 0.003 0.055 3570 Dihedral : 4.978 73.729 2731 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.58 % Allowed : 4.93 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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 aren not related in a simple way. whole: -1.75 (0.16), residues: 2507 helix: 0.84 (0.20), residues: 668 sheet: -2.19 (0.19), residues: 662 loop : -1.66 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 42 TYR 0.016 0.001 TYR a 312 PHE 0.017 0.001 PHE e 397 TRP 0.019 0.001 TRP e 63 HIS 0.007 0.001 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00254 (20580) covalent geometry : angle 0.51727 (27806) hydrogen bonds : bond 0.04702 ( 792) hydrogen bonds : angle 5.92038 ( 2274) metal coordination : bond 0.01398 ( 11) metal coordination : angle 7.00589 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 60 TYR cc_start: 0.8593 (t80) cc_final: 0.8375 (t80) REVERT: U 41 GLN cc_start: 0.8472 (mp10) cc_final: 0.8089 (mp10) outliers start: 13 outliers final: 11 residues processed: 149 average time/residue: 0.2816 time to fit residues: 68.4936 Evaluate side-chains 139 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain R residue 103 PHE Chi-restraints excluded: chain a residue 37 ASP Chi-restraints excluded: chain d residue 367 LEU Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 581 MET Chi-restraints excluded: chain d residue 587 ILE Chi-restraints excluded: chain d residue 698 THR Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 630 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 23 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 76 optimal weight: 0.0010 chunk 160 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 522 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.098462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.077904 restraints weight = 134958.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.081869 restraints weight = 53968.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084319 restraints weight = 30698.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.085833 restraints weight = 21017.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.086827 restraints weight = 16217.350| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20591 Z= 0.162 Angle : 0.527 13.829 27812 Z= 0.277 Chirality : 0.042 0.154 3134 Planarity : 0.003 0.061 3570 Dihedral : 4.898 72.923 2731 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.62 % Allowed : 6.36 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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 aren not related in a simple way. whole: -1.67 (0.16), residues: 2507 helix: 1.06 (0.20), residues: 669 sheet: -2.17 (0.19), residues: 678 loop : -1.68 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 91 TYR 0.013 0.001 TYR a 312 PHE 0.013 0.001 PHE e 397 TRP 0.019 0.001 TRP e 63 HIS 0.004 0.001 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00357 (20580) covalent geometry : angle 0.51871 (27806) hydrogen bonds : bond 0.04192 ( 792) hydrogen bonds : angle 5.64280 ( 2274) metal coordination : bond 0.01238 ( 11) metal coordination : angle 6.47705 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 41 GLN cc_start: 0.8483 (mp10) cc_final: 0.8224 (mp10) REVERT: a 114 MET cc_start: 0.7689 (mpp) cc_final: 0.7254 (mpp) outliers start: 14 outliers final: 10 residues processed: 138 average time/residue: 0.2737 time to fit residues: 61.9597 Evaluate side-chains 134 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain R residue 103 PHE Chi-restraints excluded: chain a residue 37 ASP Chi-restraints excluded: chain a residue 269 MET Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 581 MET Chi-restraints excluded: chain d residue 587 ILE Chi-restraints excluded: chain d residue 698 THR Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 630 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 65 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 467 GLN ** d 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.095318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.074519 restraints weight = 134492.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.078522 restraints weight = 54472.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.080978 restraints weight = 31180.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.082525 restraints weight = 21478.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.083543 restraints weight = 16529.885| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 20591 Z= 0.315 Angle : 0.607 14.210 27812 Z= 0.323 Chirality : 0.044 0.152 3134 Planarity : 0.004 0.055 3570 Dihedral : 5.104 68.015 2731 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.71 % Allowed : 7.78 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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 aren not related in a simple way. whole: -1.93 (0.16), residues: 2507 helix: 1.00 (0.20), residues: 669 sheet: -2.39 (0.19), residues: 691 loop : -1.90 (0.17), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 589 TYR 0.018 0.002 TYR a 312 PHE 0.016 0.002 PHE d1030 TRP 0.019 0.002 TRP e 63 HIS 0.006 0.001 HIS a 259 Details of bonding type rmsd covalent geometry : bond 0.00701 (20580) covalent geometry : angle 0.59967 (27806) hydrogen bonds : bond 0.04351 ( 792) hydrogen bonds : angle 5.68530 ( 2274) metal coordination : bond 0.01527 ( 11) metal coordination : angle 6.58917 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 551 GLN cc_start: 0.7480 (mp10) cc_final: 0.7202 (mp10) REVERT: e 623 GLU cc_start: 0.7988 (mp0) cc_final: 0.7434 (mp0) outliers start: 16 outliers final: 13 residues processed: 138 average time/residue: 0.2697 time to fit residues: 61.2353 Evaluate side-chains 136 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain R residue 103 PHE Chi-restraints excluded: chain a residue 37 ASP Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain d residue 362 MET Chi-restraints excluded: chain d residue 367 LEU Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 581 MET Chi-restraints excluded: chain d residue 587 ILE Chi-restraints excluded: chain d residue 698 THR Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 630 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 130 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 189 HIS ** d 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 522 HIS ** d 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.097998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077302 restraints weight = 135151.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.081286 restraints weight = 53964.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.083749 restraints weight = 30639.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.085271 restraints weight = 20985.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.086240 restraints weight = 16148.438| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20591 Z= 0.136 Angle : 0.523 13.145 27812 Z= 0.274 Chirality : 0.042 0.154 3134 Planarity : 0.003 0.052 3570 Dihedral : 4.894 69.235 2731 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.71 % Allowed : 8.44 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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 aren not related in a simple way. whole: -1.73 (0.16), residues: 2507 helix: 1.18 (0.20), residues: 672 sheet: -2.23 (0.19), residues: 699 loop : -1.80 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 42 TYR 0.012 0.001 TYR a 312 PHE 0.015 0.001 PHE e 397 TRP 0.019 0.001 TRP e 63 HIS 0.006 0.001 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00303 (20580) covalent geometry : angle 0.51485 (27806) hydrogen bonds : bond 0.03841 ( 792) hydrogen bonds : angle 5.40609 ( 2274) metal coordination : bond 0.01399 ( 11) metal coordination : angle 6.25684 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 551 GLN cc_start: 0.7495 (mp10) cc_final: 0.7238 (mp10) REVERT: e 623 GLU cc_start: 0.8001 (mp0) cc_final: 0.7419 (mp0) outliers start: 16 outliers final: 13 residues processed: 141 average time/residue: 0.2716 time to fit residues: 63.1576 Evaluate side-chains 138 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain R residue 103 PHE Chi-restraints excluded: chain a residue 37 ASP Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain d residue 362 MET Chi-restraints excluded: chain d residue 367 LEU Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 581 MET Chi-restraints excluded: chain d residue 587 ILE Chi-restraints excluded: chain d residue 698 THR Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 630 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 116 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 0.0270 chunk 234 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 334 GLN e 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.098086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.077618 restraints weight = 134554.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081595 restraints weight = 53570.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.084048 restraints weight = 30320.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.085572 restraints weight = 20710.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.086557 restraints weight = 15903.340| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20591 Z= 0.143 Angle : 0.508 12.079 27812 Z= 0.267 Chirality : 0.042 0.154 3134 Planarity : 0.003 0.050 3570 Dihedral : 4.779 68.301 2731 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.67 % Allowed : 8.71 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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 aren not related in a simple way. whole: -1.62 (0.17), residues: 2507 helix: 1.28 (0.20), residues: 673 sheet: -2.16 (0.19), residues: 698 loop : -1.75 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 21 TYR 0.011 0.001 TYR a 312 PHE 0.014 0.001 PHE e 397 TRP 0.018 0.001 TRP e 63 HIS 0.005 0.001 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00317 (20580) covalent geometry : angle 0.50122 (27806) hydrogen bonds : bond 0.03645 ( 792) hydrogen bonds : angle 5.27875 ( 2274) metal coordination : bond 0.01173 ( 11) metal coordination : angle 5.73990 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 54 LEU cc_start: 0.6032 (OUTLIER) cc_final: 0.5774 (mt) REVERT: e 551 GLN cc_start: 0.7414 (mp10) cc_final: 0.7197 (mp10) REVERT: e 623 GLU cc_start: 0.7918 (mp0) cc_final: 0.7134 (mp0) outliers start: 15 outliers final: 12 residues processed: 137 average time/residue: 0.2576 time to fit residues: 58.5458 Evaluate side-chains 136 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain R residue 103 PHE Chi-restraints excluded: chain a residue 37 ASP Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain d residue 367 LEU Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 581 MET Chi-restraints excluded: chain d residue 587 ILE Chi-restraints excluded: chain d residue 698 THR Chi-restraints excluded: chain e residue 54 LEU Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 630 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 72 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 0.0670 chunk 84 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 334 GLN e 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.098458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078247 restraints weight = 134448.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.082188 restraints weight = 53280.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.084627 restraints weight = 30060.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.086121 restraints weight = 20475.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.087115 restraints weight = 15724.608| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20591 Z= 0.134 Angle : 0.505 11.401 27812 Z= 0.264 Chirality : 0.042 0.154 3134 Planarity : 0.003 0.048 3570 Dihedral : 4.717 67.328 2731 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.58 % Allowed : 8.84 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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 aren not related in a simple way. whole: -1.56 (0.17), residues: 2507 helix: 1.34 (0.20), residues: 672 sheet: -2.13 (0.19), residues: 698 loop : -1.73 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 42 TYR 0.011 0.001 TYR a 312 PHE 0.014 0.001 PHE e 397 TRP 0.018 0.001 TRP e 63 HIS 0.004 0.001 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00298 (20580) covalent geometry : angle 0.49859 (27806) hydrogen bonds : bond 0.03567 ( 792) hydrogen bonds : angle 5.20013 ( 2274) metal coordination : bond 0.01101 ( 11) metal coordination : angle 5.46019 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 54 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5759 (mt) REVERT: e 547 MET cc_start: 0.7108 (tpp) cc_final: 0.6803 (tpp) REVERT: e 623 GLU cc_start: 0.7919 (mp0) cc_final: 0.7150 (mp0) outliers start: 13 outliers final: 10 residues processed: 138 average time/residue: 0.2600 time to fit residues: 59.3491 Evaluate side-chains 136 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain d residue 367 LEU Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 581 MET Chi-restraints excluded: chain d residue 587 ILE Chi-restraints excluded: chain d residue 698 THR Chi-restraints excluded: chain e residue 54 LEU Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 630 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 0.0980 chunk 209 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 211 optimal weight: 0.0370 chunk 116 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.098072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.077435 restraints weight = 134023.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.081573 restraints weight = 53243.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.084122 restraints weight = 30047.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.085653 restraints weight = 20394.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.086667 restraints weight = 15668.424| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20591 Z= 0.123 Angle : 0.499 10.720 27812 Z= 0.261 Chirality : 0.042 0.154 3134 Planarity : 0.003 0.048 3570 Dihedral : 4.650 66.217 2731 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.58 % Allowed : 8.98 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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 aren not related in a simple way. whole: -1.49 (0.17), residues: 2507 helix: 1.42 (0.20), residues: 672 sheet: -2.09 (0.19), residues: 692 loop : -1.69 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 42 TYR 0.010 0.001 TYR a 312 PHE 0.014 0.001 PHE e 397 TRP 0.018 0.001 TRP e 63 HIS 0.004 0.001 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00275 (20580) covalent geometry : angle 0.49346 (27806) hydrogen bonds : bond 0.03476 ( 792) hydrogen bonds : angle 5.11145 ( 2274) metal coordination : bond 0.01004 ( 11) metal coordination : angle 5.15813 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 114 MET cc_start: 0.7631 (mpp) cc_final: 0.7206 (mpp) REVERT: e 54 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5733 (mt) REVERT: e 623 GLU cc_start: 0.7882 (mp0) cc_final: 0.7109 (mp0) outliers start: 13 outliers final: 12 residues processed: 136 average time/residue: 0.2701 time to fit residues: 60.4537 Evaluate side-chains 139 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain d residue 367 LEU Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 581 MET Chi-restraints excluded: chain d residue 587 ILE Chi-restraints excluded: chain d residue 698 THR Chi-restraints excluded: chain e residue 54 LEU Chi-restraints excluded: chain e residue 146 MET Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 630 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 86 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 226 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 158 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.098928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.078602 restraints weight = 134752.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.082559 restraints weight = 53538.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.084998 restraints weight = 30238.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.086506 restraints weight = 20638.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.087489 restraints weight = 15846.694| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20591 Z= 0.131 Angle : 0.503 10.311 27812 Z= 0.262 Chirality : 0.042 0.153 3134 Planarity : 0.003 0.048 3570 Dihedral : 4.615 64.919 2731 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.49 % Allowed : 9.38 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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 aren not related in a simple way. whole: -1.43 (0.17), residues: 2507 helix: 1.47 (0.20), residues: 672 sheet: -2.07 (0.19), residues: 684 loop : -1.66 (0.17), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 42 TYR 0.010 0.001 TYR a 312 PHE 0.013 0.001 PHE e 397 TRP 0.018 0.001 TRP e 63 HIS 0.003 0.001 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00293 (20580) covalent geometry : angle 0.49815 (27806) hydrogen bonds : bond 0.03453 ( 792) hydrogen bonds : angle 5.07800 ( 2274) metal coordination : bond 0.00972 ( 11) metal coordination : angle 4.97650 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 63 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 114 MET cc_start: 0.7598 (mpp) cc_final: 0.7183 (mpp) REVERT: e 54 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5707 (mt) REVERT: e 623 GLU cc_start: 0.7858 (mp0) cc_final: 0.7209 (mp0) outliers start: 11 outliers final: 10 residues processed: 132 average time/residue: 0.2663 time to fit residues: 58.1626 Evaluate side-chains 137 residues out of total 2255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain a residue 152 VAL Chi-restraints excluded: chain d residue 367 LEU Chi-restraints excluded: chain d residue 562 THR Chi-restraints excluded: chain d residue 581 MET Chi-restraints excluded: chain d residue 587 ILE Chi-restraints excluded: chain d residue 698 THR Chi-restraints excluded: chain e residue 54 LEU Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 630 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 184 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.099838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.078735 restraints weight = 136674.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.082812 restraints weight = 54867.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.085307 restraints weight = 31250.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.086873 restraints weight = 21458.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.087916 restraints weight = 16507.605| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20591 Z= 0.148 Angle : 0.510 9.988 27812 Z= 0.265 Chirality : 0.042 0.153 3134 Planarity : 0.003 0.046 3570 Dihedral : 4.590 63.155 2731 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.53 % Allowed : 9.64 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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 aren not related in a simple way. whole: -1.42 (0.17), residues: 2507 helix: 1.49 (0.21), residues: 674 sheet: -2.07 (0.19), residues: 683 loop : -1.67 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 21 TYR 0.011 0.001 TYR a 312 PHE 0.013 0.001 PHE e 397 TRP 0.018 0.001 TRP e 63 HIS 0.003 0.001 HIS e 181 Details of bonding type rmsd covalent geometry : bond 0.00332 (20580) covalent geometry : angle 0.50476 (27806) hydrogen bonds : bond 0.03420 ( 792) hydrogen bonds : angle 5.04627 ( 2274) metal coordination : bond 0.00962 ( 11) metal coordination : angle 4.85402 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5370.06 seconds wall clock time: 92 minutes 32.86 seconds (5552.86 seconds total)