Starting phenix.real_space_refine on Tue Aug 26 23:19:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b3g_15827/08_2025/8b3g_15827.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b3g_15827/08_2025/8b3g_15827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b3g_15827/08_2025/8b3g_15827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b3g_15827/08_2025/8b3g_15827.map" model { file = "/net/cci-nas-00/data/ceres_data/8b3g_15827/08_2025/8b3g_15827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b3g_15827/08_2025/8b3g_15827.cif" } resolution = 4.4 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= -0.001 sd= 0.086 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 122 5.16 5 C 13572 2.51 5 N 3697 2.21 5 O 4018 1.98 5 H 21416 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s 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: 42828 Number of models: 1 Model: "" Number of chains: 9 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: "c" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 2451 Classifications: {'peptide': 148} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 140} 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 71.630 64.426 44.129 1.00520.46 S ATOM 3974 SG CYS R 45 73.593 65.299 46.143 1.00574.49 S ATOM 4437 SG CYS R 83 74.428 61.747 45.892 1.00585.86 S ATOM 4312 SG CYS R 75 62.376 58.278 35.047 1.00501.27 S ATOM 4637 SG CYS R 94 63.873 58.560 39.155 1.00542.22 S ATOM 4106 SG CYS R 53 77.711 62.359 46.631 1.00616.98 S ATOM 4150 SG CYS R 56 81.627 62.009 45.539 1.00599.97 S ATOM 4215 SG CYS R 68 79.879 63.166 43.102 1.00575.23 S Time building chain proxies: 6.34, per 1000 atoms: 0.15 Number of scatterers: 42828 At special positions: 0 Unit cell: (110.7, 150.06, 186.96, 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 122 16.00 O 4018 8.00 N 3697 7.00 C 13572 6.00 H 21416 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5046 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 44 sheets defined 31.8% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 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: 3.840A 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: 3.600A 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: 4.049A 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 'c' and resid 2 through 15 removed outlier: 3.503A pdb=" N SER c 15 " --> pdb=" O GLU c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 35 removed outlier: 4.245A pdb=" N SER c 35 " --> pdb=" O ILE c 31 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 52 removed outlier: 3.736A pdb=" N GLN c 52 " --> pdb=" O ALA c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 72 Processing helix chain 'c' and resid 73 through 81 Processing helix chain 'c' and resid 82 through 91 Processing helix chain 'c' and resid 102 through 125 Processing helix chain 'c' and resid 128 through 141 Processing helix chain 'd' and resid 251 through 255 Processing helix chain 'd' and resid 366 through 370 removed outlier: 4.122A 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: 3.987A 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: 4.103A 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: 3.801A 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: 3.512A 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: 3.600A 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: 7.632A 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: 3.526A 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: 3.893A 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: 3.581A 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: 3.910A 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: 7.825A 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: 7.400A 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: 3.813A pdb=" N VAL e 577 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL R 30 " --> pdb=" O LEU e 573 " (cutoff:3.500A) removed outlier: 6.915A 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: 10.645A 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: 3.813A pdb=" N VAL e 577 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL R 30 " --> pdb=" O LEU e 573 " (cutoff:3.500A) removed outlier: 6.915A 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: 10.645A 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: 5.881A 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: 4.875A 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: 6.420A pdb=" N LEU a 124 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 4.315A 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: 3.890A 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: 4.033A 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: 6.777A 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: 3.794A pdb=" N ALA d 104 " --> pdb=" O ILE d 88 " (cutoff:3.500A) removed outlier: 6.418A 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: 6.962A 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: 6.501A pdb=" N CYS d 179 " --> pdb=" O VAL d 167 " (cutoff:3.500A) removed outlier: 4.410A 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: 3.579A 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: 5.093A 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: 6.667A 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: 3.909A 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: 5.053A pdb=" N THR d 352 " --> pdb=" O SER d 331 " (cutoff:3.500A) removed outlier: 6.794A 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 393 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: 7.220A 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: 4.444A 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: 3.507A 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: 5.076A 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: 6.519A 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: 6.842A 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: 4.434A 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: 5.931A 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: 6.175A 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: 7.508A 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: 6.205A 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: 6.867A 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: 6.867A 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: 6.793A 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: 6.429A 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 711 905 hydrogen bonds defined for protein. 2544 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: 9.98 Time building geometry restraints manager: 4.88 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: 21370 1.03 - 1.23: 117 1.23 - 1.42: 8940 1.42 - 1.62: 12620 1.62 - 1.82: 187 Bond restraints: 43234 Sorted by residual: bond pdb=" ND2 ASN d 392 " pdb="HD21 ASN d 392 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN d 392 " pdb="HD22 ASN d 392 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" CA ASN d 392 " pdb=" C ASN d 392 " ideal model delta sigma weight residual 1.524 1.453 0.071 1.31e-02 5.83e+03 2.95e+01 bond pdb=" C PRO c 98 " pdb=" N LEU c 99 " ideal model delta sigma weight residual 1.331 1.423 -0.092 2.07e-02 2.33e+03 1.96e+01 bond pdb=" CA GLN d 708 " pdb=" CB GLN d 708 " ideal model delta sigma weight residual 1.529 1.456 0.073 1.66e-02 3.63e+03 1.93e+01 ... (remaining 43229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 77393 2.07 - 4.14: 736 4.14 - 6.20: 90 6.20 - 8.27: 7 8.27 - 10.34: 3 Bond angle restraints: 78229 Sorted by residual: angle pdb=" N ILE d 394 " pdb=" CA ILE d 394 " pdb=" C ILE d 394 " ideal model delta sigma weight residual 106.32 96.62 9.70 1.61e+00 3.86e-01 3.63e+01 angle pdb=" CA PRO e 520 " pdb=" N PRO e 520 " pdb=" CD PRO e 520 " ideal model delta sigma weight residual 112.00 103.97 8.03 1.40e+00 5.10e-01 3.29e+01 angle pdb=" C ILE d 396 " pdb=" CA ILE d 396 " pdb=" CB ILE d 396 " ideal model delta sigma weight residual 111.81 104.34 7.47 1.37e+00 5.33e-01 2.98e+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=" CA PRO c 100 " pdb=" N PRO c 100 " pdb=" CD PRO c 100 " ideal model delta sigma weight residual 112.00 106.45 5.55 1.40e+00 5.10e-01 1.57e+01 ... (remaining 78224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 18021 17.59 - 35.19: 1695 35.19 - 52.78: 363 52.78 - 70.38: 94 70.38 - 87.97: 20 Dihedral angle restraints: 20193 sinusoidal: 11109 harmonic: 9084 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 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+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 -154.83 -25.17 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 -155.42 -24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 20190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2835 0.059 - 0.118: 432 0.118 - 0.178: 45 0.178 - 0.237: 2 0.237 - 0.296: 1 Chirality restraints: 3315 Sorted by residual: chirality pdb=" CB ILE d 396 " pdb=" CA ILE d 396 " pdb=" CG1 ILE d 396 " pdb=" CG2 ILE d 396 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ILE d 396 " pdb=" N ILE d 396 " pdb=" C ILE d 396 " pdb=" CB ILE d 396 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA GLN d 708 " pdb=" N GLN d 708 " pdb=" C GLN d 708 " pdb=" CB GLN d 708 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.11e-01 ... (remaining 3312 not shown) Planarity restraints: 6360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN d 708 " -0.065 2.00e-02 2.50e+03 6.62e-02 6.56e+01 pdb=" CD GLN d 708 " 0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN d 708 " 0.055 2.00e-02 2.50e+03 pdb=" NE2 GLN d 708 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN d 708 " 0.096 2.00e-02 2.50e+03 pdb="HE22 GLN d 708 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG d 391 " -0.035 2.00e-02 2.50e+03 6.82e-02 4.66e+01 pdb=" C ARG d 391 " 0.118 2.00e-02 2.50e+03 pdb=" O ARG d 391 " -0.044 2.00e-02 2.50e+03 pdb=" N ASN d 392 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE d 396 " 0.028 2.00e-02 2.50e+03 5.44e-02 2.96e+01 pdb=" N HIS d 397 " -0.093 2.00e-02 2.50e+03 pdb=" CA HIS d 397 " 0.022 2.00e-02 2.50e+03 pdb=" H HIS d 397 " 0.043 2.00e-02 2.50e+03 ... (remaining 6357 not shown) Histogram of nonbonded interaction distances: 0.54 - 1.35: 20 1.35 - 2.16: 1670 2.16 - 2.98: 123528 2.98 - 3.79: 179859 3.79 - 4.60: 311414 Warning: very small nonbonded interaction distances. Nonbonded interactions: 616491 Sorted by model distance: nonbonded pdb="HG12 ILE d 394 " pdb=" OE1 GLN d 708 " model vdw 0.540 2.620 nonbonded pdb=" HE3 LYS a 335 " pdb=" HB3 ASN c 141 " model vdw 0.642 2.440 nonbonded pdb="HH22 ARG a 40 " pdb=" HD2 HIS c 136 " model vdw 0.644 1.680 nonbonded pdb="HH12 ARG a 40 " pdb=" CG HIS c 136 " model vdw 0.784 2.800 nonbonded pdb="HG23 ILE d 394 " pdb=" OD1 ASP d 705 " model vdw 0.856 2.620 ... (remaining 616486 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: 1.600 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: 0.250 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 42.160 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.008 0.864 21830 Z= 0.642 Angle : 0.721 30.471 29476 Z= 0.373 Chirality : 0.044 0.296 3315 Planarity : 0.005 0.136 3787 Dihedral : 13.895 87.973 8192 Min Nonbonded Distance : 0.968 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.13 % Allowed : 0.17 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.07 (0.16), residues: 2653 helix: 0.11 (0.19), residues: 759 sheet: -2.42 (0.19), residues: 667 loop : -1.62 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG c 44 TYR 0.018 0.002 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 0.00525 (21818) covalent geometry : angle 0.66974 (29470) hydrogen bonds : bond 0.23957 ( 882) hydrogen bonds : angle 9.41451 ( 2544) metal coordination : bond 0.12288 ( 11) metal coordination : angle 18.75687 ( 6) Misc. bond : bond 0.86362 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 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 169 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 1.193 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: 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: 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: 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: 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 147 MET cc_start: 0.6978 (mmt) cc_final: 0.6453 (mmp) REVERT: N 58 ASP cc_start: 0.9660 (m-30) cc_final: 0.9286 (m-30) REVERT: U 4 PHE cc_start: 0.9862 (m-80) cc_final: 0.9651 (m-10) REVERT: d 64 MET cc_start: 0.9168 (ttm) cc_final: 0.8805 (ptm) REVERT: d 437 MET cc_start: -0.2099 (tpp) cc_final: -0.2368 (tmm) REVERT: d 954 MET cc_start: 0.8616 (mmm) cc_final: 0.8323 (mmm) REVERT: d 962 ASP cc_start: 0.9722 (m-30) cc_final: 0.9494 (p0) REVERT: d 1099 ASP cc_start: 0.9541 (m-30) cc_final: 0.9283 (p0) REVERT: e 146 MET cc_start: 0.9370 (tpp) cc_final: 0.9024 (tpp) REVERT: e 251 MET cc_start: 0.9076 (tpp) cc_final: 0.8692 (mmm) REVERT: e 505 MET cc_start: 0.9592 (mmp) cc_final: 0.9325 (mmm) REVERT: e 539 MET cc_start: 0.7536 (ppp) cc_final: 0.6645 (ppp) outliers start: 3 outliers final: 2 residues processed: 169 average time/residue: 0.4727 time to fit residues: 110.4464 Evaluate side-chains 124 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 49 GLN R 98 ASN a 228 GLN ** d 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 708 GLN d 877 ASN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 GLN e 164 ASN e 309 HIS e 338 GLN e 399 ASN ** e 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.034388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.028028 restraints weight = 1424995.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.028985 restraints weight = 902809.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.029653 restraints weight = 622838.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.030126 restraints weight = 461986.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.030458 restraints weight = 361936.093| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21830 Z= 0.169 Angle : 0.603 15.866 29476 Z= 0.325 Chirality : 0.042 0.165 3315 Planarity : 0.005 0.082 3787 Dihedral : 5.221 75.555 2892 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.69 (0.16), residues: 2653 helix: 0.53 (0.18), residues: 788 sheet: -2.22 (0.19), residues: 682 loop : -1.48 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG a 40 TYR 0.012 0.001 TYR e 227 PHE 0.026 0.001 PHE c 137 TRP 0.015 0.001 TRP e 63 HIS 0.009 0.001 HIS c 136 Details of bonding type rmsd covalent geometry : bond 0.00343 (21818) covalent geometry : angle 0.59328 (29470) hydrogen bonds : bond 0.05354 ( 882) hydrogen bonds : angle 6.55855 ( 2544) metal coordination : bond 0.02336 ( 11) metal coordination : angle 7.54559 ( 6) Misc. bond : bond 0.00456 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 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 131 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.723 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: D 147 MET cc_start: 0.8465 (mmt) cc_final: 0.8001 (mmp) REVERT: d 954 MET cc_start: 0.9374 (mmm) cc_final: 0.8993 (mmm) REVERT: d 962 ASP cc_start: 0.9913 (m-30) cc_final: 0.9691 (p0) REVERT: d 1099 ASP cc_start: 0.9573 (m-30) cc_final: 0.9312 (p0) REVERT: e 146 MET cc_start: 0.9737 (tpp) cc_final: 0.9355 (tpp) REVERT: e 251 MET cc_start: 0.8853 (tpp) cc_final: 0.8440 (mmm) REVERT: e 322 MET cc_start: 0.9924 (ttm) cc_final: 0.9636 (tmm) REVERT: e 494 MET cc_start: 0.9330 (mtt) cc_final: 0.9078 (mtp) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.4532 time to fit residues: 82.5207 Evaluate side-chains 109 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 193 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 7 HIS a 183 GLN d 93 GLN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 677 ASN d 852 GLN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 603 ASN e 657 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.032199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.025971 restraints weight = 1480822.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.026879 restraints weight = 941632.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.027485 restraints weight = 654241.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.027931 restraints weight = 488605.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.028248 restraints weight = 385126.266| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21830 Z= 0.217 Angle : 0.604 15.054 29476 Z= 0.324 Chirality : 0.040 0.149 3315 Planarity : 0.004 0.059 3787 Dihedral : 4.998 74.254 2892 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.04 % Allowed : 1.89 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.16), residues: 2653 helix: 0.75 (0.18), residues: 782 sheet: -2.07 (0.20), residues: 634 loop : -1.58 (0.16), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG c 44 TYR 0.014 0.002 TYR a 100 PHE 0.017 0.001 PHE d 949 TRP 0.033 0.002 TRP d 561 HIS 0.008 0.002 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00429 (21818) covalent geometry : angle 0.59325 (29470) hydrogen bonds : bond 0.04693 ( 882) hydrogen bonds : angle 6.10173 ( 2544) metal coordination : bond 0.02171 ( 11) metal coordination : angle 8.02988 ( 6) Misc. bond : bond 0.00540 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 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 122 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 1.211 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: 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: 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: 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 147 MET cc_start: 0.8553 (mmt) cc_final: 0.8155 (mmp) REVERT: a 149 MET cc_start: 0.8837 (mtm) cc_final: 0.8629 (mtp) REVERT: d 130 MET cc_start: 0.9568 (mtm) cc_final: 0.9333 (ttm) REVERT: d 910 MET cc_start: 0.8939 (mmt) cc_final: 0.8688 (mmt) REVERT: d 954 MET cc_start: 0.9526 (mmm) cc_final: 0.9108 (mmm) REVERT: d 962 ASP cc_start: 0.9893 (m-30) cc_final: 0.9663 (p0) REVERT: e 146 MET cc_start: 0.9761 (tpp) cc_final: 0.9387 (tpp) REVERT: e 251 MET cc_start: 0.8904 (tpp) cc_final: 0.8474 (mmm) REVERT: e 322 MET cc_start: 0.9919 (ttm) cc_final: 0.9633 (tmm) REVERT: e 704 MET cc_start: 0.8424 (ttp) cc_final: 0.7955 (tpp) outliers start: 1 outliers final: 1 residues processed: 122 average time/residue: 0.4703 time to fit residues: 80.1101 Evaluate side-chains 101 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 206 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 187 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 809 GLN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 511 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.030524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.024702 restraints weight = 1516508.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.025574 restraints weight = 952032.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.026186 restraints weight = 650312.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.026612 restraints weight = 476846.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.026917 restraints weight = 374290.148| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21830 Z= 0.185 Angle : 0.560 14.951 29476 Z= 0.301 Chirality : 0.040 0.153 3315 Planarity : 0.004 0.097 3787 Dihedral : 4.948 71.583 2892 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.45 (0.16), residues: 2653 helix: 0.88 (0.18), residues: 777 sheet: -2.09 (0.19), residues: 644 loop : -1.46 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG c 44 TYR 0.013 0.002 TYR d 718 PHE 0.024 0.002 PHE D 62 TRP 0.018 0.002 TRP d1073 HIS 0.012 0.001 HIS e 511 Details of bonding type rmsd covalent geometry : bond 0.00361 (21818) covalent geometry : angle 0.54981 (29470) hydrogen bonds : bond 0.04069 ( 882) hydrogen bonds : angle 5.84253 ( 2544) metal coordination : bond 0.01585 ( 11) metal coordination : angle 7.30828 ( 6) Misc. bond : bond 0.00337 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 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 112 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.203 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 MET cc_start: 0.7383 (mmt) cc_final: 0.6651 (mmp) REVERT: U 4 PHE cc_start: 0.9886 (m-80) cc_final: 0.9639 (m-10) REVERT: a 149 MET cc_start: 0.8528 (mtm) cc_final: 0.8242 (mtp) REVERT: d 64 MET cc_start: 0.8498 (ptm) cc_final: 0.8181 (ptm) REVERT: d 873 MET cc_start: 0.8742 (ptp) cc_final: 0.8154 (ptp) REVERT: d 910 MET cc_start: 0.8389 (mmt) cc_final: 0.8153 (mmt) REVERT: d 954 MET cc_start: 0.8622 (mmm) cc_final: 0.8229 (mmm) REVERT: d 962 ASP cc_start: 0.9627 (m-30) cc_final: 0.9355 (p0) REVERT: e 146 MET cc_start: 0.9375 (tpp) cc_final: 0.9124 (tpp) REVERT: e 251 MET cc_start: 0.8895 (tpp) cc_final: 0.8584 (mmm) REVERT: e 475 MET cc_start: 0.9769 (tpp) cc_final: 0.9567 (tpp) REVERT: e 505 MET cc_start: 0.9475 (mmp) cc_final: 0.9132 (mmm) REVERT: e 704 MET cc_start: 0.8813 (ttp) cc_final: 0.8309 (tpp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.4948 time to fit residues: 77.5817 Evaluate side-chains 96 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 93 optimal weight: 9.9990 chunk 215 optimal weight: 0.0980 chunk 118 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 203 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 59 ASN d 156 ASN ** d 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 536 HIS ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 338 GLN ** 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 = 0.3272 r_free = 0.3272 target = 0.026424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.020661 restraints weight = 1462936.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.021182 restraints weight = 1090842.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.021560 restraints weight = 854701.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.021854 restraints weight = 698123.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.022074 restraints weight = 590797.978| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 21830 Z= 0.239 Angle : 0.628 15.444 29476 Z= 0.336 Chirality : 0.041 0.214 3315 Planarity : 0.004 0.078 3787 Dihedral : 5.048 70.083 2892 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.04 % Allowed : 1.68 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.52 (0.16), residues: 2653 helix: 0.77 (0.18), residues: 768 sheet: -2.09 (0.20), residues: 619 loop : -1.50 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG c 41 TYR 0.017 0.002 TYR a 100 PHE 0.022 0.002 PHE d 650 TRP 0.017 0.002 TRP e 533 HIS 0.011 0.002 HIS R 48 Details of bonding type rmsd covalent geometry : bond 0.00471 (21818) covalent geometry : angle 0.61873 (29470) hydrogen bonds : bond 0.04277 ( 882) hydrogen bonds : angle 5.91822 ( 2544) metal coordination : bond 0.01384 ( 11) metal coordination : angle 7.56269 ( 6) Misc. bond : bond 0.00410 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 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 101 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.898 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: 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: 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 147 MET cc_start: 0.7773 (mmt) cc_final: 0.7126 (mmp) REVERT: d 910 MET cc_start: 0.8663 (mmt) cc_final: 0.8354 (mmt) REVERT: d 954 MET cc_start: 0.9049 (mmm) cc_final: 0.8704 (mmm) REVERT: d 962 ASP cc_start: 0.9789 (m-30) cc_final: 0.9493 (p0) REVERT: e 146 MET cc_start: 0.9576 (tpp) cc_final: 0.9295 (tpp) REVERT: e 251 MET cc_start: 0.9142 (tpp) cc_final: 0.8692 (mmm) REVERT: e 494 MET cc_start: 0.9428 (mtt) cc_final: 0.9149 (mtt) REVERT: e 547 MET cc_start: 0.9084 (mmm) cc_final: 0.8096 (tpp) REVERT: e 704 MET cc_start: 0.8818 (ttp) cc_final: 0.8328 (tpp) outliers start: 1 outliers final: 1 residues processed: 101 average time/residue: 0.3973 time to fit residues: 58.8185 Evaluate side-chains 90 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 1 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 250 optimal weight: 30.0000 chunk 122 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 241 ASN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 481 GLN ** d 522 HIS ** 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 = 0.3456 r_free = 0.3456 target = 0.030215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.024221 restraints weight = 1524133.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.025085 restraints weight = 961737.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.025679 restraints weight = 662545.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.026100 restraints weight = 490551.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.026400 restraints weight = 385474.032| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21830 Z= 0.120 Angle : 0.519 13.782 29476 Z= 0.275 Chirality : 0.041 0.147 3315 Planarity : 0.003 0.040 3787 Dihedral : 4.859 68.261 2892 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.26 (0.16), residues: 2653 helix: 1.19 (0.18), residues: 769 sheet: -2.09 (0.19), residues: 633 loop : -1.40 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG c 44 TYR 0.013 0.001 TYR d 678 PHE 0.021 0.001 PHE c 62 TRP 0.015 0.001 TRP e 63 HIS 0.008 0.001 HIS c 136 Details of bonding type rmsd covalent geometry : bond 0.00251 (21818) covalent geometry : angle 0.50972 (29470) hydrogen bonds : bond 0.03628 ( 882) hydrogen bonds : angle 5.60274 ( 2544) metal coordination : bond 0.01533 ( 11) metal coordination : angle 6.83990 ( 6) Misc. bond : bond 0.00376 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 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 100 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.153 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 954 MET cc_start: 0.9404 (mmm) cc_final: 0.9156 (mmm) REVERT: d 962 ASP cc_start: 0.9843 (m-30) cc_final: 0.9639 (p0) REVERT: e 251 MET cc_start: 0.8879 (tpp) cc_final: 0.8542 (mmm) REVERT: e 547 MET cc_start: 0.8390 (mmm) cc_final: 0.7548 (tpp) REVERT: e 704 MET cc_start: 0.8353 (ttp) cc_final: 0.7995 (tpp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.4411 time to fit residues: 63.6833 Evaluate side-chains 90 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 170 optimal weight: 10.0000 chunk 169 optimal weight: 8.9990 chunk 110 optimal weight: 0.1980 chunk 203 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 163 GLN e 339 HIS e 722 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.030054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.024085 restraints weight = 1520155.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.024914 restraints weight = 960981.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.025518 restraints weight = 663732.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.025945 restraints weight = 491172.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.026224 restraints weight = 385029.676| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 21830 Z= 0.119 Angle : 0.498 12.532 29476 Z= 0.264 Chirality : 0.040 0.149 3315 Planarity : 0.003 0.041 3787 Dihedral : 4.706 67.761 2892 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.09 (0.16), residues: 2653 helix: 1.45 (0.19), residues: 769 sheet: -2.08 (0.19), residues: 654 loop : -1.30 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG c 44 TYR 0.012 0.001 TYR d 678 PHE 0.017 0.001 PHE e 440 TRP 0.016 0.001 TRP e 63 HIS 0.008 0.001 HIS c 136 Details of bonding type rmsd covalent geometry : bond 0.00246 (21818) covalent geometry : angle 0.48916 (29470) hydrogen bonds : bond 0.03477 ( 882) hydrogen bonds : angle 5.42228 ( 2544) metal coordination : bond 0.01320 ( 11) metal coordination : angle 6.38989 ( 6) Misc. bond : bond 0.00384 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 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 97 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.095 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: 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: 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: 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 910 MET cc_start: 0.9000 (mmt) cc_final: 0.8709 (mmt) REVERT: d 954 MET cc_start: 0.9379 (mmm) cc_final: 0.9075 (mmm) REVERT: d 962 ASP cc_start: 0.9852 (m-30) cc_final: 0.9643 (p0) REVERT: e 251 MET cc_start: 0.8882 (tpp) cc_final: 0.8534 (mmm) REVERT: e 547 MET cc_start: 0.8453 (mmm) cc_final: 0.7626 (tpp) REVERT: e 704 MET cc_start: 0.8409 (ttp) cc_final: 0.8047 (tpp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.4986 time to fit residues: 70.1755 Evaluate side-chains 89 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 260 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN a 110 HIS a 259 HIS c 49 GLN ** d 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 337 ASN d 372 GLN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 663 ASN ** d 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 759 GLN d 809 GLN d 877 ASN d 907 ASN d1049 ASN e 117 GLN e 181 HIS ** e 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 363 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.025070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.019648 restraints weight = 1526941.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.020109 restraints weight = 1146222.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.020455 restraints weight = 903596.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.020717 restraints weight = 743529.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.020917 restraints weight = 634600.568| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 21830 Z= 0.275 Angle : 0.665 20.202 29476 Z= 0.359 Chirality : 0.041 0.183 3315 Planarity : 0.004 0.044 3787 Dihedral : 5.009 66.556 2892 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.04 % Allowed : 0.88 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.53 (0.16), residues: 2653 helix: 0.72 (0.18), residues: 780 sheet: -2.08 (0.20), residues: 601 loop : -1.53 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 44 TYR 0.022 0.002 TYR a 100 PHE 0.024 0.002 PHE d 650 TRP 0.022 0.002 TRP e 533 HIS 0.008 0.002 HIS c 136 Details of bonding type rmsd covalent geometry : bond 0.00539 (21818) covalent geometry : angle 0.65676 (29470) hydrogen bonds : bond 0.04186 ( 882) hydrogen bonds : angle 5.82359 ( 2544) metal coordination : bond 0.01209 ( 11) metal coordination : angle 7.31168 ( 6) Misc. bond : bond 0.00389 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 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 96 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 1.268 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: 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: 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: symmetry clash REVERT: D 147 MET cc_start: 0.7353 (mmt) cc_final: 0.6588 (mmm) REVERT: d 954 MET cc_start: 0.9142 (mmm) cc_final: 0.8828 (mmm) REVERT: e 146 MET cc_start: 0.9549 (tpp) cc_final: 0.9208 (tpp) REVERT: e 251 MET cc_start: 0.9097 (tpp) cc_final: 0.8704 (mmm) REVERT: e 494 MET cc_start: 0.9427 (mtt) cc_final: 0.9202 (mtt) REVERT: e 547 MET cc_start: 0.9113 (mmm) cc_final: 0.8135 (tpp) REVERT: e 704 MET cc_start: 0.8785 (ttp) cc_final: 0.8301 (tpp) outliers start: 1 outliers final: 1 residues processed: 96 average time/residue: 0.4843 time to fit residues: 68.0984 Evaluate side-chains 87 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 118 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 162 optimal weight: 9.9990 chunk 95 optimal weight: 0.5980 chunk 208 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 GLN ** c 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 372 GLN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 570 GLN ** 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 = 0.3229 r_free = 0.3229 target = 0.025401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.019662 restraints weight = 1460949.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.020247 restraints weight = 1038072.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.020670 restraints weight = 783865.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.020988 restraints weight = 622379.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.021224 restraints weight = 515071.557| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21830 Z= 0.153 Angle : 0.542 13.440 29476 Z= 0.290 Chirality : 0.042 0.379 3315 Planarity : 0.004 0.040 3787 Dihedral : 4.881 64.760 2892 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.33 (0.16), residues: 2653 helix: 1.10 (0.18), residues: 776 sheet: -2.12 (0.20), residues: 624 loop : -1.45 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG c 44 TYR 0.016 0.002 TYR d 678 PHE 0.060 0.002 PHE D 69 TRP 0.014 0.001 TRP e 63 HIS 0.009 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00305 (21818) covalent geometry : angle 0.53337 (29470) hydrogen bonds : bond 0.03580 ( 882) hydrogen bonds : angle 5.56979 ( 2544) metal coordination : bond 0.01505 ( 11) metal coordination : angle 6.85059 ( 6) Misc. bond : bond 0.00373 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 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 92 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.218 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: 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: 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: symmetry clash REVERT: d 64 MET cc_start: 0.8946 (ptm) cc_final: 0.8249 (tmm) REVERT: d 954 MET cc_start: 0.8855 (mmm) cc_final: 0.8627 (mmm) REVERT: d 962 ASP cc_start: 0.9636 (m-30) cc_final: 0.9409 (p0) REVERT: e 251 MET cc_start: 0.8907 (tpp) cc_final: 0.8594 (mmm) REVERT: e 547 MET cc_start: 0.9157 (mmm) cc_final: 0.8103 (tpp) REVERT: e 704 MET cc_start: 0.8814 (ttp) cc_final: 0.8364 (tpp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.4814 time to fit residues: 65.1828 Evaluate side-chains 86 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 161 optimal weight: 9.9990 chunk 160 optimal weight: 0.0870 chunk 118 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 126 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 overall best weight: 2.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 7 HIS D 20 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 570 GLN ** 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 = 0.3231 r_free = 0.3231 target = 0.025404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.019614 restraints weight = 1449866.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.020214 restraints weight = 1036252.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.020657 restraints weight = 779171.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.020983 restraints weight = 615333.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.021226 restraints weight = 507629.377| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21830 Z= 0.128 Angle : 0.522 13.062 29476 Z= 0.278 Chirality : 0.041 0.159 3315 Planarity : 0.004 0.046 3787 Dihedral : 4.784 64.285 2892 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.22 (0.16), residues: 2653 helix: 1.28 (0.18), residues: 776 sheet: -2.14 (0.19), residues: 645 loop : -1.36 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG c 44 TYR 0.015 0.001 TYR d 678 PHE 0.031 0.001 PHE D 69 TRP 0.015 0.001 TRP e 533 HIS 0.010 0.001 HIS D 7 Details of bonding type rmsd covalent geometry : bond 0.00267 (21818) covalent geometry : angle 0.51337 (29470) hydrogen bonds : bond 0.03442 ( 882) hydrogen bonds : angle 5.47605 ( 2544) metal coordination : bond 0.01387 ( 11) metal coordination : angle 6.49011 ( 6) Misc. bond : bond 0.00368 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5306 Ramachandran restraints generated. 2653 Oldfield, 0 Emsley, 2653 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 92 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.278 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: 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: 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 64 MET cc_start: 0.8911 (ptm) cc_final: 0.8187 (tmm) REVERT: d 835 MET cc_start: 0.6590 (mmm) cc_final: 0.6238 (mmm) REVERT: d 954 MET cc_start: 0.8787 (mmm) cc_final: 0.8547 (mmm) REVERT: d 962 ASP cc_start: 0.9626 (m-30) cc_final: 0.9397 (p0) REVERT: e 251 MET cc_start: 0.8837 (tpp) cc_final: 0.8510 (mmm) REVERT: e 505 MET cc_start: 0.9530 (mmt) cc_final: 0.9037 (mmm) REVERT: e 547 MET cc_start: 0.9172 (mmm) cc_final: 0.8143 (tpp) REVERT: e 704 MET cc_start: 0.8820 (ttp) cc_final: 0.8368 (tpp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.4794 time to fit residues: 64.5653 Evaluate side-chains 86 residues out of total 2387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 150 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 240 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN ** d 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 332 GLN ** d 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d1106 GLN e 115 GLN ** e 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 309 HIS ** e 542 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.024482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.019076 restraints weight = 1529064.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.019834 restraints weight = 1114071.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.020219 restraints weight = 800744.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.020578 restraints weight = 590726.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.020815 restraints weight = 471356.378| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 21830 Z= 0.285 Angle : 0.684 14.559 29476 Z= 0.373 Chirality : 0.042 0.243 3315 Planarity : 0.005 0.046 3787 Dihedral : 5.182 63.298 2892 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2653 helix: 0.31 (0.18), residues: 790 sheet: -2.37 (0.19), residues: 664 loop : -1.63 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG c 44 TYR 0.025 0.003 TYR a 100 PHE 0.026 0.003 PHE d 949 TRP 0.025 0.002 TRP e 533 HIS 0.009 0.002 HIS d 189 Details of bonding type rmsd covalent geometry : bond 0.00553 (21818) covalent geometry : angle 0.67529 (29470) hydrogen bonds : bond 0.04273 ( 882) hydrogen bonds : angle 5.98087 ( 2544) metal coordination : bond 0.01476 ( 11) metal coordination : angle 7.45673 ( 6) Misc. bond : bond 0.00368 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7187.46 seconds wall clock time: 123 minutes 51.21 seconds (7431.21 seconds total)