Starting phenix.real_space_refine on Thu Mar 5 03:47:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6loe_0937/03_2026/6loe_0937.cif Found real_map, /net/cci-nas-00/data/ceres_data/6loe_0937/03_2026/6loe_0937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6loe_0937/03_2026/6loe_0937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6loe_0937/03_2026/6loe_0937.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6loe_0937/03_2026/6loe_0937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6loe_0937/03_2026/6loe_0937.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians Fe 21 7.16 5 S 106 5.16 5 C 12235 2.51 5 N 3163 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18785 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1763 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "B" Number of atoms: 7176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7176 Classifications: {'peptide': 929} Link IDs: {'PTRANS': 54, 'TRANS': 874} Chain: "C" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3728 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 22, 'TRANS': 433} Chain: "D" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1348 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 13, 'TRANS': 160} Chain: "E" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1253 Unusual residues: {'ACE': 1} Classifications: {'peptide': 157, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 11, 'TRANS': 145} Chain: "F" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3159 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 21, 'TRANS': 373} Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {'HEC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {'EL6': 1, 'F3S': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'EL6': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7079 SG CYS B 772 44.642 62.351 45.588 1.00 5.32 S ATOM 8511 SG CYS B 952 44.756 61.852 50.721 1.00 6.62 S ATOM 7098 SG CYS B 775 49.722 62.205 47.271 1.00 5.50 S ATOM 7059 SG CYS B 769 47.536 57.136 48.142 1.00 6.47 S ATOM 8265 SG CYS B 921 55.418 69.826 53.259 1.00 5.04 S ATOM 8241 SG CYS B 918 57.887 64.114 52.522 1.00 6.02 S ATOM 7123 SG CYS B 779 56.767 67.351 48.402 1.00 5.35 S ATOM 8480 SG CYS B 948 52.480 64.905 52.339 1.00 5.40 S ATOM 7499 SG CYS B 824 63.216 61.122 54.019 1.00 5.24 S ATOM 7560 SG CYS B 832 68.738 59.364 54.348 1.00 3.74 S ATOM 7813 SG CYS B 866 66.309 56.854 50.988 1.00 5.53 S ATOM 7523 SG CYS B 827 64.450 56.126 56.803 1.00 4.46 S ATOM 7785 SG CYS B 862 72.524 61.822 49.307 1.00 5.33 S ATOM 7740 SG CYS B 856 73.695 67.329 47.823 1.00 5.51 S ATOM 7590 SG CYS B 836 76.283 64.552 52.718 1.00 5.66 S Time building chain proxies: 4.26, per 1000 atoms: 0.23 Number of scatterers: 18785 At special positions: 0 Unit cell: (161.2, 131.04, 95.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 21 26.01 S 106 16.00 O 3260 8.00 N 3163 7.00 C 12235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 713.0 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B1104 " pdb="FE1 F3S B1104 " - pdb=" SG CYS B 862 " pdb="FE3 F3S B1104 " - pdb=" SG CYS B 856 " pdb="FE4 F3S B1104 " - pdb=" SG CYS B 836 " pdb=" SF4 B1101 " pdb="FE2 SF4 B1101 " - pdb=" SG CYS B 952 " pdb="FE3 SF4 B1101 " - pdb=" SG CYS B 775 " pdb="FE1 SF4 B1101 " - pdb=" SG CYS B 772 " pdb="FE4 SF4 B1101 " - pdb=" SG CYS B 769 " pdb=" SF4 B1102 " pdb="FE3 SF4 B1102 " - pdb=" SG CYS B 779 " pdb="FE2 SF4 B1102 " - pdb=" SG CYS B 918 " pdb="FE1 SF4 B1102 " - pdb=" SG CYS B 921 " pdb="FE4 SF4 B1102 " - pdb=" SG CYS B 948 " pdb=" SF4 B1103 " pdb="FE2 SF4 B1103 " - pdb=" SG CYS B 832 " pdb="FE4 SF4 B1103 " - pdb=" SG CYS B 827 " pdb="FE3 SF4 B1103 " - pdb=" SG CYS B 866 " pdb="FE1 SF4 B1103 " - pdb=" SG CYS B 824 " Number of angles added : 45 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4306 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 15 sheets defined 48.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 14 through 25 removed outlier: 3.966A pdb=" N SER A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 43 removed outlier: 3.544A pdb=" N LEU A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.584A pdb=" N HIS A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.968A pdb=" N CYS A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.814A pdb=" N TRP A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.613A pdb=" N CYS A 174 " --> pdb=" O TRP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.582A pdb=" N LYS A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.649A pdb=" N VAL A 188 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE A 189 " --> pdb=" O GLU A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 185 through 189' Processing helix chain 'A' and resid 202 through 211 removed outlier: 3.817A pdb=" N GLN A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.877A pdb=" N ILE B 153 " --> pdb=" O GLN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 removed outlier: 3.641A pdb=" N PHE B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 234 through 244 removed outlier: 3.679A pdb=" N ARG B 240 " --> pdb=" O ASN B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 282 removed outlier: 3.707A pdb=" N LEU B 280 " --> pdb=" O MET B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 323 Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 345 through 359 removed outlier: 3.709A pdb=" N LYS B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 386 removed outlier: 3.580A pdb=" N HIS B 378 " --> pdb=" O PRO B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 420 removed outlier: 3.508A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 487 through 489 No H-bonds generated for 'chain 'B' and resid 487 through 489' Processing helix chain 'B' and resid 506 through 516 removed outlier: 4.232A pdb=" N VAL B 513 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 534 removed outlier: 4.583A pdb=" N THR B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 550 removed outlier: 3.515A pdb=" N ASN B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR B 545 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 604 Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 680 through 685 removed outlier: 3.775A pdb=" N ARG B 683 " --> pdb=" O ASN B 680 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 684 " --> pdb=" O ALA B 681 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 685 " --> pdb=" O TYR B 682 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 680 through 685' Processing helix chain 'B' and resid 766 through 769 removed outlier: 3.575A pdb=" N CYS B 769 " --> pdb=" O LEU B 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 766 through 769' Processing helix chain 'B' and resid 773 through 784 removed outlier: 3.508A pdb=" N VAL B 777 " --> pdb=" O ASN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 860 through 866 removed outlier: 4.070A pdb=" N ASN B 864 " --> pdb=" O LYS B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 902 removed outlier: 3.670A pdb=" N MET B 901 " --> pdb=" O VAL B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 935 removed outlier: 3.907A pdb=" N GLU B 927 " --> pdb=" O GLN B 923 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 931 " --> pdb=" O GLU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1006 removed outlier: 3.509A pdb=" N ALA B1005 " --> pdb=" O ASN B1001 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU B1006 " --> pdb=" O PRO B1002 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1001 through 1006' Processing helix chain 'C' and resid 11 through 16 Processing helix chain 'C' and resid 24 through 36 removed outlier: 3.505A pdb=" N ILE C 32 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE C 35 " --> pdb=" O THR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 72 removed outlier: 4.431A pdb=" N ILE C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 76 removed outlier: 3.790A pdb=" N TRP C 76 " --> pdb=" O VAL C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 73 through 76' Processing helix chain 'C' and resid 85 through 98 removed outlier: 3.630A pdb=" N PHE C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 106 removed outlier: 3.813A pdb=" N THR C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.632A pdb=" N PHE C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 132 removed outlier: 4.115A pdb=" N MET C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 144 through 152 removed outlier: 4.597A pdb=" N TYR C 149 " --> pdb=" O TRP C 146 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP C 150 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET C 151 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 183 removed outlier: 3.668A pdb=" N VAL C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'C' and resid 206 through 214 Processing helix chain 'C' and resid 220 through 255 removed outlier: 3.555A pdb=" N ASN C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Proline residue: C 240 - end of helix removed outlier: 3.781A pdb=" N HIS C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE C 253 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 292 removed outlier: 4.140A pdb=" N ALA C 272 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 280 " --> pdb=" O TYR C 276 " (cutoff:3.500A) Proline residue: C 288 - end of helix Processing helix chain 'C' and resid 300 through 322 removed outlier: 3.874A pdb=" N PHE C 304 " --> pdb=" O THR C 300 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 334 through 345 removed outlier: 3.557A pdb=" N LEU C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 361 removed outlier: 3.755A pdb=" N TYR C 353 " --> pdb=" O TYR C 349 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 373 removed outlier: 3.684A pdb=" N GLN C 365 " --> pdb=" O ALA C 362 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 367 " --> pdb=" O PRO C 364 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LYS C 370 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG C 371 " --> pdb=" O TRP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 403 removed outlier: 3.684A pdb=" N ARG C 394 " --> pdb=" O MET C 390 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 400 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.767A pdb=" N TRP C 411 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 425 removed outlier: 3.545A pdb=" N ILE C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 423 " --> pdb=" O TRP C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 442 removed outlier: 3.714A pdb=" N LEU C 434 " --> pdb=" O TRP C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 452 Processing helix chain 'C' and resid 454 through 464 removed outlier: 4.028A pdb=" N LEU C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 464 " --> pdb=" O GLU C 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 39 Processing helix chain 'D' and resid 69 through 83 removed outlier: 3.671A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 94 Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.740A pdb=" N GLY D 103 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG D 104 " --> pdb=" O ILE D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 104' Processing helix chain 'D' and resid 112 through 118 removed outlier: 3.999A pdb=" N GLU D 118 " --> pdb=" O PRO D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 134 removed outlier: 3.595A pdb=" N MET D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 154 Processing helix chain 'D' and resid 173 through 182 removed outlier: 3.805A pdb=" N GLN D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 112 removed outlier: 3.557A pdb=" N LEU E 102 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU E 103 " --> pdb=" O PRO E 99 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 118 Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'E' and resid 140 through 145 removed outlier: 3.951A pdb=" N ASP E 145 " --> pdb=" O GLN E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 158 removed outlier: 3.614A pdb=" N LEU E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 186 removed outlier: 3.658A pdb=" N VAL E 179 " --> pdb=" O ARG E 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 36 removed outlier: 3.886A pdb=" N MET F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 58 removed outlier: 3.693A pdb=" N PHE F 42 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 70 Processing helix chain 'F' and resid 72 through 77 removed outlier: 3.968A pdb=" N LEU F 76 " --> pdb=" O GLY F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 86 removed outlier: 3.536A pdb=" N GLU F 83 " --> pdb=" O ARG F 79 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA F 85 " --> pdb=" O LEU F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 96 removed outlier: 3.889A pdb=" N ILE F 94 " --> pdb=" O PRO F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 117 through 122 Processing helix chain 'F' and resid 133 through 165 removed outlier: 4.185A pdb=" N ILE F 149 " --> pdb=" O PHE F 145 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG F 156 " --> pdb=" O ALA F 152 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER F 159 " --> pdb=" O LEU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 189 Proline residue: F 181 - end of helix removed outlier: 3.791A pdb=" N VAL F 184 " --> pdb=" O GLY F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 236 removed outlier: 3.570A pdb=" N ILE F 215 " --> pdb=" O PRO F 211 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER F 217 " --> pdb=" O THR F 213 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE F 220 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG F 236 " --> pdb=" O VAL F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 276 removed outlier: 3.515A pdb=" N HIS F 249 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 288 removed outlier: 4.590A pdb=" N HIS F 285 " --> pdb=" O LEU F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 303 removed outlier: 4.094A pdb=" N LEU F 296 " --> pdb=" O GLY F 292 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 311 Processing helix chain 'F' and resid 312 through 314 No H-bonds generated for 'chain 'F' and resid 312 through 314' Processing helix chain 'F' and resid 320 through 344 removed outlier: 3.723A pdb=" N ALA F 326 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE F 327 " --> pdb=" O ASN F 323 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL F 337 " --> pdb=" O LEU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 347 No H-bonds generated for 'chain 'F' and resid 345 through 347' Processing helix chain 'F' and resid 356 through 361 Processing helix chain 'F' and resid 361 through 379 removed outlier: 4.057A pdb=" N ARG F 379 " --> pdb=" O TRP F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 394 Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA2, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.721A pdb=" N LYS B 131 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 166 through 167 Processing sheet with id=AA4, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA5, first strand: chain 'B' and resid 258 through 259 removed outlier: 6.446A pdb=" N VAL B 258 " --> pdb=" O VAL B 366 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 426 through 429 Processing sheet with id=AA7, first strand: chain 'B' and resid 482 through 485 Processing sheet with id=AA8, first strand: chain 'B' and resid 658 through 662 Processing sheet with id=AA9, first strand: chain 'B' and resid 617 through 619 removed outlier: 5.856A pdb=" N ALA B 617 " --> pdb=" O TRP B 649 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 642 through 643 removed outlier: 3.518A pdb=" N ARG B 642 " --> pdb=" O TYR B 639 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 726 through 727 Processing sheet with id=AB3, first strand: chain 'B' and resid 760 through 764 Processing sheet with id=AB4, first strand: chain 'B' and resid 872 through 873 Processing sheet with id=AB5, first strand: chain 'B' and resid 978 through 979 Processing sheet with id=AB6, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.598A pdb=" N GLY D 22 " --> pdb=" O VAL D 190 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1944 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: 2.94 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.79: 19210 1.79 - 2.40: 161 2.40 - 3.01: 0 3.01 - 3.61: 0 3.61 - 4.22: 3 Bond restraints: 19374 Sorted by residual: bond pdb=" S4 F3S B1104 " pdb="FE1 F3S B1104 " ideal model delta sigma weight residual 2.233 4.217 -1.984 2.00e-02 2.50e+03 9.84e+03 bond pdb=" S1 F3S B1104 " pdb="FE4 F3S B1104 " ideal model delta sigma weight residual 2.258 4.212 -1.954 2.00e-02 2.50e+03 9.55e+03 bond pdb=" S2 F3S B1104 " pdb="FE3 F3S B1104 " ideal model delta sigma weight residual 2.300 4.221 -1.921 2.00e-02 2.50e+03 9.23e+03 bond pdb=" S2 F3S B1104 " pdb="FE4 F3S B1104 " ideal model delta sigma weight residual 2.317 2.205 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" S3 F3S B1104 " pdb="FE1 F3S B1104 " ideal model delta sigma weight residual 2.296 2.193 0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 19369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.83: 26507 14.83 - 29.67: 11 29.67 - 44.50: 2 44.50 - 59.33: 0 59.33 - 74.17: 2 Bond angle restraints: 26522 Sorted by residual: angle pdb=" S1 F3S B1104 " pdb="FE4 F3S B1104 " pdb=" S3 F3S B1104 " ideal model delta sigma weight residual 114.75 40.58 74.17 3.00e+00 1.11e-01 6.11e+02 angle pdb=" S3 F3S B1104 " pdb="FE1 F3S B1104 " pdb=" S4 F3S B1104 " ideal model delta sigma weight residual 112.59 40.74 71.85 3.00e+00 1.11e-01 5.74e+02 angle pdb=" S1 F3S B1104 " pdb="FE3 F3S B1104 " pdb=" S4 F3S B1104 " ideal model delta sigma weight residual 112.54 145.94 -33.40 3.00e+00 1.11e-01 1.24e+02 angle pdb="FE1 F3S B1104 " pdb=" S4 F3S B1104 " pdb="FE3 F3S B1104 " ideal model delta sigma weight residual 74.86 44.67 30.19 3.00e+00 1.11e-01 1.01e+02 angle pdb=" S1 F3S B1104 " pdb="FE4 F3S B1104 " pdb=" S2 F3S B1104 " ideal model delta sigma weight residual 103.63 74.90 28.73 3.00e+00 1.11e-01 9.17e+01 ... (remaining 26517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.86: 10509 25.86 - 51.72: 545 51.72 - 77.58: 53 77.58 - 103.44: 16 103.44 - 129.31: 4 Dihedral angle restraints: 11127 sinusoidal: 4407 harmonic: 6720 Sorted by residual: dihedral pdb=" C PRO B 588 " pdb=" N PRO B 588 " pdb=" CA PRO B 588 " pdb=" CB PRO B 588 " ideal model delta harmonic sigma weight residual -120.70 -103.04 -17.66 0 2.50e+00 1.60e-01 4.99e+01 dihedral pdb=" N PRO B 588 " pdb=" C PRO B 588 " pdb=" CA PRO B 588 " pdb=" CB PRO B 588 " ideal model delta harmonic sigma weight residual 115.10 98.34 16.76 0 2.50e+00 1.60e-01 4.50e+01 dihedral pdb=" CA GLY C 216 " pdb=" C GLY C 216 " pdb=" N TRP C 217 " pdb=" CA TRP C 217 " ideal model delta harmonic sigma weight residual -180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 11124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.744: 2855 2.744 - 5.488: 0 5.488 - 8.232: 0 8.232 - 10.976: 0 10.976 - 13.720: 1 Chirality restraints: 2856 Sorted by residual: chirality pdb=" S2 F3S B1104 " pdb="FE1 F3S B1104 " pdb="FE3 F3S B1104 " pdb="FE4 F3S B1104 " both_signs ideal model delta sigma weight residual False 10.77 -2.95 13.72 2.00e-01 2.50e+01 4.71e+03 chirality pdb=" CA LEU B 298 " pdb=" N LEU B 298 " pdb=" C LEU B 298 " pdb=" CB LEU B 298 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.97e+00 chirality pdb=" CA ARG E 80 " pdb=" N ARG E 80 " pdb=" C ARG E 80 " pdb=" CB ARG E 80 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 2853 not shown) Planarity restraints: 3339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC E 201 " 0.015 2.00e-02 2.50e+03 5.63e-02 7.14e+01 pdb=" C2C HEC E 201 " -0.154 2.00e-02 2.50e+03 pdb=" C3C HEC E 201 " 0.019 2.00e-02 2.50e+03 pdb=" C4C HEC E 201 " 0.005 2.00e-02 2.50e+03 pdb=" CAC HEC E 201 " 0.035 2.00e-02 2.50e+03 pdb=" CHC HEC E 201 " 0.031 2.00e-02 2.50e+03 pdb=" CHD HEC E 201 " -0.006 2.00e-02 2.50e+03 pdb=" CMC HEC E 201 " 0.044 2.00e-02 2.50e+03 pdb=" NC HEC E 201 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 305 " -0.015 2.00e-02 2.50e+03 4.30e-02 4.16e+01 pdb=" C2C HEC A 305 " 0.118 2.00e-02 2.50e+03 pdb=" C3C HEC A 305 " -0.011 2.00e-02 2.50e+03 pdb=" C4C HEC A 305 " -0.005 2.00e-02 2.50e+03 pdb=" CAC HEC A 305 " -0.028 2.00e-02 2.50e+03 pdb=" CHC HEC A 305 " -0.022 2.00e-02 2.50e+03 pdb=" CHD HEC A 305 " 0.005 2.00e-02 2.50e+03 pdb=" CMC HEC A 305 " -0.033 2.00e-02 2.50e+03 pdb=" NC HEC A 305 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 303 " 0.015 2.00e-02 2.50e+03 3.77e-02 3.21e+01 pdb=" C2C HEC A 303 " -0.102 2.00e-02 2.50e+03 pdb=" C3C HEC A 303 " 0.009 2.00e-02 2.50e+03 pdb=" C4C HEC A 303 " -0.006 2.00e-02 2.50e+03 pdb=" CAC HEC A 303 " 0.030 2.00e-02 2.50e+03 pdb=" CHC HEC A 303 " 0.026 2.00e-02 2.50e+03 pdb=" CHD HEC A 303 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEC A 303 " 0.023 2.00e-02 2.50e+03 pdb=" NC HEC A 303 " 0.003 2.00e-02 2.50e+03 ... (remaining 3336 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 213 2.56 - 3.15: 15444 3.15 - 3.73: 31842 3.73 - 4.32: 46970 4.32 - 4.90: 75982 Nonbonded interactions: 170451 Sorted by model distance: nonbonded pdb=" NE2 HIS A 225 " pdb="FE HEC A 301 " model vdw 1.981 3.080 nonbonded pdb=" NE2 HIS A 66 " pdb="FE HEC A 305 " model vdw 2.003 3.080 nonbonded pdb=" NE2 HIS A 140 " pdb="FE HEC A 302 " model vdw 2.024 3.080 nonbonded pdb=" NE2 HIS A 63 " pdb="FE HEC A 304 " model vdw 2.131 3.080 nonbonded pdb=" OG1 THR B 145 " pdb=" OE1 GLN B 150 " model vdw 2.168 3.040 ... (remaining 170446 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=1.00 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: 0.680 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.790 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.027 1.984 19410 Z= 1.305 Angle : 1.478 74.167 26567 Z= 0.557 Chirality : 0.262 13.720 2856 Planarity : 0.006 0.074 3339 Dihedral : 15.691 129.306 6821 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 0.21 % Allowed : 7.43 % Favored : 92.36 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.41 (0.14), residues: 2317 helix: -4.11 (0.09), residues: 1037 sheet: -4.01 (0.31), residues: 164 loop : -2.91 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 903 TYR 0.020 0.002 TYR A 134 PHE 0.022 0.002 PHE C 266 TRP 0.028 0.001 TRP C 170 HIS 0.006 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.02507 (19374) covalent geometry : angle 1.20547 (26522) hydrogen bonds : bond 0.27775 ( 678) hydrogen bonds : angle 11.88879 ( 1944) metal coordination : bond 0.26090 ( 15) metal coordination : angle 20.80558 ( 45) Misc. bond : bond 0.14846 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 300 time to evaluate : 0.670 Fit side-chains REVERT: A 205 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7900 (ttp80) REVERT: A 210 TYR cc_start: 0.8940 (m-10) cc_final: 0.8691 (m-10) REVERT: B 83 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7923 (mttp) REVERT: B 223 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8638 (mttp) REVERT: B 252 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7540 (ttp-110) REVERT: B 541 VAL cc_start: 0.9141 (p) cc_final: 0.8890 (t) REVERT: B 988 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8540 (mtpt) REVERT: D 132 MET cc_start: 0.7545 (tmm) cc_final: 0.7177 (tmm) REVERT: E 84 ASP cc_start: 0.8036 (p0) cc_final: 0.7161 (p0) REVERT: F 388 TYR cc_start: 0.8467 (p90) cc_final: 0.8216 (p90) outliers start: 4 outliers final: 2 residues processed: 303 average time/residue: 0.1652 time to fit residues: 73.5334 Evaluate side-chains 246 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 862 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 100 GLN A 127 HIS A 156 GLN A 190 ASN A 198 ASN A 199 GLN B 279 GLN B 294 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN B 602 GLN B 625 ASN B 654 HIS B 816 ASN B 874 ASN B 955 GLN B 975 GLN ** B 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 365 GLN E 107 GLN E 181 HIS ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS F 68 HIS F 176 GLN F 249 HIS F 386 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.112804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.100381 restraints weight = 23969.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.099889 restraints weight = 28632.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.100924 restraints weight = 25302.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.100915 restraints weight = 17752.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.100837 restraints weight = 18128.240| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.691 19410 Z= 0.236 Angle : 1.367 76.978 26567 Z= 0.436 Chirality : 0.054 1.477 2856 Planarity : 0.006 0.066 3339 Dihedral : 9.377 103.317 2655 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 2.18 % Allowed : 12.01 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.15), residues: 2317 helix: -2.54 (0.13), residues: 1070 sheet: -3.66 (0.32), residues: 162 loop : -2.60 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 910 TYR 0.017 0.002 TYR A 134 PHE 0.017 0.002 PHE F 267 TRP 0.013 0.001 TRP F 284 HIS 0.006 0.001 HIS B 548 Details of bonding type rmsd covalent geometry : bond 0.00526 (19374) covalent geometry : angle 1.02862 (26522) hydrogen bonds : bond 0.04550 ( 678) hydrogen bonds : angle 6.33070 ( 1944) metal coordination : bond 0.02279 ( 15) metal coordination : angle 21.89164 ( 45) Misc. bond : bond 0.20784 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 269 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 150 GLN cc_start: 0.9272 (tp40) cc_final: 0.9019 (mm-40) REVERT: B 223 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8609 (mttp) REVERT: B 820 MET cc_start: 0.8680 (ttp) cc_final: 0.8417 (ttp) REVERT: B 988 LYS cc_start: 0.8755 (mmtt) cc_final: 0.8495 (mtpt) REVERT: F 388 TYR cc_start: 0.8384 (p90) cc_final: 0.8142 (p90) outliers start: 42 outliers final: 27 residues processed: 294 average time/residue: 0.1453 time to fit residues: 65.2277 Evaluate side-chains 266 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 185 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 211 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 198 ASN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN B 816 ASN B 966 GLN ** B 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 365 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.116371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.104436 restraints weight = 23887.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.103548 restraints weight = 24597.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.103892 restraints weight = 21880.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.104008 restraints weight = 19171.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.104061 restraints weight = 17964.008| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.567 19410 Z= 0.153 Angle : 1.225 84.763 26567 Z= 0.377 Chirality : 0.052 1.429 2856 Planarity : 0.005 0.063 3339 Dihedral : 8.696 85.089 2655 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 2.70 % Allowed : 14.45 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.16), residues: 2317 helix: -1.57 (0.14), residues: 1083 sheet: -3.51 (0.32), residues: 161 loop : -2.35 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 320 TYR 0.016 0.001 TYR A 134 PHE 0.016 0.001 PHE F 373 TRP 0.012 0.001 TRP F 284 HIS 0.005 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00346 (19374) covalent geometry : angle 0.86745 (26522) hydrogen bonds : bond 0.03980 ( 678) hydrogen bonds : angle 5.62566 ( 1944) metal coordination : bond 0.01104 ( 15) metal coordination : angle 21.04615 ( 45) Misc. bond : bond 0.16066 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 255 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 223 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8505 (mttp) REVERT: B 300 GLU cc_start: 0.8008 (pt0) cc_final: 0.7770 (pt0) REVERT: B 317 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7288 (ttp-110) REVERT: B 820 MET cc_start: 0.8544 (ttp) cc_final: 0.8206 (ttp) REVERT: B 990 ARG cc_start: 0.9207 (tpp80) cc_final: 0.8345 (tpp80) REVERT: C 110 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7985 (mt) outliers start: 52 outliers final: 29 residues processed: 288 average time/residue: 0.1459 time to fit residues: 64.2858 Evaluate side-chains 263 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 348 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 104 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 155 optimal weight: 0.6980 chunk 162 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 198 ASN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 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 = 0.3085 r_free = 0.3085 target = 0.114581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.102404 restraints weight = 23981.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.101554 restraints weight = 26282.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.102037 restraints weight = 23572.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.102176 restraints weight = 20842.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.102234 restraints weight = 18530.596| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.592 19410 Z= 0.181 Angle : 1.189 83.648 26567 Z= 0.376 Chirality : 0.053 1.471 2856 Planarity : 0.005 0.062 3339 Dihedral : 8.501 79.933 2654 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 2.86 % Allowed : 15.80 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.17), residues: 2317 helix: -1.15 (0.15), residues: 1089 sheet: -3.37 (0.32), residues: 161 loop : -2.20 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 94 TYR 0.015 0.001 TYR A 134 PHE 0.016 0.001 PHE B 539 TRP 0.012 0.001 TRP F 284 HIS 0.005 0.001 HIS B 548 Details of bonding type rmsd covalent geometry : bond 0.00426 (19374) covalent geometry : angle 0.86974 (26522) hydrogen bonds : bond 0.03787 ( 678) hydrogen bonds : angle 5.33814 ( 1944) metal coordination : bond 0.01199 ( 15) metal coordination : angle 19.72660 ( 45) Misc. bond : bond 0.16861 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 251 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8236 (ttmm) REVERT: B 196 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7758 (tt) REVERT: B 223 LYS cc_start: 0.8729 (mtpt) cc_final: 0.8491 (mttp) REVERT: B 300 GLU cc_start: 0.8051 (pt0) cc_final: 0.7823 (pt0) REVERT: B 317 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.7322 (ttp-110) REVERT: B 820 MET cc_start: 0.8644 (ttp) cc_final: 0.8293 (ttp) REVERT: B 990 ARG cc_start: 0.9218 (tpp80) cc_final: 0.8363 (tpp80) REVERT: C 110 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8077 (mt) REVERT: D 132 MET cc_start: 0.7261 (tmm) cc_final: 0.7043 (ptm) REVERT: F 65 MET cc_start: 0.8918 (mtt) cc_final: 0.8691 (mtt) outliers start: 55 outliers final: 39 residues processed: 284 average time/residue: 0.1411 time to fit residues: 61.8406 Evaluate side-chains 276 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 348 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 3 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 160 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 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 = 0.3113 r_free = 0.3113 target = 0.116806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.105260 restraints weight = 23866.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.104562 restraints weight = 23871.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.104728 restraints weight = 21654.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.104825 restraints weight = 19166.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.104879 restraints weight = 17880.551| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.502 19410 Z= 0.154 Angle : 1.133 83.265 26567 Z= 0.364 Chirality : 0.052 1.483 2856 Planarity : 0.005 0.063 3339 Dihedral : 8.238 79.833 2654 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.48 % Allowed : 16.79 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.17), residues: 2317 helix: -0.80 (0.16), residues: 1073 sheet: -3.25 (0.32), residues: 172 loop : -2.10 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 110 TYR 0.013 0.001 TYR A 134 PHE 0.014 0.001 PHE C 433 TRP 0.011 0.001 TRP C 186 HIS 0.005 0.001 HIS E 181 Details of bonding type rmsd covalent geometry : bond 0.00357 (19374) covalent geometry : angle 0.85229 (26522) hydrogen bonds : bond 0.03566 ( 678) hydrogen bonds : angle 5.10858 ( 1944) metal coordination : bond 0.00874 ( 15) metal coordination : angle 18.14268 ( 45) Misc. bond : bond 0.14229 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 254 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8102 (ttt) REVERT: B 196 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7703 (tt) REVERT: B 223 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8433 (mttp) REVERT: B 317 ARG cc_start: 0.7999 (mtp-110) cc_final: 0.7189 (ttp-110) REVERT: B 387 GLN cc_start: 0.7920 (tp40) cc_final: 0.7310 (tp40) REVERT: B 549 ASP cc_start: 0.8055 (m-30) cc_final: 0.7843 (m-30) REVERT: B 739 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8153 (pp) REVERT: B 918 CYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8287 (t) REVERT: B 990 ARG cc_start: 0.9192 (tpp80) cc_final: 0.8296 (tpp80) REVERT: C 110 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8079 (mt) REVERT: C 160 MET cc_start: 0.7814 (mmm) cc_final: 0.7431 (tpt) REVERT: D 172 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7088 (tt) REVERT: F 65 MET cc_start: 0.8864 (mtt) cc_final: 0.8641 (mtt) REVERT: F 320 ARG cc_start: 0.8239 (tpp80) cc_final: 0.7809 (mmt90) outliers start: 67 outliers final: 44 residues processed: 300 average time/residue: 0.1448 time to fit residues: 66.8404 Evaluate side-chains 286 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 206 PHE Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 348 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 32 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 169 optimal weight: 0.0670 chunk 62 optimal weight: 0.3980 chunk 159 optimal weight: 8.9990 chunk 182 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 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 = 0.3125 r_free = 0.3125 target = 0.117770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.105159 restraints weight = 23673.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.104711 restraints weight = 28252.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.105057 restraints weight = 27243.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.105187 restraints weight = 22912.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.105271 restraints weight = 21140.879| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.467 19410 Z= 0.146 Angle : 1.104 83.633 26567 Z= 0.361 Chirality : 0.052 1.462 2856 Planarity : 0.005 0.062 3339 Dihedral : 8.072 80.605 2654 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.64 % Allowed : 17.15 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.17), residues: 2317 helix: -0.64 (0.16), residues: 1086 sheet: -3.14 (0.33), residues: 172 loop : -2.00 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 288 TYR 0.013 0.001 TYR A 134 PHE 0.014 0.001 PHE C 433 TRP 0.011 0.001 TRP B 600 HIS 0.004 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00337 (19374) covalent geometry : angle 0.84337 (26522) hydrogen bonds : bond 0.03459 ( 678) hydrogen bonds : angle 5.00322 ( 1944) metal coordination : bond 0.00769 ( 15) metal coordination : angle 17.34676 ( 45) Misc. bond : bond 0.12984 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 248 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 156 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8092 (ttt) REVERT: B 196 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7671 (tt) REVERT: B 223 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8411 (mttp) REVERT: B 317 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7177 (ttp-110) REVERT: B 387 GLN cc_start: 0.7848 (tp40) cc_final: 0.7263 (tp40) REVERT: B 549 ASP cc_start: 0.8022 (m-30) cc_final: 0.7726 (m-30) REVERT: B 739 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8132 (pp) REVERT: B 918 CYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8244 (t) REVERT: B 990 ARG cc_start: 0.9179 (tpp80) cc_final: 0.8304 (tpp80) REVERT: C 110 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8059 (mt) REVERT: C 160 MET cc_start: 0.7863 (mmm) cc_final: 0.7468 (tpt) REVERT: D 172 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7058 (tt) REVERT: F 65 MET cc_start: 0.8852 (mtt) cc_final: 0.8577 (mtp) REVERT: F 320 ARG cc_start: 0.8223 (tpp80) cc_final: 0.7878 (mmt90) outliers start: 70 outliers final: 53 residues processed: 299 average time/residue: 0.1401 time to fit residues: 65.0985 Evaluate side-chains 295 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 236 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 206 PHE Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 348 HIS Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 38 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 0.0050 chunk 157 optimal weight: 0.9990 chunk 192 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 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 = 0.3096 r_free = 0.3096 target = 0.115529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.105788 restraints weight = 23919.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.106035 restraints weight = 28414.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.104868 restraints weight = 20172.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.104897 restraints weight = 18828.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.104967 restraints weight = 16554.298| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.519 19410 Z= 0.181 Angle : 1.116 83.994 26567 Z= 0.370 Chirality : 0.053 1.460 2856 Planarity : 0.005 0.064 3339 Dihedral : 8.091 80.399 2654 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.79 % Allowed : 17.36 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.17), residues: 2317 helix: -0.53 (0.16), residues: 1080 sheet: -3.15 (0.33), residues: 172 loop : -1.98 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 110 TYR 0.013 0.001 TYR C 414 PHE 0.016 0.001 PHE A 167 TRP 0.012 0.001 TRP B 600 HIS 0.005 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00431 (19374) covalent geometry : angle 0.86355 (26522) hydrogen bonds : bond 0.03533 ( 678) hydrogen bonds : angle 4.99158 ( 1944) metal coordination : bond 0.01133 ( 15) metal coordination : angle 17.18584 ( 45) Misc. bond : bond 0.14916 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 245 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8397 (ttt) REVERT: B 223 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8436 (mttp) REVERT: B 317 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7182 (ttp-110) REVERT: B 387 GLN cc_start: 0.7845 (tp40) cc_final: 0.7243 (tp40) REVERT: B 549 ASP cc_start: 0.8061 (m-30) cc_final: 0.7709 (m-30) REVERT: B 918 CYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8351 (t) REVERT: B 990 ARG cc_start: 0.9190 (tpp80) cc_final: 0.8341 (tpp80) REVERT: C 110 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8095 (mt) REVERT: C 160 MET cc_start: 0.7839 (mmm) cc_final: 0.7451 (tpt) REVERT: D 172 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7062 (tt) REVERT: F 65 MET cc_start: 0.8875 (mtt) cc_final: 0.8619 (mtp) REVERT: F 320 ARG cc_start: 0.8270 (tpp80) cc_final: 0.7796 (mmt90) outliers start: 73 outliers final: 56 residues processed: 297 average time/residue: 0.1313 time to fit residues: 61.2313 Evaluate side-chains 296 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 236 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 206 PHE Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 110 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.118669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.107208 restraints weight = 23842.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.106065 restraints weight = 36794.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.106628 restraints weight = 30445.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.106841 restraints weight = 22133.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.106908 restraints weight = 21102.320| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.425 19410 Z= 0.145 Angle : 1.083 83.602 26567 Z= 0.359 Chirality : 0.052 1.470 2856 Planarity : 0.005 0.062 3339 Dihedral : 7.950 81.841 2654 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.74 % Allowed : 17.67 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.18), residues: 2317 helix: -0.38 (0.16), residues: 1085 sheet: -3.03 (0.33), residues: 170 loop : -1.92 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 110 TYR 0.012 0.001 TYR A 134 PHE 0.015 0.001 PHE A 167 TRP 0.013 0.001 TRP B 600 HIS 0.004 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00341 (19374) covalent geometry : angle 0.83927 (26522) hydrogen bonds : bond 0.03360 ( 678) hydrogen bonds : angle 4.90802 ( 1944) metal coordination : bond 0.00713 ( 15) metal coordination : angle 16.65659 ( 45) Misc. bond : bond 0.12041 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 255 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8301 (t0) cc_final: 0.7700 (p0) REVERT: B 156 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8031 (ttt) REVERT: B 196 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7662 (tt) REVERT: B 223 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8386 (mttp) REVERT: B 317 ARG cc_start: 0.7943 (mtp-110) cc_final: 0.7116 (ttp-110) REVERT: B 387 GLN cc_start: 0.7729 (tp40) cc_final: 0.7160 (tp40) REVERT: B 549 ASP cc_start: 0.7958 (m-30) cc_final: 0.7643 (m-30) REVERT: B 918 CYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8254 (t) REVERT: C 110 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8108 (mt) REVERT: C 160 MET cc_start: 0.7687 (mmm) cc_final: 0.7316 (tpt) REVERT: D 172 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6992 (tt) REVERT: F 65 MET cc_start: 0.8865 (mtt) cc_final: 0.8585 (mtp) REVERT: F 320 ARG cc_start: 0.8274 (tpp80) cc_final: 0.7795 (mmt90) outliers start: 72 outliers final: 61 residues processed: 307 average time/residue: 0.1374 time to fit residues: 66.0472 Evaluate side-chains 314 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 248 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 206 PHE Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 348 HIS Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 68 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.118674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.108263 restraints weight = 23803.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.108020 restraints weight = 35099.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.108518 restraints weight = 27376.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.108279 restraints weight = 19455.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.108477 restraints weight = 18169.792| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.430 19410 Z= 0.149 Angle : 1.081 83.637 26567 Z= 0.361 Chirality : 0.052 1.470 2856 Planarity : 0.005 0.062 3339 Dihedral : 7.910 82.422 2654 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.90 % Allowed : 17.78 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.18), residues: 2317 helix: -0.24 (0.16), residues: 1072 sheet: -2.97 (0.34), residues: 170 loop : -1.84 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 319 TYR 0.011 0.001 TYR C 414 PHE 0.014 0.001 PHE A 61 TRP 0.014 0.001 TRP B 600 HIS 0.005 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00352 (19374) covalent geometry : angle 0.84436 (26522) hydrogen bonds : bond 0.03346 ( 678) hydrogen bonds : angle 4.88184 ( 1944) metal coordination : bond 0.00765 ( 15) metal coordination : angle 16.42952 ( 45) Misc. bond : bond 0.11952 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 251 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ARG cc_start: 0.4873 (mtm-85) cc_final: 0.4600 (mtm180) REVERT: A 190 ASN cc_start: 0.8224 (t0) cc_final: 0.7788 (p0) REVERT: B 156 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8012 (ttt) REVERT: B 196 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7671 (tt) REVERT: B 223 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8369 (mttp) REVERT: B 317 ARG cc_start: 0.7939 (mtp-110) cc_final: 0.7119 (ttp-110) REVERT: B 387 GLN cc_start: 0.7673 (tp40) cc_final: 0.7139 (tp40) REVERT: B 549 ASP cc_start: 0.7976 (m-30) cc_final: 0.7645 (m-30) REVERT: B 918 CYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8274 (t) REVERT: C 110 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8116 (mt) REVERT: C 160 MET cc_start: 0.7676 (mmm) cc_final: 0.7292 (tpt) REVERT: D 85 MET cc_start: 0.8277 (mmm) cc_final: 0.8015 (tpt) REVERT: D 172 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6923 (tt) REVERT: F 65 MET cc_start: 0.8865 (mtt) cc_final: 0.8579 (mtp) REVERT: F 320 ARG cc_start: 0.8281 (tpp80) cc_final: 0.7786 (mmt90) outliers start: 75 outliers final: 63 residues processed: 305 average time/residue: 0.1369 time to fit residues: 65.4576 Evaluate side-chains 316 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 248 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 206 PHE Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 89 optimal weight: 2.9990 chunk 129 optimal weight: 0.0970 chunk 211 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 199 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN F 353 HIS F 386 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.120903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.110801 restraints weight = 23850.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.110976 restraints weight = 32439.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.111107 restraints weight = 22947.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.110906 restraints weight = 17531.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.111079 restraints weight = 16066.075| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.382 19410 Z= 0.138 Angle : 1.059 83.385 26567 Z= 0.357 Chirality : 0.052 1.482 2856 Planarity : 0.004 0.062 3339 Dihedral : 7.816 84.171 2654 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.69 % Allowed : 18.04 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.18), residues: 2317 helix: -0.07 (0.16), residues: 1066 sheet: -2.87 (0.34), residues: 170 loop : -1.77 (0.20), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 319 TYR 0.012 0.001 TYR C 349 PHE 0.015 0.001 PHE A 61 TRP 0.015 0.001 TRP B 600 HIS 0.004 0.001 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00321 (19374) covalent geometry : angle 0.83625 (26522) hydrogen bonds : bond 0.03252 ( 678) hydrogen bonds : angle 4.81929 ( 1944) metal coordination : bond 0.00684 ( 15) metal coordination : angle 15.81935 ( 45) Misc. bond : bond 0.10317 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 263 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ARG cc_start: 0.4699 (mtm-85) cc_final: 0.4482 (mtm-85) REVERT: A 190 ASN cc_start: 0.8151 (t0) cc_final: 0.7877 (p0) REVERT: B 133 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7267 (mm-30) REVERT: B 156 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7960 (ttt) REVERT: B 196 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7730 (tt) REVERT: B 317 ARG cc_start: 0.7914 (mtp-110) cc_final: 0.7130 (ttp-110) REVERT: B 387 GLN cc_start: 0.7650 (tp40) cc_final: 0.7168 (tp40) REVERT: B 549 ASP cc_start: 0.7912 (m-30) cc_final: 0.7593 (m-30) REVERT: B 649 TRP cc_start: 0.9024 (t-100) cc_final: 0.8728 (t-100) REVERT: B 918 CYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8253 (t) REVERT: C 110 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8089 (mt) REVERT: C 160 MET cc_start: 0.7539 (mmm) cc_final: 0.7182 (tpt) REVERT: D 100 ASN cc_start: 0.8913 (t0) cc_final: 0.8632 (t0) REVERT: D 172 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6881 (tt) REVERT: F 46 TYR cc_start: 0.8752 (t80) cc_final: 0.8481 (t80) REVERT: F 65 MET cc_start: 0.8833 (mtt) cc_final: 0.8556 (mtp) outliers start: 71 outliers final: 57 residues processed: 313 average time/residue: 0.1378 time to fit residues: 67.2157 Evaluate side-chains 314 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 252 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 880 ASP Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 206 PHE Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 348 HIS Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 31 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 65 optimal weight: 0.0970 chunk 59 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 0.0570 chunk 213 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 ASN ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.123020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.113104 restraints weight = 23752.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.113185 restraints weight = 32098.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.112900 restraints weight = 22867.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.112765 restraints weight = 17834.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.112913 restraints weight = 16227.286| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.354 19410 Z= 0.132 Angle : 1.044 83.133 26567 Z= 0.357 Chirality : 0.052 1.499 2856 Planarity : 0.005 0.061 3339 Dihedral : 7.736 85.720 2654 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.38 % Allowed : 18.61 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.18), residues: 2317 helix: 0.05 (0.16), residues: 1061 sheet: -2.80 (0.35), residues: 170 loop : -1.72 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 94 TYR 0.009 0.001 TYR B 157 PHE 0.014 0.001 PHE A 167 TRP 0.019 0.001 TRP A 193 HIS 0.004 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00306 (19374) covalent geometry : angle 0.83604 (26522) hydrogen bonds : bond 0.03211 ( 678) hydrogen bonds : angle 4.73589 ( 1944) metal coordination : bond 0.00505 ( 15) metal coordination : angle 15.21576 ( 45) Misc. bond : bond 0.09257 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2686.49 seconds wall clock time: 47 minutes 40.29 seconds (2860.29 seconds total)