Starting phenix.real_space_refine on Sat Jul 4 18:44:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dxe_30906/07_2026/7dxe_30906.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dxe_30906/07_2026/7dxe_30906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dxe_30906/07_2026/7dxe_30906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dxe_30906/07_2026/7dxe_30906.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7dxe_30906/07_2026/7dxe_30906.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dxe_30906/07_2026/7dxe_30906.cif" model { file = "/net/cci-nas-00/data/ceres_data/7dxe_30906/07_2026/7dxe_30906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dxe_30906/07_2026/7dxe_30906.cif" } resolution = 3.2 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= 0.015 sd= 0.131 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 Zn 4 6.06 5 S 112 5.16 5 C 14708 2.51 5 N 3544 2.21 5 O 3912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22280 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5434 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 26, 'TRANS': 658} Chain breaks: 4 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 6, 'ASP:plan': 9, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "B" Number of atoms: 5434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5434 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 26, 'TRANS': 658} Chain breaks: 4 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 6, 'ASP:plan': 9, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 136 Unusual residues: {' ZN': 1, '98R': 1, 'POV': 1, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'98R:plan-4': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 136 Unusual residues: {' ZN': 1, '98R': 1, 'POV': 1, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'98R:plan-4': 1} Unresolved non-hydrogen planarities: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6645 SG CYS A 182 86.145 23.760 58.138 1.00188.23 S ATOM 6660 SG CYS A 184 88.564 23.555 55.319 1.00186.39 S ATOM 6678 SG CYS A 187 87.207 27.048 55.640 1.00178.79 S ATOM 12079 SG CYS B 182 37.181 99.560 58.138 1.00188.23 S ATOM 12094 SG CYS B 184 34.763 99.766 55.319 1.00186.39 S ATOM 12112 SG CYS B 187 36.119 96.273 55.639 1.00178.79 S Restraints were copied for chains: C, D Time building chain proxies: 10.52, per 1000 atoms: 0.47 Number of scatterers: 22280 At special positions: 0 Unit cell: (124.355, 124.355, 145.255, 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) Zn 4 29.99 S 112 16.00 O 3912 8.00 N 3544 7.00 C 14708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.53 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" ND1 HIS A 178 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 187 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 184 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 182 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" ND1 HIS B 178 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 187 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 184 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 182 " pdb=" ZN C 904 " pdb="ZN ZN C 904 " - pdb=" ND1 HIS C 178 " pdb="ZN ZN C 904 " - pdb=" SG CYS C 187 " pdb="ZN ZN C 904 " - pdb=" SG CYS C 184 " pdb="ZN ZN C 904 " - pdb=" SG CYS C 182 " pdb=" ZN D 902 " pdb="ZN ZN D 902 " - pdb=" ND1 HIS D 178 " pdb="ZN ZN D 902 " - pdb=" SG CYS D 187 " pdb="ZN ZN D 902 " - pdb=" SG CYS D 184 " pdb="ZN ZN D 902 " - pdb=" SG CYS D 182 " Number of angles added : 12 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5248 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 0 sheets defined 76.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'D' and resid 25 through 38 removed outlier: 3.580A pdb=" N ALA D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 48 Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.824A pdb=" N ASN D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 83 Processing helix chain 'D' and resid 89 through 100 Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 112 through 117 removed outlier: 3.758A pdb=" N ALA D 117 " --> pdb=" O PRO D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 159 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 184 through 193 removed outlier: 3.764A pdb=" N HIS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 210 Processing helix chain 'D' and resid 211 through 219 removed outlier: 4.480A pdb=" N SER D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 241 removed outlier: 3.555A pdb=" N THR D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 264 Processing helix chain 'D' and resid 267 through 276 Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.618A pdb=" N VAL D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.955A pdb=" N GLN D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.501A pdb=" N GLU D 331 " --> pdb=" O GLY D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 355 Proline residue: D 349 - end of helix Processing helix chain 'D' and resid 356 through 360 Proline residue: D 359 - end of helix No H-bonds generated for 'chain 'D' and resid 356 through 360' Processing helix chain 'D' and resid 361 through 369 removed outlier: 3.717A pdb=" N LYS D 365 " --> pdb=" O SER D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 392 removed outlier: 3.841A pdb=" N ALA D 392 " --> pdb=" O LEU D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 423 through 448 Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.638A pdb=" N LEU D 454 " --> pdb=" O ARG D 450 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN D 455 " --> pdb=" O GLU D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 493 Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 510 through 512 No H-bonds generated for 'chain 'D' and resid 510 through 512' Processing helix chain 'D' and resid 521 through 538 Processing helix chain 'D' and resid 539 through 548 removed outlier: 4.087A pdb=" N LEU D 545 " --> pdb=" O ALA D 542 " (cutoff:3.500A) Proline residue: D 546 - end of helix Processing helix chain 'D' and resid 551 through 588 removed outlier: 4.291A pdb=" N LYS D 567 " --> pdb=" O LYS D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 591 No H-bonds generated for 'chain 'D' and resid 589 through 591' Processing helix chain 'D' and resid 601 through 612 Processing helix chain 'D' and resid 628 through 662 removed outlier: 3.891A pdb=" N GLU D 632 " --> pdb=" O HIS D 628 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR D 662 " --> pdb=" O ILE D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 686 removed outlier: 3.648A pdb=" N TRP D 673 " --> pdb=" O SER D 669 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR D 684 " --> pdb=" O LEU D 680 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP D 686 " --> pdb=" O LEU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 785 Processing helix chain 'A' and resid 25 through 38 removed outlier: 3.580A pdb=" N ALA A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 64 through 72 removed outlier: 3.824A pdb=" N ASN A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.758A pdb=" N ALA A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 160 through 170 Processing helix chain 'A' and resid 184 through 193 removed outlier: 3.764A pdb=" N HIS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 210 Processing helix chain 'A' and resid 211 through 219 removed outlier: 4.480A pdb=" N SER A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.556A pdb=" N THR A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 264 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.618A pdb=" N VAL A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.955A pdb=" N GLN A 317 " --> pdb=" O ASN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.503A pdb=" N GLU A 331 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 355 Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 356 through 360 Proline residue: A 359 - end of helix No H-bonds generated for 'chain 'A' and resid 356 through 360' Processing helix chain 'A' and resid 361 through 369 removed outlier: 3.718A pdb=" N LYS A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 392 removed outlier: 3.841A pdb=" N ALA A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 423 through 448 Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.638A pdb=" N LEU A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 493 Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 521 through 538 Processing helix chain 'A' and resid 539 through 548 removed outlier: 4.087A pdb=" N LEU A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Proline residue: A 546 - end of helix Processing helix chain 'A' and resid 551 through 588 removed outlier: 4.291A pdb=" N LYS A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 601 through 612 Processing helix chain 'A' and resid 628 through 662 removed outlier: 3.891A pdb=" N GLU A 632 " --> pdb=" O HIS A 628 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR A 662 " --> pdb=" O ILE A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.648A pdb=" N TRP A 673 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 785 Processing helix chain 'B' and resid 25 through 38 removed outlier: 3.580A pdb=" N ALA B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 48 Processing helix chain 'B' and resid 64 through 72 removed outlier: 3.824A pdb=" N ASN B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 83 Processing helix chain 'B' and resid 89 through 100 Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.758A pdb=" N ALA B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 184 through 193 removed outlier: 3.765A pdb=" N HIS B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 210 Processing helix chain 'B' and resid 211 through 219 removed outlier: 4.480A pdb=" N SER B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.556A pdb=" N THR B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 264 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.618A pdb=" N VAL B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.956A pdb=" N GLN B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.501A pdb=" N GLU B 331 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 355 Proline residue: B 349 - end of helix Processing helix chain 'B' and resid 356 through 360 Proline residue: B 359 - end of helix No H-bonds generated for 'chain 'B' and resid 356 through 360' Processing helix chain 'B' and resid 361 through 369 removed outlier: 3.719A pdb=" N LYS B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 392 removed outlier: 3.841A pdb=" N ALA B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 Processing helix chain 'B' and resid 423 through 448 Processing helix chain 'B' and resid 448 through 455 removed outlier: 3.639A pdb=" N LEU B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 493 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 521 through 538 Processing helix chain 'B' and resid 539 through 548 removed outlier: 4.087A pdb=" N LEU B 545 " --> pdb=" O ALA B 542 " (cutoff:3.500A) Proline residue: B 546 - end of helix Processing helix chain 'B' and resid 551 through 588 removed outlier: 4.291A pdb=" N LYS B 567 " --> pdb=" O LYS B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 591 No H-bonds generated for 'chain 'B' and resid 589 through 591' Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 628 through 662 removed outlier: 3.891A pdb=" N GLU B 632 " --> pdb=" O HIS B 628 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR B 662 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.648A pdb=" N TRP B 673 " --> pdb=" O SER B 669 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 684 " --> pdb=" O LEU B 680 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP B 686 " --> pdb=" O LEU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 785 Processing helix chain 'C' and resid 25 through 38 removed outlier: 3.580A pdb=" N ALA C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 48 Processing helix chain 'C' and resid 64 through 72 removed outlier: 3.824A pdb=" N ASN C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 83 Processing helix chain 'C' and resid 89 through 100 Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 112 through 117 removed outlier: 3.758A pdb=" N ALA C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 Processing helix chain 'C' and resid 160 through 170 Processing helix chain 'C' and resid 184 through 193 removed outlier: 3.765A pdb=" N HIS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 210 Processing helix chain 'C' and resid 211 through 219 removed outlier: 4.480A pdb=" N SER C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 241 removed outlier: 3.556A pdb=" N THR C 225 " --> pdb=" O ASP C 221 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 264 Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.618A pdb=" N VAL C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 323 removed outlier: 3.955A pdb=" N GLN C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 331 removed outlier: 3.502A pdb=" N GLU C 331 " --> pdb=" O GLY C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 355 Proline residue: C 349 - end of helix Processing helix chain 'C' and resid 356 through 360 Proline residue: C 359 - end of helix No H-bonds generated for 'chain 'C' and resid 356 through 360' Processing helix chain 'C' and resid 361 through 369 removed outlier: 3.718A pdb=" N LYS C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 392 removed outlier: 3.841A pdb=" N ALA C 392 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 423 through 448 Processing helix chain 'C' and resid 448 through 455 removed outlier: 3.639A pdb=" N LEU C 454 " --> pdb=" O ARG C 450 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 493 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 510 through 512 No H-bonds generated for 'chain 'C' and resid 510 through 512' Processing helix chain 'C' and resid 521 through 538 Processing helix chain 'C' and resid 539 through 548 removed outlier: 4.087A pdb=" N LEU C 545 " --> pdb=" O ALA C 542 " (cutoff:3.500A) Proline residue: C 546 - end of helix Processing helix chain 'C' and resid 551 through 588 removed outlier: 4.291A pdb=" N LYS C 567 " --> pdb=" O LYS C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 591 No H-bonds generated for 'chain 'C' and resid 589 through 591' Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 628 through 662 removed outlier: 3.891A pdb=" N GLU C 632 " --> pdb=" O HIS C 628 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR C 662 " --> pdb=" O ILE C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 686 removed outlier: 3.648A pdb=" N TRP C 673 " --> pdb=" O SER C 669 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP C 686 " --> pdb=" O LEU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 785 1416 hydrogen bonds defined for protein. 4200 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: 3.98 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4757 1.33 - 1.45: 4843 1.45 - 1.57: 12996 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 22780 Sorted by residual: bond pdb=" C21 POV A 901 " pdb=" O21 POV A 901 " ideal model delta sigma weight residual 1.330 1.456 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C21 POV B 904 " pdb=" O21 POV B 904 " ideal model delta sigma weight residual 1.330 1.456 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C21 POV C 901 " pdb=" O21 POV C 901 " ideal model delta sigma weight residual 1.330 1.456 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C21 POV D 904 " pdb=" O21 POV D 904 " ideal model delta sigma weight residual 1.330 1.456 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C31 POV D 904 " pdb=" O31 POV D 904 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.95e+01 ... (remaining 22775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 30053 2.01 - 4.01: 528 4.01 - 6.02: 187 6.02 - 8.02: 60 8.02 - 10.03: 32 Bond angle restraints: 30860 Sorted by residual: angle pdb=" C ILE C 357 " pdb=" N ALA C 358 " pdb=" CA ALA C 358 " ideal model delta sigma weight residual 120.09 124.71 -4.62 1.25e+00 6.40e-01 1.36e+01 angle pdb=" C ILE B 357 " pdb=" N ALA B 358 " pdb=" CA ALA B 358 " ideal model delta sigma weight residual 120.09 124.71 -4.62 1.25e+00 6.40e-01 1.36e+01 angle pdb=" C ILE A 357 " pdb=" N ALA A 358 " pdb=" CA ALA A 358 " ideal model delta sigma weight residual 120.09 124.71 -4.62 1.25e+00 6.40e-01 1.36e+01 angle pdb=" C ILE D 357 " pdb=" N ALA D 358 " pdb=" CA ALA D 358 " ideal model delta sigma weight residual 120.09 124.71 -4.62 1.25e+00 6.40e-01 1.36e+01 angle pdb=" N TRP D 517 " pdb=" CA TRP D 517 " pdb=" C TRP D 517 " ideal model delta sigma weight residual 110.24 115.35 -5.11 1.41e+00 5.03e-01 1.31e+01 ... (remaining 30855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.89: 12732 23.89 - 47.77: 692 47.77 - 71.66: 92 71.66 - 95.54: 32 95.54 - 119.43: 24 Dihedral angle restraints: 13572 sinusoidal: 5480 harmonic: 8092 Sorted by residual: dihedral pdb=" CA TYR C 138 " pdb=" C TYR C 138 " pdb=" N ASP C 139 " pdb=" CA ASP C 139 " ideal model delta harmonic sigma weight residual 180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA TYR A 138 " pdb=" C TYR A 138 " pdb=" N ASP A 139 " pdb=" CA ASP A 139 " ideal model delta harmonic sigma weight residual 180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA TYR B 138 " pdb=" C TYR B 138 " pdb=" N ASP B 139 " pdb=" CA ASP B 139 " ideal model delta harmonic sigma weight residual -180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 13569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2930 0.056 - 0.112: 546 0.112 - 0.168: 32 0.168 - 0.224: 12 0.224 - 0.281: 12 Chirality restraints: 3532 Sorted by residual: chirality pdb=" C2 98R D 905 " pdb=" C1 98R D 905 " pdb=" C3 98R D 905 " pdb=" O2 98R D 905 " both_signs ideal model delta sigma weight residual False -2.31 -2.59 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C2 98R C 902 " pdb=" C1 98R C 902 " pdb=" C3 98R C 902 " pdb=" O2 98R C 902 " both_signs ideal model delta sigma weight residual False -2.31 -2.59 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C2 98R B 905 " pdb=" C1 98R B 905 " pdb=" C3 98R B 905 " pdb=" O2 98R B 905 " both_signs ideal model delta sigma weight residual False -2.31 -2.59 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 3529 not shown) Planarity restraints: 3792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 518 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO D 519 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 519 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 519 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 518 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO B 519 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 519 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 519 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 518 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO C 519 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 519 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 519 " 0.018 5.00e-02 4.00e+02 ... (remaining 3789 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2301 2.75 - 3.28: 23391 3.28 - 3.82: 36140 3.82 - 4.36: 42068 4.36 - 4.90: 73638 Nonbonded interactions: 177538 Sorted by model distance: nonbonded pdb=" O PRO C 760 " pdb=" OG1 THR C 761 " model vdw 2.208 3.040 nonbonded pdb=" O PRO D 760 " pdb=" OG1 THR D 761 " model vdw 2.208 3.040 nonbonded pdb=" O PRO B 760 " pdb=" OG1 THR B 761 " model vdw 2.208 3.040 nonbonded pdb=" O PRO A 760 " pdb=" OG1 THR A 761 " model vdw 2.208 3.040 nonbonded pdb=" O ASN B 72 " pdb=" ND1 HIS B 74 " model vdw 2.310 3.120 ... (remaining 177533 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 785 or resid 903)) selection = (chain 'B' and (resid 22 through 785 or resid 903)) selection = (chain 'C' and (resid 22 through 785 or resid 903)) selection = (chain 'D' and (resid 22 through 785 or resid 903)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 29.620 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 22796 Z= 0.291 Angle : 0.838 12.668 30872 Z= 0.378 Chirality : 0.044 0.281 3532 Planarity : 0.004 0.033 3792 Dihedral : 15.814 119.429 8324 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.37 % Favored : 97.48 % Rotamer: Outliers : 0.35 % Allowed : 5.55 % Favored : 94.11 % 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: -0.46 (0.14), residues: 2700 helix: 0.37 (0.11), residues: 1872 sheet: None (None), residues: 0 loop : -1.74 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 769 TYR 0.011 0.001 TYR A 323 PHE 0.015 0.001 PHE C 568 TRP 0.014 0.002 TRP C 322 HIS 0.002 0.001 HIS C 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.28 (22780) covalent geometry : angle 0.80846 / 0.37 (30860) hydrogen bonds : bond 0.12945 / 9.03 ( 1416) hydrogen bonds : angle 4.64430 / 3.34 ( 4200) metal coordination : bond 0.08403 / 5.43 ( 16) metal coordination : angle 11.28676 / 6.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 335 time to evaluate : 0.871 Fit side-chains REVERT: D 104 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7883 (mtm180) REVERT: D 120 ARG cc_start: 0.7376 (mmt90) cc_final: 0.7113 (mtt-85) REVERT: D 563 LYS cc_start: 0.6912 (mmtt) cc_final: 0.6626 (ttmm) REVERT: D 583 MET cc_start: 0.7761 (mmm) cc_final: 0.7214 (mmt) REVERT: D 646 MET cc_start: 0.7403 (mmt) cc_final: 0.6912 (mmt) REVERT: A 104 ARG cc_start: 0.8262 (mtt180) cc_final: 0.7884 (mtm180) REVERT: A 120 ARG cc_start: 0.7332 (mmt90) cc_final: 0.7090 (mtt-85) REVERT: A 563 LYS cc_start: 0.6903 (mmtt) cc_final: 0.6618 (ttmm) REVERT: A 583 MET cc_start: 0.7772 (mmm) cc_final: 0.7232 (mmt) REVERT: A 646 MET cc_start: 0.7397 (mmt) cc_final: 0.6929 (mmt) REVERT: B 104 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7857 (mtm180) REVERT: B 120 ARG cc_start: 0.7322 (mmt90) cc_final: 0.7072 (mtt-85) REVERT: B 563 LYS cc_start: 0.6908 (mmtt) cc_final: 0.6619 (ttmm) REVERT: B 583 MET cc_start: 0.7816 (mmm) cc_final: 0.7263 (mmt) REVERT: B 646 MET cc_start: 0.7406 (mmt) cc_final: 0.6945 (mmt) REVERT: C 104 ARG cc_start: 0.8260 (mtt180) cc_final: 0.7874 (mtm180) REVERT: C 120 ARG cc_start: 0.7356 (mmt90) cc_final: 0.7111 (mtt-85) REVERT: C 563 LYS cc_start: 0.6906 (mmtt) cc_final: 0.6620 (ttmm) REVERT: C 583 MET cc_start: 0.7819 (mmm) cc_final: 0.7270 (mmt) REVERT: C 646 MET cc_start: 0.7405 (mmt) cc_final: 0.6906 (mmt) outliers start: 8 outliers final: 8 residues processed: 339 average time/residue: 0.1747 time to fit residues: 90.8121 Evaluate side-chains 226 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 218 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 554 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 ASN D 652 ASN D 659 ASN ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 652 ASN A 659 ASN ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 ASN B 652 ASN B 659 ASN ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 ASN C 652 ASN C 659 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.094885 restraints weight = 31996.365| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.93 r_work: 0.2978 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22796 Z= 0.167 Angle : 0.608 6.534 30872 Z= 0.314 Chirality : 0.040 0.140 3532 Planarity : 0.004 0.034 3792 Dihedral : 11.731 113.391 3280 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.33 % Favored : 97.52 % Rotamer: Outliers : 2.34 % Allowed : 9.88 % Favored : 87.78 % 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: 0.99 (0.16), residues: 2700 helix: 1.43 (0.11), residues: 1912 sheet: None (None), residues: 0 loop : -1.27 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 192 TYR 0.025 0.002 TYR A 452 PHE 0.014 0.001 PHE D 31 TRP 0.017 0.002 TRP B 322 HIS 0.003 0.001 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (22780) covalent geometry : angle 0.60650 / 0.31 (30860) hydrogen bonds : bond 0.05509 / 3.80 ( 1416) hydrogen bonds : angle 3.82069 / 2.74 ( 4200) metal coordination : bond 0.00386 / 0.27 ( 16) metal coordination : angle 2.10421 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 0.890 Fit side-chains REVERT: D 236 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8625 (tt) REVERT: D 563 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7655 (ttmm) REVERT: D 583 MET cc_start: 0.9330 (mmm) cc_final: 0.8821 (mmt) REVERT: A 236 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8617 (tt) REVERT: A 437 MET cc_start: 0.8673 (tpt) cc_final: 0.8411 (tpp) REVERT: A 563 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7645 (ttmm) REVERT: A 583 MET cc_start: 0.9332 (mmm) cc_final: 0.8827 (mmt) REVERT: B 563 LYS cc_start: 0.7978 (mmtt) cc_final: 0.7654 (ttmm) REVERT: B 583 MET cc_start: 0.9335 (mmm) cc_final: 0.8821 (mmt) REVERT: C 236 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8636 (tt) REVERT: C 437 MET cc_start: 0.8676 (tpt) cc_final: 0.8423 (tpp) REVERT: C 563 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7649 (ttmm) REVERT: C 583 MET cc_start: 0.9339 (mmm) cc_final: 0.8826 (mmt) outliers start: 54 outliers final: 34 residues processed: 251 average time/residue: 0.1579 time to fit residues: 63.2909 Evaluate side-chains 217 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 554 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 2 optimal weight: 8.9990 chunk 198 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 264 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 230 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 267 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 ASN ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.089046 restraints weight = 32351.027| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.33 r_work: 0.2887 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22796 Z= 0.176 Angle : 0.584 6.961 30872 Z= 0.303 Chirality : 0.039 0.117 3532 Planarity : 0.004 0.032 3792 Dihedral : 10.229 109.803 3280 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.63 % Favored : 97.22 % Rotamer: Outliers : 2.17 % Allowed : 12.00 % Favored : 85.83 % 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: 1.38 (0.16), residues: 2700 helix: 1.76 (0.12), residues: 1936 sheet: None (None), residues: 0 loop : -1.31 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 192 TYR 0.016 0.001 TYR B 452 PHE 0.015 0.001 PHE C 31 TRP 0.019 0.002 TRP C 322 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (22780) covalent geometry : angle 0.58302 / 0.30 (30860) hydrogen bonds : bond 0.05371 / 3.70 ( 1416) hydrogen bonds : angle 3.68948 / 2.65 ( 4200) metal coordination : bond 0.00473 / 0.33 ( 16) metal coordination : angle 1.72253 / 1.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 236 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8485 (tt) REVERT: D 437 MET cc_start: 0.8622 (tpt) cc_final: 0.8387 (tpp) REVERT: D 563 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7514 (ttpp) REVERT: A 236 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8476 (tt) REVERT: A 437 MET cc_start: 0.8618 (tpt) cc_final: 0.8391 (tpp) REVERT: A 563 LYS cc_start: 0.7838 (mmtt) cc_final: 0.7499 (ttpp) REVERT: B 437 MET cc_start: 0.8614 (tpt) cc_final: 0.8387 (tpp) REVERT: B 563 LYS cc_start: 0.7904 (mmtt) cc_final: 0.7524 (ttpp) REVERT: C 236 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8486 (tt) REVERT: C 437 MET cc_start: 0.8622 (tpt) cc_final: 0.8400 (tpp) REVERT: C 563 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7521 (ttpp) outliers start: 50 outliers final: 36 residues processed: 233 average time/residue: 0.1114 time to fit residues: 43.7479 Evaluate side-chains 224 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 759 GLN Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain A residue 131 GLN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 759 GLN Chi-restraints excluded: chain C residue 761 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 172 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 136 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 413 GLN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 ASN A 413 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN B 413 GLN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN C 276 ASN C 413 GLN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.099244 restraints weight = 31787.881| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.79 r_work: 0.3055 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22796 Z= 0.136 Angle : 0.553 9.050 30872 Z= 0.284 Chirality : 0.038 0.114 3532 Planarity : 0.004 0.032 3792 Dihedral : 9.666 109.066 3280 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.56 % Favored : 97.30 % Rotamer: Outliers : 3.16 % Allowed : 12.65 % Favored : 84.19 % 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: 1.71 (0.16), residues: 2700 helix: 2.07 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -1.27 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.013 0.001 TYR A 452 PHE 0.012 0.001 PHE A 31 TRP 0.015 0.001 TRP C 322 HIS 0.004 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (22780) covalent geometry : angle 0.55236 / 0.28 (30860) hydrogen bonds : bond 0.04832 / 3.33 ( 1416) hydrogen bonds : angle 3.57353 / 2.56 ( 4200) metal coordination : bond 0.00425 / 0.30 ( 16) metal coordination : angle 1.27744 / 0.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 195 time to evaluate : 0.797 Fit side-chains REVERT: D 563 LYS cc_start: 0.7974 (mmtt) cc_final: 0.7659 (ttpp) REVERT: A 563 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7652 (ttpp) REVERT: B 563 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7652 (ttpp) REVERT: C 236 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8733 (tt) REVERT: C 563 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7648 (ttpp) outliers start: 73 outliers final: 40 residues processed: 252 average time/residue: 0.1246 time to fit residues: 53.9104 Evaluate side-chains 232 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 554 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 243 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 240 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 78 optimal weight: 0.0060 chunk 34 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 276 ASN ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 ASN A 276 ASN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN B 276 ASN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.100578 restraints weight = 31491.789| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.74 r_work: 0.3098 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22796 Z= 0.114 Angle : 0.554 15.973 30872 Z= 0.278 Chirality : 0.037 0.111 3532 Planarity : 0.004 0.034 3792 Dihedral : 9.268 109.829 3280 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.52 % Favored : 97.37 % Rotamer: Outliers : 3.08 % Allowed : 12.87 % Favored : 84.06 % 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: 1.95 (0.16), residues: 2700 helix: 2.18 (0.12), residues: 1936 sheet: None (None), residues: 0 loop : -1.11 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.011 0.001 TYR A 452 PHE 0.010 0.001 PHE A 31 TRP 0.012 0.001 TRP B 322 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (22780) covalent geometry : angle 0.55334 / 0.28 (30860) hydrogen bonds : bond 0.04444 / 3.06 ( 1416) hydrogen bonds : angle 3.46600 / 2.49 ( 4200) metal coordination : bond 0.00424 / 0.30 ( 16) metal coordination : angle 1.06869 / 0.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 203 time to evaluate : 0.874 Fit side-chains REVERT: D 186 ASP cc_start: 0.8150 (t0) cc_final: 0.7882 (t0) REVERT: D 563 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7692 (ttpp) REVERT: A 186 ASP cc_start: 0.8139 (t0) cc_final: 0.7873 (t0) REVERT: A 563 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7743 (ttpp) REVERT: B 186 ASP cc_start: 0.8153 (t0) cc_final: 0.7881 (t0) REVERT: B 563 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7752 (ttpp) REVERT: C 186 ASP cc_start: 0.8154 (t0) cc_final: 0.7838 (t0) REVERT: C 563 LYS cc_start: 0.8078 (mmtt) cc_final: 0.7739 (ttpp) outliers start: 71 outliers final: 51 residues processed: 268 average time/residue: 0.1216 time to fit residues: 55.6509 Evaluate side-chains 240 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 761 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 257 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 652 ASN D 759 GLN A 652 ASN A 659 ASN A 759 GLN B 652 ASN B 759 GLN C 652 ASN C 759 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.094019 restraints weight = 32195.548| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.75 r_work: 0.2991 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 22796 Z= 0.257 Angle : 0.655 16.336 30872 Z= 0.328 Chirality : 0.042 0.128 3532 Planarity : 0.004 0.034 3792 Dihedral : 9.358 105.330 3274 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.07 % Favored : 96.78 % Rotamer: Outliers : 3.42 % Allowed : 12.56 % Favored : 84.01 % 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: 1.73 (0.16), residues: 2700 helix: 1.97 (0.11), residues: 1912 sheet: None (None), residues: 0 loop : -0.93 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 773 TYR 0.010 0.002 TYR D 138 PHE 0.017 0.002 PHE B 572 TRP 0.021 0.002 TRP C 322 HIS 0.005 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.26 (22780) covalent geometry : angle 0.65378 / 0.33 (30860) hydrogen bonds : bond 0.05705 / 3.92 ( 1416) hydrogen bonds : angle 3.68748 / 2.64 ( 4200) metal coordination : bond 0.00215 / 0.15 ( 16) metal coordination : angle 1.69255 / 1.00 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 201 time to evaluate : 0.930 Fit side-chains REVERT: D 563 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7727 (ttpp) REVERT: A 563 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7748 (ttpp) REVERT: B 563 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7723 (ttpp) REVERT: C 563 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7718 (ttpp) outliers start: 79 outliers final: 57 residues processed: 265 average time/residue: 0.1292 time to fit residues: 58.3428 Evaluate side-chains 247 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 618 GLU Chi-restraints excluded: chain D residue 759 GLN Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 618 GLU Chi-restraints excluded: chain C residue 759 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 180 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 247 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 268 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 chunk 260 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 ASN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN B 759 GLN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.129388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.098288 restraints weight = 31650.562| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.74 r_work: 0.3063 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22796 Z= 0.123 Angle : 0.574 16.474 30872 Z= 0.285 Chirality : 0.037 0.111 3532 Planarity : 0.004 0.034 3792 Dihedral : 9.036 106.370 3272 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.30 % Favored : 97.67 % Rotamer: Outliers : 3.08 % Allowed : 13.65 % Favored : 83.28 % 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: 2.10 (0.16), residues: 2700 helix: 2.33 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -0.94 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 192 TYR 0.010 0.001 TYR A 410 PHE 0.009 0.001 PHE D 568 TRP 0.015 0.001 TRP C 322 HIS 0.003 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (22780) covalent geometry : angle 0.57413 / 0.29 (30860) hydrogen bonds : bond 0.04701 / 3.24 ( 1416) hydrogen bonds : angle 3.51553 / 2.52 ( 4200) metal coordination : bond 0.00438 / 0.31 ( 16) metal coordination : angle 1.00641 / 0.57 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 206 time to evaluate : 0.872 Fit side-chains REVERT: D 186 ASP cc_start: 0.8277 (t0) cc_final: 0.7948 (t0) REVERT: D 563 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7876 (ttpp) REVERT: A 186 ASP cc_start: 0.8263 (t0) cc_final: 0.7937 (t0) REVERT: A 563 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7846 (ttpp) REVERT: B 186 ASP cc_start: 0.8268 (t0) cc_final: 0.7938 (t0) REVERT: B 563 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7861 (ttpp) REVERT: C 186 ASP cc_start: 0.8259 (t0) cc_final: 0.7928 (t0) REVERT: C 563 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7859 (ttpp) outliers start: 71 outliers final: 44 residues processed: 261 average time/residue: 0.1301 time to fit residues: 57.8128 Evaluate side-chains 245 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 595 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 80 optimal weight: 2.9990 chunk 181 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 206 optimal weight: 7.9990 chunk 223 optimal weight: 0.0670 chunk 45 optimal weight: 0.0270 chunk 150 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 ASN D 759 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN A 659 ASN A 759 GLN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN B 759 GLN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN C 759 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099686 restraints weight = 31600.986| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.76 r_work: 0.3083 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 22796 Z= 0.115 Angle : 0.557 17.730 30872 Z= 0.278 Chirality : 0.037 0.128 3532 Planarity : 0.003 0.034 3792 Dihedral : 8.786 108.446 3272 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.64 % Allowed : 14.30 % Favored : 83.06 % 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: 2.28 (0.16), residues: 2700 helix: 2.39 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -0.74 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 192 TYR 0.009 0.001 TYR B 452 PHE 0.008 0.001 PHE A 568 TRP 0.014 0.001 TRP D 322 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (22780) covalent geometry : angle 0.55632 / 0.28 (30860) hydrogen bonds : bond 0.04385 / 3.02 ( 1416) hydrogen bonds : angle 3.42916 / 2.46 ( 4200) metal coordination : bond 0.00378 / 0.27 ( 16) metal coordination : angle 0.93710 / 0.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 218 time to evaluate : 0.873 Fit side-chains REVERT: D 186 ASP cc_start: 0.8236 (t0) cc_final: 0.7901 (t0) REVERT: D 563 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7695 (ttpp) REVERT: A 186 ASP cc_start: 0.8219 (t0) cc_final: 0.7884 (t0) REVERT: A 236 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8698 (tt) REVERT: A 563 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7714 (ttpp) REVERT: B 186 ASP cc_start: 0.8236 (t0) cc_final: 0.7908 (t0) REVERT: B 563 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7691 (ttpp) REVERT: C 236 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8696 (tt) REVERT: C 563 LYS cc_start: 0.8026 (mmtt) cc_final: 0.7692 (ttpp) outliers start: 61 outliers final: 41 residues processed: 262 average time/residue: 0.1355 time to fit residues: 59.3713 Evaluate side-chains 244 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 759 GLN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 759 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 77 optimal weight: 0.0870 chunk 133 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 178 optimal weight: 0.8980 chunk 207 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 204 optimal weight: 20.0000 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 652 ASN D 759 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN A 659 ASN A 759 GLN B 652 ASN B 759 GLN C 652 ASN C 759 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098090 restraints weight = 31858.552| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.78 r_work: 0.3035 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22796 Z= 0.160 Angle : 0.593 16.402 30872 Z= 0.293 Chirality : 0.038 0.117 3532 Planarity : 0.004 0.034 3792 Dihedral : 8.785 107.614 3272 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.51 % Allowed : 14.73 % Favored : 82.76 % 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: 2.18 (0.16), residues: 2700 helix: 2.31 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -0.77 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.010 0.001 TYR A 452 PHE 0.011 0.001 PHE A 568 TRP 0.014 0.001 TRP A 322 HIS 0.003 0.001 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (22780) covalent geometry : angle 0.59219 / 0.29 (30860) hydrogen bonds : bond 0.04724 / 3.25 ( 1416) hydrogen bonds : angle 3.47220 / 2.49 ( 4200) metal coordination : bond 0.00279 / 0.20 ( 16) metal coordination : angle 1.16765 / 0.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 204 time to evaluate : 0.993 Fit side-chains REVERT: D 186 ASP cc_start: 0.8240 (t0) cc_final: 0.7889 (t0) REVERT: D 563 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7704 (ttpt) REVERT: A 186 ASP cc_start: 0.8226 (t0) cc_final: 0.7879 (t0) REVERT: A 563 LYS cc_start: 0.8042 (mmtt) cc_final: 0.7703 (ttpt) REVERT: B 186 ASP cc_start: 0.8244 (t0) cc_final: 0.7895 (t0) REVERT: B 563 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7698 (ttpt) REVERT: C 563 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7671 (ttpt) outliers start: 58 outliers final: 49 residues processed: 247 average time/residue: 0.1256 time to fit residues: 53.0879 Evaluate side-chains 252 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 618 GLU Chi-restraints excluded: chain D residue 759 GLN Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 759 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 260 optimal weight: 0.0980 chunk 268 optimal weight: 0.9980 chunk 267 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 214 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 ASN D 759 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN A 759 GLN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN B 759 GLN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN C 759 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.099546 restraints weight = 31734.618| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.76 r_work: 0.3075 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22796 Z= 0.117 Angle : 0.580 18.631 30872 Z= 0.286 Chirality : 0.037 0.136 3532 Planarity : 0.003 0.035 3792 Dihedral : 8.627 108.521 3272 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.17 % Allowed : 15.25 % Favored : 82.58 % 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: 2.29 (0.16), residues: 2700 helix: 2.38 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -0.72 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.009 0.001 TYR C 410 PHE 0.008 0.001 PHE A 568 TRP 0.015 0.001 TRP A 322 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (22780) covalent geometry : angle 0.57979 / 0.29 (30860) hydrogen bonds : bond 0.04385 / 3.02 ( 1416) hydrogen bonds : angle 3.43072 / 2.46 ( 4200) metal coordination : bond 0.00347 / 0.25 ( 16) metal coordination : angle 0.86786 / 0.49 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 212 time to evaluate : 0.887 Fit side-chains REVERT: D 341 VAL cc_start: 0.8616 (t) cc_final: 0.8359 (t) REVERT: D 563 LYS cc_start: 0.8026 (mmtt) cc_final: 0.7709 (ttpt) REVERT: A 341 VAL cc_start: 0.8613 (t) cc_final: 0.8371 (t) REVERT: A 563 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7705 (ttpt) REVERT: B 563 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7713 (ttpt) REVERT: C 563 LYS cc_start: 0.8023 (mmtt) cc_final: 0.7706 (ttpt) outliers start: 50 outliers final: 46 residues processed: 247 average time/residue: 0.1234 time to fit residues: 52.2891 Evaluate side-chains 250 residues out of total 2424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 759 GLN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 574 MET Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 759 GLN Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 618 GLU Chi-restraints excluded: chain C residue 759 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 50 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 204 optimal weight: 20.0000 chunk 242 optimal weight: 0.8980 chunk 218 optimal weight: 4.9990 chunk 184 optimal weight: 0.0000 chunk 99 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 ASN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN A 659 ASN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN B 759 GLN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.130695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100247 restraints weight = 31743.207| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.79 r_work: 0.3065 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.212 22796 Z= 0.228 Angle : 0.858 59.160 30872 Z= 0.483 Chirality : 0.039 0.429 3532 Planarity : 0.005 0.151 3792 Dihedral : 8.624 108.517 3272 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.25 % Allowed : 15.25 % Favored : 82.50 % Cbeta Deviations : 0.04 % 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: 2.28 (0.16), residues: 2700 helix: 2.38 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -0.72 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 192 TYR 0.009 0.001 TYR C 410 PHE 0.009 0.001 PHE A 568 TRP 0.014 0.001 TRP A 322 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.23 (22780) covalent geometry : angle 0.85775 / 0.48 (30860) hydrogen bonds : bond 0.04396 / 3.03 ( 1416) hydrogen bonds : angle 3.43100 / 2.46 ( 4200) metal coordination : bond 0.00339 / 0.24 ( 16) metal coordination : angle 0.86758 / 0.49 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5091.92 seconds wall clock time: 88 minutes 16.37 seconds (5296.37 seconds total)