Starting phenix.real_space_refine on Fri Mar 6 09:18:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5d_10694/03_2026/6y5d_10694.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5d_10694/03_2026/6y5d_10694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y5d_10694/03_2026/6y5d_10694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5d_10694/03_2026/6y5d_10694.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y5d_10694/03_2026/6y5d_10694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5d_10694/03_2026/6y5d_10694.map" } resolution = 4.1 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= 0.006 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 612 5.49 5 S 54 5.16 5 C 17252 2.51 5 N 5588 2.21 5 O 6864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30372 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3119 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "J" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3154 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "K" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2980 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "L" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2980 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "M" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "N" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "O" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "P" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 698 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "Q" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 772 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "R" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 618 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "S" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 787 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "T" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "U" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3119 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "V" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3154 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-1': 2, 'PTD:plan-2': 2} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "O" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "S" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-1': 2, 'PTD:plan-2': 2} Unresolved non-hydrogen planarities: 4 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14165 SG CYS K 396 76.480 20.279 43.285 0.00566.57 S ATOM 14171 SG CYS K 397 78.707 19.449 46.231 0.00570.62 S ATOM 14230 SG CYS K 404 80.023 21.567 43.400 0.00566.15 S ATOM 17145 SG CYS L 396 99.066 112.815 22.367 0.00600.00 S ATOM 17151 SG CYS L 397 96.012 114.889 23.197 0.00600.00 S ATOM 17210 SG CYS L 404 95.615 111.456 21.678 0.00600.00 S Time building chain proxies: 6.56, per 1000 atoms: 0.22 Number of scatterers: 30372 At special positions: 0 Unit cell: (163.4, 157.38, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 54 16.00 P 612 15.00 O 6864 8.00 N 5588 7.00 C 17252 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 390 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 397 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 404 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 396 " pdb=" ZN L 601 " pdb="ZN ZN L 601 " - pdb=" NE2 HIS L 390 " pdb="ZN ZN L 601 " - pdb=" SG CYS L 397 " pdb="ZN ZN L 601 " - pdb=" SG CYS L 404 " pdb="ZN ZN L 601 " - pdb=" SG CYS L 396 " Number of angles added : 6 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4176 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 28 sheets defined 65.1% alpha, 7.8% beta 306 base pairs and 562 stacking pairs defined. Time for finding SS restraints: 4.97 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.551A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.043A pdb=" N VAL B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.423A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.501A pdb=" N LYS D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 105 through 125 removed outlier: 3.596A pdb=" N LYS D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.934A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.928A pdb=" N VAL F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 28 through 35 Processing helix chain 'G' and resid 47 through 74 Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 106 through 123 Processing helix chain 'K' and resid 162 through 175 Processing helix chain 'K' and resid 176 through 178 No H-bonds generated for 'chain 'K' and resid 176 through 178' Processing helix chain 'K' and resid 179 through 200 removed outlier: 3.517A pdb=" N ARG K 196 " --> pdb=" O HIS K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 264 removed outlier: 3.990A pdb=" N GLN K 264 " --> pdb=" O PRO K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 289 Processing helix chain 'K' and resid 331 through 335 Processing helix chain 'K' and resid 345 through 353 Processing helix chain 'K' and resid 379 through 388 Processing helix chain 'K' and resid 399 through 403 Processing helix chain 'K' and resid 405 through 424 Processing helix chain 'K' and resid 434 through 449 Processing helix chain 'K' and resid 451 through 458 removed outlier: 3.660A pdb=" N ASP K 456 " --> pdb=" O SER K 453 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ARG K 457 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LYS K 458 " --> pdb=" O TRP K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 478 Processing helix chain 'K' and resid 497 through 513 Processing helix chain 'K' and resid 514 through 515 No H-bonds generated for 'chain 'K' and resid 514 through 515' Processing helix chain 'K' and resid 516 through 520 Processing helix chain 'L' and resid 162 through 175 Processing helix chain 'L' and resid 176 through 178 No H-bonds generated for 'chain 'L' and resid 176 through 178' Processing helix chain 'L' and resid 179 through 200 Processing helix chain 'L' and resid 260 through 264 removed outlier: 4.036A pdb=" N GLN L 264 " --> pdb=" O PRO L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 272 through 288 removed outlier: 3.680A pdb=" N GLU L 286 " --> pdb=" O LYS L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 289 through 291 No H-bonds generated for 'chain 'L' and resid 289 through 291' Processing helix chain 'L' and resid 331 through 335 Processing helix chain 'L' and resid 345 through 353 Processing helix chain 'L' and resid 379 through 389 Processing helix chain 'L' and resid 399 through 403 Processing helix chain 'L' and resid 405 through 424 Processing helix chain 'L' and resid 434 through 449 Processing helix chain 'L' and resid 451 through 458 removed outlier: 3.877A pdb=" N ASP L 456 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ARG L 457 " --> pdb=" O GLN L 454 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS L 458 " --> pdb=" O TRP L 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 459 through 477 Processing helix chain 'L' and resid 497 through 514 Processing helix chain 'L' and resid 515 through 520 removed outlier: 6.002A pdb=" N VAL L 518 " --> pdb=" O GLU L 515 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 58 Processing helix chain 'M' and resid 64 through 77 Processing helix chain 'M' and resid 86 through 115 Processing helix chain 'M' and resid 121 through 132 Processing helix chain 'N' and resid 26 through 30 Processing helix chain 'N' and resid 31 through 42 Processing helix chain 'N' and resid 50 through 77 removed outlier: 3.517A pdb=" N GLU N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL N 61 " --> pdb=" O GLY N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 93 Processing helix chain 'O' and resid 17 through 22 Processing helix chain 'O' and resid 28 through 37 Processing helix chain 'O' and resid 47 through 74 Processing helix chain 'O' and resid 80 through 90 Processing helix chain 'O' and resid 91 through 98 Processing helix chain 'O' and resid 113 through 117 Processing helix chain 'P' and resid 38 through 50 Processing helix chain 'P' and resid 56 through 85 Processing helix chain 'P' and resid 91 through 103 Processing helix chain 'P' and resid 105 through 125 removed outlier: 3.616A pdb=" N LYS P 109 " --> pdb=" O GLY P 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 58 Processing helix chain 'Q' and resid 64 through 77 Processing helix chain 'Q' and resid 86 through 115 Processing helix chain 'Q' and resid 121 through 132 Processing helix chain 'R' and resid 25 through 30 Processing helix chain 'R' and resid 31 through 42 Processing helix chain 'R' and resid 50 through 77 removed outlier: 4.133A pdb=" N VAL R 61 " --> pdb=" O GLY R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 93 Processing helix chain 'S' and resid 17 through 23 Processing helix chain 'S' and resid 28 through 37 Processing helix chain 'S' and resid 47 through 74 Processing helix chain 'S' and resid 80 through 90 Processing helix chain 'S' and resid 91 through 98 Processing helix chain 'T' and resid 38 through 50 Processing helix chain 'T' and resid 56 through 85 Processing helix chain 'T' and resid 91 through 103 Processing helix chain 'T' and resid 105 through 125 removed outlier: 3.896A pdb=" N LYS T 109 " --> pdb=" O GLY T 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.933A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.090A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.968A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.999A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.033A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'K' and resid 207 through 208 removed outlier: 7.205A pdb=" N LEU K 322 " --> pdb=" O PRO K 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 207 through 208 Processing sheet with id=AB4, first strand: chain 'K' and resid 266 through 267 Processing sheet with id=AB5, first strand: chain 'K' and resid 364 through 366 removed outlier: 3.619A pdb=" N GLY K 369 " --> pdb=" O GLU K 366 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 206 through 208 removed outlier: 6.891A pdb=" N LEU L 322 " --> pdb=" O PRO L 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 206 through 208 Processing sheet with id=AB8, first strand: chain 'L' and resid 266 through 267 Processing sheet with id=AB9, first strand: chain 'L' and resid 364 through 365 Processing sheet with id=AC1, first strand: chain 'M' and resid 84 through 85 removed outlier: 7.020A pdb=" N ARG M 84 " --> pdb=" O VAL N 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'M' and resid 119 through 120 Processing sheet with id=AC3, first strand: chain 'N' and resid 98 through 99 Processing sheet with id=AC4, first strand: chain 'O' and resid 43 through 44 removed outlier: 6.957A pdb=" N ARG O 43 " --> pdb=" O ILE P 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'O' and resid 78 through 79 Processing sheet with id=AC6, first strand: chain 'O' and resid 102 through 103 removed outlier: 6.960A pdb=" N THR O 102 " --> pdb=" O TYR R 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'Q' and resid 84 through 85 removed outlier: 6.928A pdb=" N ARG Q 84 " --> pdb=" O VAL R 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'Q' and resid 119 through 120 Processing sheet with id=AC9, first strand: chain 'S' and resid 43 through 44 removed outlier: 7.176A pdb=" N ARG S 43 " --> pdb=" O ILE T 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'S' and resid 78 through 79 1133 hydrogen bonds defined for protein. 3261 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 782 hydrogen bonds 1564 hydrogen bond angles 0 basepair planarities 306 basepair parallelities 562 stacking parallelities Total time for adding SS restraints: 8.36 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5979 1.33 - 1.46: 12378 1.46 - 1.59: 12863 1.59 - 1.72: 857 1.72 - 1.86: 87 Bond restraints: 32164 Sorted by residual: bond pdb=" NE ARG L 423 " pdb=" CZ ARG L 423 " ideal model delta sigma weight residual 1.326 1.388 -0.062 1.10e-02 8.26e+03 3.22e+01 bond pdb=" CG ARG G 30 " pdb=" CD ARG G 30 " ideal model delta sigma weight residual 1.520 1.384 0.136 3.00e-02 1.11e+03 2.06e+01 bond pdb=" CG ARG G 33 " pdb=" CD ARG G 33 " ideal model delta sigma weight residual 1.520 1.387 0.133 3.00e-02 1.11e+03 1.98e+01 bond pdb=" NE ARG K 423 " pdb=" CZ ARG K 423 " ideal model delta sigma weight residual 1.326 1.375 -0.049 1.10e-02 8.26e+03 1.97e+01 bond pdb=" CD ARG B 96 " pdb=" NE ARG B 96 " ideal model delta sigma weight residual 1.458 1.396 0.062 1.40e-02 5.10e+03 1.94e+01 ... (remaining 32159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 43295 2.39 - 4.78: 2449 4.78 - 7.17: 214 7.17 - 9.56: 23 9.56 - 11.95: 5 Bond angle restraints: 45986 Sorted by residual: angle pdb=" N THR L 395 " pdb=" CA THR L 395 " pdb=" C THR L 395 " ideal model delta sigma weight residual 113.61 101.66 11.95 1.50e+00 4.44e-01 6.35e+01 angle pdb=" N GLY C 38 " pdb=" CA GLY C 38 " pdb=" C GLY C 38 " ideal model delta sigma weight residual 115.30 104.35 10.95 1.39e+00 5.18e-01 6.20e+01 angle pdb=" C HIS D 50 " pdb=" N PRO D 51 " pdb=" CA PRO D 51 " ideal model delta sigma weight residual 119.47 128.45 -8.98 1.16e+00 7.43e-01 5.99e+01 angle pdb=" C LYS L 355 " pdb=" N PRO L 356 " pdb=" CA PRO L 356 " ideal model delta sigma weight residual 119.84 129.45 -9.61 1.25e+00 6.40e-01 5.91e+01 angle pdb=" C HIS T 50 " pdb=" N PRO T 51 " pdb=" CA PRO T 51 " ideal model delta sigma weight residual 119.47 128.29 -8.82 1.16e+00 7.43e-01 5.78e+01 ... (remaining 45981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 15087 35.76 - 71.53: 2699 71.53 - 107.29: 47 107.29 - 143.05: 0 143.05 - 178.82: 6 Dihedral angle restraints: 17839 sinusoidal: 11381 harmonic: 6458 Sorted by residual: dihedral pdb=" C4' DC I 81 " pdb=" C3' DC I 81 " pdb=" O3' DC I 81 " pdb=" P DC I 82 " ideal model delta sinusoidal sigma weight residual 220.00 41.18 178.82 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC U 81 " pdb=" C3' DC U 81 " pdb=" O3' DC U 81 " pdb=" P DC U 82 " ideal model delta sinusoidal sigma weight residual 220.00 41.36 178.64 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT V 60 " pdb=" C3' DT V 60 " pdb=" O3' DT V 60 " pdb=" P DT V 61 " ideal model delta sinusoidal sigma weight residual 220.00 44.45 175.55 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 17836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4271 0.093 - 0.187: 807 0.187 - 0.280: 73 0.280 - 0.374: 20 0.374 - 0.467: 3 Chirality restraints: 5174 Sorted by residual: chirality pdb=" C3' DA J 4 " pdb=" C4' DA J 4 " pdb=" O3' DA J 4 " pdb=" C2' DA J 4 " both_signs ideal model delta sigma weight residual False -2.66 -2.19 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA LYS B 32 " pdb=" N LYS B 32 " pdb=" C LYS B 32 " pdb=" CB LYS B 32 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" C3' DA V 4 " pdb=" C4' DA V 4 " pdb=" O3' DA V 4 " pdb=" C2' DA V 4 " both_signs ideal model delta sigma weight residual False -2.66 -2.26 -0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 5171 not shown) Planarity restraints: 3704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 265 " 0.073 2.00e-02 2.50e+03 4.45e-02 3.46e+01 pdb=" CG PHE K 265 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE K 265 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE K 265 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE K 265 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE K 265 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE K 265 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 71 " 0.069 2.00e-02 2.50e+03 4.40e-02 3.39e+01 pdb=" CG PHE P 71 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE P 71 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE P 71 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE P 71 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE P 71 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE P 71 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 103 " -0.028 2.00e-02 2.50e+03 5.59e-02 3.12e+01 pdb=" C GLY B 103 " 0.097 2.00e-02 2.50e+03 pdb=" O GLY B 103 " -0.035 2.00e-02 2.50e+03 pdb=" OXT GLY B 103 " -0.034 2.00e-02 2.50e+03 ... (remaining 3701 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6182 2.78 - 3.31: 26394 3.31 - 3.84: 58583 3.84 - 4.37: 74446 4.37 - 4.90: 101288 Nonbonded interactions: 266893 Sorted by model distance: nonbonded pdb=" O TYR C 40 " pdb=" OG SER D 79 " model vdw 2.251 3.040 nonbonded pdb=" O GLY B 102 " pdb=" OG SER H 65 " model vdw 2.287 3.040 nonbonded pdb=" O ASN K 260 " pdb=" OG SER K 263 " model vdw 2.303 3.040 nonbonded pdb=" NH2 ARG Q 43 " pdb=" OP1 DG V 72 " model vdw 2.390 3.120 nonbonded pdb=" O PHE L 491 " pdb=" NZ LYS L 501 " model vdw 2.394 3.120 ... (remaining 266888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 41 through 134) selection = (chain 'E' and resid 41 through 134) selection = (chain 'M' and resid 41 through 134) selection = chain 'Q' } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = (chain 'F' and resid 25 through 101) selection = (chain 'N' and resid 25 through 101) selection = chain 'R' } ncs_group { reference = (chain 'C' and (resid 14 through 113 or resid 201)) selection = (chain 'G' and (resid 14 through 113 or resid 701)) selection = (chain 'O' and (resid 14 through 113 or resid 201)) selection = (chain 'S' and (resid 14 through 113 or resid 702)) } ncs_group { reference = (chain 'D' and resid 36 through 125) selection = (chain 'H' and resid 36 through 125) selection = chain 'P' selection = (chain 'T' and resid 36 through 125) } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.84 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 36.550 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 : 0.013 0.171 32190 Z= 0.784 Angle : 1.229 11.949 45992 Z= 0.833 Chirality : 0.074 0.467 5174 Planarity : 0.011 0.068 3704 Dihedral : 25.763 178.819 13663 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.97 % Favored : 97.94 % Rotamer: Outliers : 0.11 % Allowed : 0.95 % Favored : 98.95 % 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: 0.59 (0.16), residues: 2182 helix: 0.70 (0.13), residues: 1384 sheet: -0.06 (0.44), residues: 92 loop : 0.10 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG F 68 TYR 0.064 0.010 TYR L 436 PHE 0.073 0.010 PHE K 265 TRP 0.059 0.016 TRP K 455 HIS 0.018 0.004 HIS L 390 Details of bonding type rmsd covalent geometry : bond 0.01279 (32164) covalent geometry : angle 1.22875 (45986) hydrogen bonds : bond 0.15706 ( 1895) hydrogen bonds : angle 5.76161 ( 4825) metal coordination : bond 0.01954 ( 8) metal coordination : angle 2.69578 ( 6) Misc. bond : bond 0.16973 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 445 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8004 (mtt) cc_final: 0.7672 (mpp) REVERT: C 19 SER cc_start: 0.8358 (m) cc_final: 0.8123 (t) REVERT: C 39 ASN cc_start: 0.7804 (m-40) cc_final: 0.7233 (m110) REVERT: C 84 LEU cc_start: 0.9563 (mt) cc_final: 0.9193 (mp) REVERT: C 91 ASP cc_start: 0.8232 (t70) cc_final: 0.7882 (t0) REVERT: C 94 LEU cc_start: 0.9606 (mt) cc_final: 0.9398 (mm) REVERT: E 75 ILE cc_start: 0.9428 (mt) cc_final: 0.9113 (mm) REVERT: F 67 ILE cc_start: 0.9079 (mt) cc_final: 0.8867 (pt) REVERT: F 69 ASP cc_start: 0.8240 (m-30) cc_final: 0.7886 (m-30) REVERT: F 99 TYR cc_start: 0.8825 (m-10) cc_final: 0.8275 (m-80) REVERT: G 26 PHE cc_start: 0.8461 (m-80) cc_final: 0.8134 (m-10) REVERT: G 31 VAL cc_start: 0.8422 (t) cc_final: 0.8161 (t) REVERT: G 56 LEU cc_start: 0.9700 (mt) cc_final: 0.9471 (mt) REVERT: G 57 GLU cc_start: 0.8649 (tt0) cc_final: 0.7694 (tt0) REVERT: H 88 SER cc_start: 0.8448 (m) cc_final: 0.8050 (p) REVERT: N 66 VAL cc_start: 0.9021 (t) cc_final: 0.8807 (m) REVERT: P 55 ILE cc_start: 0.4843 (tt) cc_final: 0.4640 (tt) outliers start: 2 outliers final: 1 residues processed: 447 average time/residue: 0.1887 time to fit residues: 137.4468 Evaluate side-chains 223 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN H 83 HIS O 39 ASN Q 94 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.093915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.061647 restraints weight = 292350.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.061915 restraints weight = 145464.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.061360 restraints weight = 108831.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.061745 restraints weight = 84671.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.061726 restraints weight = 71834.028| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 32190 Z= 0.242 Angle : 0.694 10.396 45992 Z= 0.401 Chirality : 0.040 0.230 5174 Planarity : 0.005 0.057 3704 Dihedral : 29.399 179.569 9158 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.05 % Favored : 98.85 % Rotamer: Outliers : 0.11 % Allowed : 1.89 % Favored : 98.00 % 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: 1.75 (0.17), residues: 2182 helix: 1.84 (0.13), residues: 1391 sheet: -0.37 (0.44), residues: 92 loop : 0.09 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.001 ARG O 30 TYR 0.028 0.002 TYR O 51 PHE 0.041 0.003 PHE P 71 TRP 0.049 0.006 TRP K 375 HIS 0.009 0.002 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00519 (32164) covalent geometry : angle 0.69329 (45986) hydrogen bonds : bond 0.05998 ( 1895) hydrogen bonds : angle 3.92295 ( 4825) metal coordination : bond 0.02657 ( 8) metal coordination : angle 2.25399 ( 6) Misc. bond : bond 0.00205 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 309 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.9124 (mppt) cc_final: 0.8851 (mmtm) REVERT: B 85 MET cc_start: 0.8130 (tpt) cc_final: 0.7819 (mmm) REVERT: C 39 ASN cc_start: 0.7834 (m-40) cc_final: 0.7631 (m110) REVERT: E 52 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9080 (mm) REVERT: E 98 GLU cc_start: 0.8945 (mp0) cc_final: 0.8424 (mp0) REVERT: F 69 ASP cc_start: 0.8581 (m-30) cc_final: 0.8316 (m-30) REVERT: F 85 MET cc_start: 0.8948 (tpt) cc_final: 0.8658 (tpp) REVERT: F 99 TYR cc_start: 0.9117 (m-10) cc_final: 0.8643 (m-10) REVERT: G 26 PHE cc_start: 0.8500 (m-80) cc_final: 0.7983 (m-10) REVERT: G 31 VAL cc_start: 0.8603 (t) cc_final: 0.8362 (t) REVERT: G 50 VAL cc_start: 0.9447 (t) cc_final: 0.9185 (p) REVERT: G 57 GLU cc_start: 0.8745 (tt0) cc_final: 0.7761 (tt0) REVERT: G 60 THR cc_start: 0.9932 (m) cc_final: 0.9723 (p) REVERT: G 62 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8841 (mm-30) REVERT: N 38 LEU cc_start: 0.8468 (mt) cc_final: 0.8262 (mm) outliers start: 2 outliers final: 1 residues processed: 309 average time/residue: 0.1841 time to fit residues: 93.6597 Evaluate side-chains 197 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 175 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 165 optimal weight: 40.0000 chunk 207 optimal weight: 10.0000 chunk 270 optimal weight: 20.0000 chunk 172 optimal weight: 40.0000 chunk 102 optimal weight: 40.0000 chunk 73 optimal weight: 20.0000 chunk 258 optimal weight: 40.0000 overall best weight: 7.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS F 94 GLN M 114 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.090482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.056736 restraints weight = 298812.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.057091 restraints weight = 153209.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.056483 restraints weight = 117221.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.056919 restraints weight = 97849.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.056836 restraints weight = 77763.914| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 32190 Z= 0.271 Angle : 0.684 10.884 45992 Z= 0.397 Chirality : 0.039 0.238 5174 Planarity : 0.006 0.077 3704 Dihedral : 29.485 177.890 9158 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.83 % Favored : 98.08 % Rotamer: Outliers : 0.42 % Allowed : 2.58 % Favored : 97.00 % 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: 1.54 (0.17), residues: 2182 helix: 1.71 (0.13), residues: 1402 sheet: -0.62 (0.43), residues: 94 loop : -0.08 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 36 TYR 0.040 0.002 TYR R 73 PHE 0.023 0.002 PHE L 280 TRP 0.006 0.001 TRP K 375 HIS 0.012 0.002 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00582 (32164) covalent geometry : angle 0.68162 (45986) hydrogen bonds : bond 0.07043 ( 1895) hydrogen bonds : angle 3.97909 ( 4825) metal coordination : bond 0.01720 ( 8) metal coordination : angle 4.71963 ( 6) Misc. bond : bond 0.00091 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 259 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9435 (mm-30) cc_final: 0.8967 (mm-30) REVERT: A 65 LYS cc_start: 0.9226 (mppt) cc_final: 0.8921 (mmtm) REVERT: A 107 ASP cc_start: 0.8911 (m-30) cc_final: 0.8602 (m-30) REVERT: C 39 ASN cc_start: 0.8223 (m-40) cc_final: 0.7984 (m110) REVERT: D 77 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9166 (tp30) REVERT: E 98 GLU cc_start: 0.8938 (mp0) cc_final: 0.8395 (mp0) REVERT: E 106 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8485 (tm-30) REVERT: E 107 ASP cc_start: 0.9546 (m-30) cc_final: 0.9268 (m-30) REVERT: F 30 ILE cc_start: 0.9305 (mp) cc_final: 0.9058 (mp) REVERT: F 38 LEU cc_start: 0.9577 (mp) cc_final: 0.9289 (tt) REVERT: F 85 MET cc_start: 0.9098 (tpt) cc_final: 0.8793 (tpp) REVERT: F 99 TYR cc_start: 0.9304 (m-10) cc_final: 0.8914 (m-10) REVERT: G 31 VAL cc_start: 0.9008 (t) cc_final: 0.8588 (p) REVERT: G 57 GLU cc_start: 0.8758 (tt0) cc_final: 0.7714 (tt0) REVERT: G 62 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8931 (mm-30) REVERT: G 91 ASP cc_start: 0.8939 (t0) cc_final: 0.8675 (t70) REVERT: H 38 TYR cc_start: 0.9437 (m-80) cc_final: 0.9225 (m-10) outliers start: 8 outliers final: 2 residues processed: 264 average time/residue: 0.1867 time to fit residues: 81.5079 Evaluate side-chains 176 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 82 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 243 optimal weight: 7.9990 chunk 235 optimal weight: 7.9990 chunk 218 optimal weight: 6.9990 chunk 268 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 256 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.089415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.052877 restraints weight = 295328.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.053854 restraints weight = 147003.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.054044 restraints weight = 98678.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.055202 restraints weight = 84940.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.055320 restraints weight = 73405.123| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 32190 Z= 0.268 Angle : 0.659 11.501 45992 Z= 0.382 Chirality : 0.038 0.172 5174 Planarity : 0.005 0.057 3704 Dihedral : 29.696 177.357 9158 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.70 % Favored : 98.21 % Rotamer: Outliers : 0.16 % Allowed : 2.00 % Favored : 97.84 % 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: 1.48 (0.17), residues: 2182 helix: 1.69 (0.13), residues: 1392 sheet: -0.37 (0.46), residues: 92 loop : -0.20 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 80 TYR 0.034 0.002 TYR G 40 PHE 0.026 0.002 PHE K 433 TRP 0.008 0.001 TRP L 375 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00580 (32164) covalent geometry : angle 0.65785 (45986) hydrogen bonds : bond 0.06320 ( 1895) hydrogen bonds : angle 3.98765 ( 4825) metal coordination : bond 0.01878 ( 8) metal coordination : angle 4.08374 ( 6) Misc. bond : bond 0.00063 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 229 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9409 (mm-30) cc_final: 0.8981 (mm-30) REVERT: A 52 ILE cc_start: 0.9511 (mt) cc_final: 0.9295 (mm) REVERT: A 65 LYS cc_start: 0.9281 (mppt) cc_final: 0.8942 (mmtm) REVERT: A 95 GLU cc_start: 0.8933 (tt0) cc_final: 0.8668 (tt0) REVERT: A 107 ASP cc_start: 0.8880 (m-30) cc_final: 0.8583 (m-30) REVERT: D 77 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8961 (tp30) REVERT: D 101 LEU cc_start: 0.9530 (mm) cc_final: 0.8931 (tp) REVERT: E 98 GLU cc_start: 0.8907 (mp0) cc_final: 0.8347 (mp0) REVERT: E 106 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8507 (tm-30) REVERT: E 107 ASP cc_start: 0.9485 (m-30) cc_final: 0.9189 (m-30) REVERT: F 85 MET cc_start: 0.8988 (tpt) cc_final: 0.8745 (tpp) REVERT: F 99 TYR cc_start: 0.9229 (m-10) cc_final: 0.8915 (m-80) REVERT: G 31 VAL cc_start: 0.9302 (t) cc_final: 0.9071 (p) REVERT: G 62 GLU cc_start: 0.9251 (mm-30) cc_final: 0.9012 (mm-30) REVERT: G 105 GLN cc_start: 0.8678 (mm-40) cc_final: 0.7795 (tm-30) REVERT: H 38 TYR cc_start: 0.9471 (m-80) cc_final: 0.9129 (m-10) outliers start: 3 outliers final: 1 residues processed: 230 average time/residue: 0.1799 time to fit residues: 69.2331 Evaluate side-chains 168 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 136 optimal weight: 30.0000 chunk 3 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 269 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 122 optimal weight: 50.0000 chunk 96 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 overall best weight: 5.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.089161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.052585 restraints weight = 296218.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.053567 restraints weight = 146568.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.054539 restraints weight = 98317.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.054734 restraints weight = 79058.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.054963 restraints weight = 72567.584| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 32190 Z= 0.220 Angle : 0.615 10.188 45992 Z= 0.359 Chirality : 0.036 0.148 5174 Planarity : 0.005 0.064 3704 Dihedral : 29.613 177.376 9158 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.83 % Favored : 98.08 % Rotamer: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.18), residues: 2182 helix: 1.86 (0.13), residues: 1396 sheet: -0.42 (0.48), residues: 88 loop : -0.27 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 93 TYR 0.023 0.002 TYR R 73 PHE 0.029 0.002 PHE M 105 TRP 0.005 0.001 TRP L 375 HIS 0.013 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00472 (32164) covalent geometry : angle 0.61116 (45986) hydrogen bonds : bond 0.05525 ( 1895) hydrogen bonds : angle 3.88315 ( 4825) metal coordination : bond 0.01976 ( 8) metal coordination : angle 5.80230 ( 6) Misc. bond : bond 0.00067 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9001 (mm-30) REVERT: A 65 LYS cc_start: 0.9293 (mppt) cc_final: 0.8957 (mmtm) REVERT: A 98 GLU cc_start: 0.8879 (mp0) cc_final: 0.8554 (mp0) REVERT: A 107 ASP cc_start: 0.8850 (m-30) cc_final: 0.8542 (m-30) REVERT: D 77 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8925 (tp30) REVERT: D 101 LEU cc_start: 0.9540 (mm) cc_final: 0.9120 (tp) REVERT: E 98 GLU cc_start: 0.8901 (mp0) cc_final: 0.8279 (mp0) REVERT: E 106 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8530 (tm-30) REVERT: E 107 ASP cc_start: 0.9495 (m-30) cc_final: 0.9267 (m-30) REVERT: F 99 TYR cc_start: 0.9369 (m-10) cc_final: 0.8992 (m-10) REVERT: G 57 GLU cc_start: 0.8854 (tt0) cc_final: 0.8362 (tt0) REVERT: G 62 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8950 (mm-30) REVERT: G 105 GLN cc_start: 0.8756 (mm-40) cc_final: 0.7847 (tm-30) REVERT: H 38 TYR cc_start: 0.9483 (m-80) cc_final: 0.9133 (m-10) REVERT: H 103 LEU cc_start: 0.9467 (mp) cc_final: 0.9256 (mp) REVERT: N 38 LEU cc_start: 0.8456 (mm) cc_final: 0.8201 (mm) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.1711 time to fit residues: 63.5484 Evaluate side-chains 156 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 10 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 257 optimal weight: 20.0000 chunk 273 optimal weight: 40.0000 chunk 46 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 116 optimal weight: 0.4980 chunk 233 optimal weight: 8.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.090476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.057122 restraints weight = 291538.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.057066 restraints weight = 150611.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.056986 restraints weight = 119581.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.056995 restraints weight = 87602.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.056958 restraints weight = 83509.609| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32190 Z= 0.154 Angle : 0.576 10.687 45992 Z= 0.337 Chirality : 0.035 0.149 5174 Planarity : 0.004 0.081 3704 Dihedral : 29.385 177.738 9158 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.79 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 1.78 (0.18), residues: 2182 helix: 1.99 (0.14), residues: 1404 sheet: -0.28 (0.49), residues: 86 loop : -0.27 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG P 80 TYR 0.023 0.001 TYR G 40 PHE 0.030 0.002 PHE A 105 TRP 0.005 0.001 TRP K 375 HIS 0.005 0.001 HIS T 83 Details of bonding type rmsd covalent geometry : bond 0.00324 (32164) covalent geometry : angle 0.57378 (45986) hydrogen bonds : bond 0.04081 ( 1895) hydrogen bonds : angle 3.61004 ( 4825) metal coordination : bond 0.01849 ( 8) metal coordination : angle 4.53240 ( 6) Misc. bond : bond 0.00022 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9404 (mm-30) cc_final: 0.8957 (mm-30) REVERT: A 65 LYS cc_start: 0.9227 (mppt) cc_final: 0.8946 (mmtm) REVERT: A 95 GLU cc_start: 0.8827 (tt0) cc_final: 0.8611 (tt0) REVERT: A 107 ASP cc_start: 0.8621 (m-30) cc_final: 0.8300 (m-30) REVERT: D 60 MET cc_start: 0.9165 (tpp) cc_final: 0.8867 (tpp) REVERT: D 77 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8955 (tp30) REVERT: E 98 GLU cc_start: 0.8955 (mp0) cc_final: 0.8309 (mp0) REVERT: E 106 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8442 (tm-30) REVERT: F 69 ASP cc_start: 0.8827 (m-30) cc_final: 0.8522 (m-30) REVERT: F 99 TYR cc_start: 0.9294 (m-10) cc_final: 0.8789 (m-10) REVERT: G 52 MET cc_start: 0.9211 (ttm) cc_final: 0.8994 (ttm) REVERT: G 57 GLU cc_start: 0.8813 (tt0) cc_final: 0.8320 (tt0) REVERT: G 62 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8790 (mm-30) REVERT: G 105 GLN cc_start: 0.8707 (mm-40) cc_final: 0.7682 (tm-30) REVERT: H 38 TYR cc_start: 0.9418 (m-80) cc_final: 0.9127 (m-10) REVERT: H 103 LEU cc_start: 0.9385 (mp) cc_final: 0.9166 (mp) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1785 time to fit residues: 68.3534 Evaluate side-chains 164 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 137 optimal weight: 4.9990 chunk 210 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 270 optimal weight: 20.0000 chunk 231 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 230 optimal weight: 6.9990 chunk 173 optimal weight: 0.0670 chunk 110 optimal weight: 30.0000 chunk 125 optimal weight: 0.0020 chunk 19 optimal weight: 0.9990 overall best weight: 2.6132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.090109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.057086 restraints weight = 293577.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.056879 restraints weight = 166275.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.056914 restraints weight = 126323.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.057355 restraints weight = 90557.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.056761 restraints weight = 83905.668| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32190 Z= 0.159 Angle : 0.574 10.313 45992 Z= 0.337 Chirality : 0.034 0.152 5174 Planarity : 0.004 0.047 3704 Dihedral : 29.200 177.175 9158 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.83 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: 1.84 (0.18), residues: 2182 helix: 2.06 (0.14), residues: 1393 sheet: -0.17 (0.48), residues: 86 loop : -0.26 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 93 TYR 0.023 0.001 TYR O 51 PHE 0.029 0.001 PHE K 280 TRP 0.005 0.001 TRP K 375 HIS 0.007 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00338 (32164) covalent geometry : angle 0.57215 (45986) hydrogen bonds : bond 0.04462 ( 1895) hydrogen bonds : angle 3.56903 ( 4825) metal coordination : bond 0.01397 ( 8) metal coordination : angle 3.79000 ( 6) Misc. bond : bond 0.00018 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9484 (mm-30) cc_final: 0.9015 (mm-30) REVERT: A 65 LYS cc_start: 0.9293 (mppt) cc_final: 0.8983 (mmtm) REVERT: A 75 ILE cc_start: 0.9780 (mm) cc_final: 0.9570 (tp) REVERT: A 95 GLU cc_start: 0.8980 (tt0) cc_final: 0.8537 (tt0) REVERT: A 98 GLU cc_start: 0.8923 (mp0) cc_final: 0.8590 (mp0) REVERT: A 107 ASP cc_start: 0.8684 (m-30) cc_final: 0.8355 (m-30) REVERT: B 75 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8341 (tm-30) REVERT: D 60 MET cc_start: 0.9212 (tpp) cc_final: 0.8814 (tpp) REVERT: D 77 GLU cc_start: 0.9382 (mm-30) cc_final: 0.8999 (tp30) REVERT: E 98 GLU cc_start: 0.8889 (mp0) cc_final: 0.8291 (mp0) REVERT: E 107 ASP cc_start: 0.9497 (m-30) cc_final: 0.9257 (m-30) REVERT: F 99 TYR cc_start: 0.9431 (m-10) cc_final: 0.8783 (m-10) REVERT: G 57 GLU cc_start: 0.8880 (tt0) cc_final: 0.8395 (tt0) REVERT: G 62 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8859 (mm-30) REVERT: G 105 GLN cc_start: 0.8798 (mm-40) cc_final: 0.7786 (tm-30) REVERT: H 38 TYR cc_start: 0.9506 (m-80) cc_final: 0.9004 (m-10) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1760 time to fit residues: 64.2066 Evaluate side-chains 156 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 238 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 174 optimal weight: 80.0000 chunk 209 optimal weight: 30.0000 chunk 14 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 overall best weight: 6.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.088479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.054394 restraints weight = 295819.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.054424 restraints weight = 150820.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.053559 restraints weight = 135374.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.053801 restraints weight = 100811.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.053838 restraints weight = 85411.074| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 32190 Z= 0.252 Angle : 0.637 16.323 45992 Z= 0.370 Chirality : 0.037 0.196 5174 Planarity : 0.005 0.061 3704 Dihedral : 29.444 177.794 9158 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.20 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: 1.54 (0.18), residues: 2182 helix: 1.80 (0.14), residues: 1394 sheet: -0.35 (0.47), residues: 86 loop : -0.33 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 87 TYR 0.021 0.002 TYR O 51 PHE 0.032 0.002 PHE M 105 TRP 0.012 0.001 TRP K 330 HIS 0.010 0.002 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00543 (32164) covalent geometry : angle 0.63521 (45986) hydrogen bonds : bond 0.06762 ( 1895) hydrogen bonds : angle 3.91362 ( 4825) metal coordination : bond 0.01442 ( 8) metal coordination : angle 4.41123 ( 6) Misc. bond : bond 0.00097 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9473 (mm-30) cc_final: 0.9079 (tp30) REVERT: A 65 LYS cc_start: 0.9271 (mppt) cc_final: 0.8938 (mmtm) REVERT: A 95 GLU cc_start: 0.8868 (tt0) cc_final: 0.8614 (tt0) REVERT: A 98 GLU cc_start: 0.8765 (mp0) cc_final: 0.8474 (mp0) REVERT: A 107 ASP cc_start: 0.8801 (m-30) cc_final: 0.8525 (m-30) REVERT: D 60 MET cc_start: 0.9114 (tpp) cc_final: 0.8652 (tpp) REVERT: D 77 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9017 (tp30) REVERT: E 98 GLU cc_start: 0.9060 (mp0) cc_final: 0.8472 (mp0) REVERT: E 107 ASP cc_start: 0.9423 (m-30) cc_final: 0.9172 (m-30) REVERT: E 126 GLN cc_start: 0.9343 (mp10) cc_final: 0.9086 (mp10) REVERT: F 99 TYR cc_start: 0.9251 (m-10) cc_final: 0.8784 (m-10) REVERT: G 57 GLU cc_start: 0.8883 (tt0) cc_final: 0.8401 (tt0) REVERT: G 105 GLN cc_start: 0.8640 (mm-40) cc_final: 0.7778 (tm-30) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1722 time to fit residues: 54.3210 Evaluate side-chains 135 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 23 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 263 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 chunk 225 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.088850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.054493 restraints weight = 296829.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.054568 restraints weight = 151629.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.053891 restraints weight = 114179.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.054204 restraints weight = 91611.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.054146 restraints weight = 80435.862| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32190 Z= 0.201 Angle : 0.604 12.388 45992 Z= 0.353 Chirality : 0.036 0.161 5174 Planarity : 0.004 0.049 3704 Dihedral : 29.526 177.635 9158 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.20 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 1.56 (0.18), residues: 2182 helix: 1.82 (0.14), residues: 1391 sheet: -0.33 (0.47), residues: 88 loop : -0.33 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 80 TYR 0.020 0.001 TYR R 73 PHE 0.037 0.001 PHE Q 68 TRP 0.006 0.001 TRP K 330 HIS 0.011 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00430 (32164) covalent geometry : angle 0.60151 (45986) hydrogen bonds : bond 0.04932 ( 1895) hydrogen bonds : angle 3.83481 ( 4825) metal coordination : bond 0.01345 ( 8) metal coordination : angle 4.38975 ( 6) Misc. bond : bond 0.00034 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9441 (mm-30) cc_final: 0.9009 (tp30) REVERT: A 95 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8521 (tt0) REVERT: A 98 GLU cc_start: 0.8781 (mp0) cc_final: 0.8465 (mp0) REVERT: A 107 ASP cc_start: 0.8759 (m-30) cc_final: 0.8458 (m-30) REVERT: D 60 MET cc_start: 0.9097 (tpp) cc_final: 0.8684 (tpp) REVERT: D 77 GLU cc_start: 0.9306 (mm-30) cc_final: 0.9032 (tp30) REVERT: E 98 GLU cc_start: 0.8936 (mp0) cc_final: 0.8291 (mp0) REVERT: E 106 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8474 (tm-30) REVERT: E 107 ASP cc_start: 0.9432 (m-30) cc_final: 0.9198 (m-30) REVERT: F 60 LYS cc_start: 0.9407 (ptpp) cc_final: 0.9162 (ptpp) REVERT: F 99 TYR cc_start: 0.9259 (m-10) cc_final: 0.8865 (m-80) REVERT: G 57 GLU cc_start: 0.8860 (tt0) cc_final: 0.8372 (tt0) REVERT: G 96 LYS cc_start: 0.9596 (tmtt) cc_final: 0.9341 (mmtt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1738 time to fit residues: 54.5469 Evaluate side-chains 137 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 15 optimal weight: 10.0000 chunk 234 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 134 optimal weight: 40.0000 chunk 61 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 256 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.088339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.053662 restraints weight = 296064.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.053602 restraints weight = 153634.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.053163 restraints weight = 110410.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.053378 restraints weight = 91358.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.053439 restraints weight = 83818.612| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 32190 Z= 0.232 Angle : 0.631 14.974 45992 Z= 0.365 Chirality : 0.036 0.157 5174 Planarity : 0.005 0.050 3704 Dihedral : 29.554 177.684 9158 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.38 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 1.45 (0.18), residues: 2182 helix: 1.76 (0.14), residues: 1390 sheet: -0.37 (0.47), residues: 88 loop : -0.42 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 87 TYR 0.031 0.002 TYR R 89 PHE 0.030 0.002 PHE M 105 TRP 0.012 0.001 TRP K 330 HIS 0.011 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00499 (32164) covalent geometry : angle 0.62855 (45986) hydrogen bonds : bond 0.06164 ( 1895) hydrogen bonds : angle 3.93259 ( 4825) metal coordination : bond 0.01352 ( 8) metal coordination : angle 4.43213 ( 6) Misc. bond : bond 0.00030 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9498 (mm-30) cc_final: 0.9067 (tp30) REVERT: A 65 LYS cc_start: 0.9301 (mppt) cc_final: 0.8930 (mmtm) REVERT: A 107 ASP cc_start: 0.8779 (m-30) cc_final: 0.8486 (m-30) REVERT: D 60 MET cc_start: 0.9206 (tpp) cc_final: 0.8706 (tpp) REVERT: D 77 GLU cc_start: 0.9354 (mm-30) cc_final: 0.9094 (tp30) REVERT: E 98 GLU cc_start: 0.8997 (mp0) cc_final: 0.8380 (mp0) REVERT: E 107 ASP cc_start: 0.9458 (m-30) cc_final: 0.9208 (m-30) REVERT: E 126 GLN cc_start: 0.9372 (mp10) cc_final: 0.9143 (mp10) REVERT: F 97 THR cc_start: 0.9593 (p) cc_final: 0.9378 (p) REVERT: F 99 TYR cc_start: 0.9273 (m-10) cc_final: 0.8766 (m-80) REVERT: G 57 GLU cc_start: 0.8858 (tt0) cc_final: 0.8377 (tt0) REVERT: G 96 LYS cc_start: 0.9583 (tmtt) cc_final: 0.9312 (mmtt) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1738 time to fit residues: 53.7250 Evaluate side-chains 135 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 128 optimal weight: 30.0000 chunk 115 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 134 optimal weight: 40.0000 chunk 104 optimal weight: 40.0000 chunk 130 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.088606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.054478 restraints weight = 297291.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.054408 restraints weight = 155245.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.054009 restraints weight = 135208.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.054108 restraints weight = 105629.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.054044 restraints weight = 88671.021| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 32190 Z= 0.218 Angle : 0.625 10.663 45992 Z= 0.362 Chirality : 0.036 0.146 5174 Planarity : 0.005 0.064 3704 Dihedral : 29.638 177.176 9158 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 1.41 (0.18), residues: 2182 helix: 1.70 (0.14), residues: 1394 sheet: -0.38 (0.48), residues: 88 loop : -0.38 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 87 TYR 0.023 0.002 TYR R 89 PHE 0.023 0.002 PHE M 105 TRP 0.010 0.001 TRP K 330 HIS 0.010 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00468 (32164) covalent geometry : angle 0.62202 (45986) hydrogen bonds : bond 0.05560 ( 1895) hydrogen bonds : angle 3.91282 ( 4825) metal coordination : bond 0.01302 ( 8) metal coordination : angle 5.31551 ( 6) Misc. bond : bond 0.00031 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7951.75 seconds wall clock time: 136 minutes 5.77 seconds (8165.77 seconds total)