Starting phenix.real_space_refine on Mon Sep 14 10:11:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6y5d_10694/09_2026/6y5d_10694.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5d_10694/09_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_10694/09_2026/6y5d_10694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5d_10694/09_2026/6y5d_10694.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y5d_10694/09_2026/6y5d_10694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5d_10694/09_2026/6y5d_10694.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6y5d_10694/09_2026/6y5d_10694.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6y5d_10694/09_2026/6y5d_10694.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 5.37, per 1000 atoms: 0.18 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: 2.40 Conformation dependent library (CDL) restraints added in 670.0 milliseconds 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: 4.42 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: 7.07 Time building geometry restraints manager: 3.20 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: 43153 2.39 - 4.78: 2587 4.78 - 7.17: 217 7.17 - 9.56: 24 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 - 0.108: 4510 0.108 - 0.215: 603 0.215 - 0.323: 49 0.323 - 0.430: 8 0.430 - 0.538: 4 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 -2.73 -2.19 -0.54 2.00e-01 2.50e+01 7.22e+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 -2.73 -2.26 -0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" C3' DT J 60 " pdb=" C4' DT J 60 " pdb=" O3' DT J 60 " pdb=" C2' DT J 60 " both_signs ideal model delta sigma weight residual False -2.73 -2.29 -0.44 2.00e-01 2.50e+01 4.85e+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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 32.540 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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= 0.848 Angle : 1.223 11.949 45992 Z= 0.903 Chirality : 0.075 0.538 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/Z covalent geometry : bond 0.01252 / 0.75 (32164) covalent geometry : angle 1.22308 / 0.90 (45986) hydrogen bonds : bond 0.15706 / 10.61 ( 1895) hydrogen bonds : angle 5.76161 / 4.17 ( 4825) metal coordination : bond 0.01954 / 1.14 ( 8) metal coordination : angle 2.69578 / 1.77 ( 6) Misc. bond : bond 0.16973 / 12.15 ( 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 : 0.759 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: A 121 MET cc_start: 0.8004 (mtt) cc_final: 0.7672 (mpp) REVERT: C 19 SER cc_start: 0.8358 (m) cc_final: 0.8122 (t) REVERT: C 39 ASN cc_start: 0.7804 (m-40) cc_final: 0.7231 (m110) REVERT: C 84 LEU cc_start: 0.9563 (mt) cc_final: 0.9192 (mp) REVERT: C 91 ASP cc_start: 0.8232 (t70) cc_final: 0.7881 (t0) REVERT: C 94 LEU cc_start: 0.9606 (mt) cc_final: 0.9397 (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: 0.8868 (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: 0.8276 (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: 0.8156 (t) REVERT: G 56 LEU cc_start: 0.9700 (mt) cc_final: 0.9472 (mt) REVERT: G 57 GLU cc_start: 0.8649 (tt0) cc_final: 0.7692 (tt0) REVERT: H 88 SER cc_start: 0.8448 (m) cc_final: 0.8046 (p) REVERT: N 66 VAL cc_start: 0.9021 (t) cc_final: 0.8806 (m) REVERT: P 55 ILE cc_start: 0.4843 (tt) cc_final: 0.4635 (tt) outliers start: 2 outliers final: 1 residues processed: 447 average time/residue: 0.1746 time to fit residues: 127.9522 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 : 0.796 ------------------------------------------------------------------------------- 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: 50.0000 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 50.0000 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... 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 H 110 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.094503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.062368 restraints weight = 291881.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.062678 restraints weight = 146238.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.062249 restraints weight = 106704.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.062449 restraints weight = 82626.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.062467 restraints weight = 67667.080| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 32190 Z= 0.209 Angle : 0.806 10.982 45992 Z= 0.450 Chirality : 0.049 0.297 5174 Planarity : 0.006 0.071 3704 Dihedral : 29.716 179.423 9158 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.10 % Favored : 98.81 % Rotamer: Outliers : 0.16 % Allowed : 2.37 % Favored : 97.48 % 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: 1.55 (0.17), residues: 2182 helix: 1.70 (0.13), residues: 1382 sheet: -0.81 (0.44), residues: 96 loop : 0.07 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG R 41 TYR 0.024 0.002 TYR R 73 PHE 0.041 0.003 PHE P 71 TRP 0.024 0.004 TRP K 375 HIS 0.010 0.001 HIS T 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 (32164) covalent geometry : angle 0.80615 / 0.45 (45986) hydrogen bonds : bond 0.06905 / 4.65 ( 1895) hydrogen bonds : angle 4.06650 / 2.99 ( 4825) metal coordination : bond 0.02476 / 1.48 ( 8) metal coordination : angle 1.89042 / 1.14 ( 6) Misc. bond : bond 0.00290 / 0.23 ( 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 322 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 319 time to evaluate : 0.702 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 121 MET cc_start: 0.8066 (mtt) cc_final: 0.7833 (mpp) REVERT: C 39 ASN cc_start: 0.7665 (m-40) cc_final: 0.7442 (m110) REVERT: C 63 ILE cc_start: 0.9745 (tp) cc_final: 0.9533 (tp) REVERT: E 52 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9041 (mp) REVERT: E 56 GLN cc_start: 0.8369 (mt0) cc_final: 0.8156 (mt0) REVERT: E 98 GLU cc_start: 0.8922 (mp0) cc_final: 0.8476 (mp0) REVERT: E 107 ASP cc_start: 0.9410 (m-30) cc_final: 0.9185 (m-30) REVERT: F 85 MET cc_start: 0.8875 (tpt) cc_final: 0.8606 (tpp) REVERT: F 99 TYR cc_start: 0.9111 (m-10) cc_final: 0.8508 (m-80) REVERT: G 26 PHE cc_start: 0.8497 (m-80) cc_final: 0.8026 (m-10) REVERT: G 31 VAL cc_start: 0.8529 (t) cc_final: 0.8088 (p) REVERT: G 57 GLU cc_start: 0.8731 (tt0) cc_final: 0.7756 (tt0) REVERT: G 60 THR cc_start: 0.9931 (m) cc_final: 0.9722 (p) REVERT: G 90 ASN cc_start: 0.9195 (m-40) cc_final: 0.8828 (m-40) REVERT: N 38 LEU cc_start: 0.8448 (mt) cc_final: 0.8233 (mt) REVERT: N 66 VAL cc_start: 0.9304 (t) cc_final: 0.9037 (m) outliers start: 3 outliers final: 1 residues processed: 319 average time/residue: 0.1653 time to fit residues: 88.2374 Evaluate side-chains 196 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 194 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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: 6.9990 chunk 82 optimal weight: 40.0000 chunk 16 optimal weight: 0.9990 chunk 75 optimal weight: 40.0000 chunk 165 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 270 optimal weight: 50.0000 chunk 172 optimal weight: 2.9990 chunk 102 optimal weight: 50.0000 chunk 73 optimal weight: 50.0000 chunk 258 optimal weight: 50.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 ASN Q 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.091582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.058226 restraints weight = 298012.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.058372 restraints weight = 148786.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.057718 restraints weight = 114796.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.058293 restraints weight = 94035.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.058157 restraints weight = 72820.516| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 32190 Z= 0.258 Angle : 0.751 9.718 45992 Z= 0.428 Chirality : 0.046 0.268 5174 Planarity : 0.005 0.050 3704 Dihedral : 29.980 179.784 9158 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.65 % Favored : 98.26 % Rotamer: Outliers : 0.42 % Allowed : 3.21 % Favored : 96.37 % 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: 1.28 (0.17), residues: 2182 helix: 1.49 (0.13), residues: 1398 sheet: -0.84 (0.42), residues: 110 loop : -0.07 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG N 40 TYR 0.027 0.002 TYR O 51 PHE 0.036 0.003 PHE P 71 TRP 0.033 0.003 TRP K 375 HIS 0.009 0.002 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.26 (32164) covalent geometry : angle 0.75002 / 0.43 (45986) hydrogen bonds : bond 0.07701 / 5.17 ( 1895) hydrogen bonds : angle 4.12464 / 3.05 ( 4825) metal coordination : bond 0.03241 / 1.58 ( 8) metal coordination : angle 2.99423 / 1.94 ( 6) Misc. bond : bond 0.01100 / 0.79 ( 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 : 0.822 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: A 95 GLU cc_start: 0.9019 (tt0) cc_final: 0.8802 (tt0) REVERT: A 107 ASP cc_start: 0.8846 (m-30) cc_final: 0.8567 (m-30) REVERT: C 39 ASN cc_start: 0.8172 (m-40) cc_final: 0.7950 (m110) REVERT: D 63 MET cc_start: 0.9581 (mmm) cc_final: 0.9364 (mmm) REVERT: E 52 ILE cc_start: 0.9552 (OUTLIER) cc_final: 0.9247 (mm) REVERT: E 56 GLN cc_start: 0.8580 (mt0) cc_final: 0.8361 (mt0) REVERT: E 106 GLU cc_start: 0.9590 (tt0) cc_final: 0.9042 (tm-30) REVERT: F 54 GLU cc_start: 0.9377 (mm-30) cc_final: 0.8926 (mt-10) REVERT: F 85 MET cc_start: 0.9058 (tpt) cc_final: 0.8725 (tpp) REVERT: F 99 TYR cc_start: 0.9098 (m-10) cc_final: 0.8413 (m-80) REVERT: G 31 VAL cc_start: 0.8909 (t) cc_final: 0.8591 (p) REVERT: G 57 GLU cc_start: 0.8728 (tt0) cc_final: 0.7713 (tt0) REVERT: G 62 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8854 (mm-30) outliers start: 8 outliers final: 1 residues processed: 264 average time/residue: 0.1685 time to fit residues: 74.8082 Evaluate side-chains 171 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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: 40.0000 chunk 180 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 chunk 235 optimal weight: 0.9980 chunk 218 optimal weight: 30.0000 chunk 268 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 256 optimal weight: 50.0000 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 50.0000 chunk 257 optimal weight: 50.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.090506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.054095 restraints weight = 294628.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.055102 restraints weight = 145174.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.056102 restraints weight = 96097.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.056610 restraints weight = 76768.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.056708 restraints weight = 68867.417| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32190 Z= 0.231 Angle : 0.733 12.303 45992 Z= 0.414 Chirality : 0.044 0.278 5174 Planarity : 0.005 0.069 3704 Dihedral : 30.092 179.991 9158 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.51 % Favored : 98.40 % Rotamer: Outliers : 0.21 % Allowed : 2.68 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.17), residues: 2182 helix: 1.51 (0.13), residues: 1385 sheet: -0.62 (0.45), residues: 96 loop : -0.19 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 79 TYR 0.032 0.002 TYR S 51 PHE 0.049 0.002 PHE E 68 TRP 0.007 0.001 TRP K 375 HIS 0.007 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.23 (32164) covalent geometry : angle 0.73243 / 0.41 (45986) hydrogen bonds : bond 0.06771 / 4.52 ( 1895) hydrogen bonds : angle 4.12646 / 3.04 ( 4825) metal coordination : bond 0.01894 / 0.99 ( 8) metal coordination : angle 3.42491 / 2.06 ( 6) Misc. bond : bond 0.00504 / 0.42 ( 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 252 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 248 time to evaluate : 0.824 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: 0.9373 (mm-30) cc_final: 0.8915 (mm-30) REVERT: A 107 ASP cc_start: 0.8804 (m-30) cc_final: 0.8510 (m-30) REVERT: D 60 MET cc_start: 0.9102 (tpp) cc_final: 0.8670 (tpp) REVERT: D 63 MET cc_start: 0.9566 (mmm) cc_final: 0.9351 (mmp) REVERT: E 98 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8242 (mt-10) REVERT: E 106 GLU cc_start: 0.9586 (tt0) cc_final: 0.9040 (tm-30) REVERT: F 38 LEU cc_start: 0.9651 (mt) cc_final: 0.9443 (tt) REVERT: F 69 ASP cc_start: 0.8852 (m-30) cc_final: 0.8567 (m-30) REVERT: F 86 ASP cc_start: 0.8965 (m-30) cc_final: 0.8575 (t0) REVERT: F 99 TYR cc_start: 0.9186 (m-10) cc_final: 0.8909 (m-80) REVERT: G 31 VAL cc_start: 0.9087 (t) cc_final: 0.8710 (p) REVERT: G 62 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8910 (mm-30) REVERT: G 105 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8106 (tm-30) REVERT: H 103 LEU cc_start: 0.9387 (mp) cc_final: 0.9139 (mp) outliers start: 4 outliers final: 0 residues processed: 249 average time/residue: 0.1701 time to fit residues: 71.4633 Evaluate side-chains 167 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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: 20.0000 chunk 3 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 95 optimal weight: 40.0000 chunk 269 optimal weight: 50.0000 chunk 25 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 96 optimal weight: 40.0000 chunk 104 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4231 r_free = 0.4231 target = 0.090975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.054665 restraints weight = 292912.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.055705 restraints weight = 142585.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.056608 restraints weight = 94203.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.057250 restraints weight = 75881.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.057358 restraints weight = 67169.618| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4254 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= 0.160 Angle : 0.647 9.350 45992 Z= 0.375 Chirality : 0.042 0.269 5174 Planarity : 0.004 0.056 3704 Dihedral : 29.950 179.900 9158 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.88 % Favored : 98.03 % Rotamer: Outliers : 0.05 % Allowed : 1.74 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.18), residues: 2182 helix: 1.70 (0.13), residues: 1387 sheet: -0.31 (0.46), residues: 92 loop : -0.20 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG O 30 TYR 0.030 0.002 TYR G 51 PHE 0.022 0.002 PHE K 280 TRP 0.005 0.001 TRP K 375 HIS 0.005 0.001 HIS T 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 (32164) covalent geometry : angle 0.64349 / 0.37 (45986) hydrogen bonds : bond 0.05297 / 3.53 ( 1895) hydrogen bonds : angle 3.91349 / 2.89 ( 4825) metal coordination : bond 0.01446 / 0.69 ( 8) metal coordination : angle 6.01742 / 4.01 ( 6) Misc. bond : bond 0.00277 / 0.25 ( 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 235 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.825 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 51 GLU cc_start: 0.9401 (mm-30) cc_final: 0.8907 (mm-30) REVERT: A 94 GLN cc_start: 0.9395 (tt0) cc_final: 0.9041 (tp40) REVERT: A 95 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8956 (mm-30) REVERT: A 107 ASP cc_start: 0.8809 (m-30) cc_final: 0.8497 (m-30) REVERT: C 52 MET cc_start: 0.9231 (tpp) cc_final: 0.9026 (tpt) REVERT: D 63 MET cc_start: 0.9585 (mmm) cc_final: 0.9336 (mmp) REVERT: E 106 GLU cc_start: 0.9597 (tt0) cc_final: 0.9047 (tm-30) REVERT: F 60 LYS cc_start: 0.9550 (mtmm) cc_final: 0.9336 (ptpp) REVERT: F 85 MET cc_start: 0.8879 (tpt) cc_final: 0.8645 (tpp) REVERT: F 86 ASP cc_start: 0.8893 (m-30) cc_final: 0.8693 (t0) REVERT: F 99 TYR cc_start: 0.9396 (m-10) cc_final: 0.8668 (m-80) REVERT: G 62 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8815 (mm-30) REVERT: G 91 ASP cc_start: 0.8781 (t0) cc_final: 0.8428 (t70) REVERT: N 38 LEU cc_start: 0.8464 (mm) cc_final: 0.8199 (mm) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.1685 time to fit residues: 66.9601 Evaluate side-chains 171 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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: 1.9990 chunk 70 optimal weight: 3.9990 chunk 257 optimal weight: 50.0000 chunk 273 optimal weight: 50.0000 chunk 46 optimal weight: 4.9990 chunk 148 optimal weight: 40.0000 chunk 154 optimal weight: 20.0000 chunk 172 optimal weight: 50.0000 chunk 99 optimal weight: 50.0000 chunk 116 optimal weight: 0.0970 chunk 233 optimal weight: 20.0000 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN E 114 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.089935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.053272 restraints weight = 295461.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.054138 restraints weight = 146440.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.054991 restraints weight = 99135.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.055826 restraints weight = 80308.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.055951 restraints weight = 70354.615| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32190 Z= 0.200 Angle : 0.667 12.410 45992 Z= 0.385 Chirality : 0.041 0.269 5174 Planarity : 0.005 0.053 3704 Dihedral : 29.890 179.892 9158 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.97 % Favored : 97.94 % Rotamer: Outliers : 0.11 % Allowed : 2.05 % 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: 1.43 (0.18), residues: 2182 helix: 1.66 (0.14), residues: 1391 sheet: -0.32 (0.45), residues: 92 loop : -0.23 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 80 TYR 0.033 0.002 TYR G 40 PHE 0.033 0.002 PHE K 280 TRP 0.014 0.002 TRP L 375 HIS 0.008 0.001 HIS G 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.20 (32164) covalent geometry : angle 0.66529 / 0.38 (45986) hydrogen bonds : bond 0.06480 / 4.33 ( 1895) hydrogen bonds : angle 3.95473 / 2.91 ( 4825) metal coordination : bond 0.01772 / 0.87 ( 8) metal coordination : angle 4.32586 / 2.66 ( 6) Misc. bond : bond 0.00217 / 0.19 ( 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 206 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 0.819 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: 0.9421 (mm-30) cc_final: 0.8944 (mm-30) REVERT: A 107 ASP cc_start: 0.8818 (m-30) cc_final: 0.8502 (m-30) REVERT: D 63 MET cc_start: 0.9577 (mmm) cc_final: 0.9346 (mmp) REVERT: E 106 GLU cc_start: 0.9596 (tt0) cc_final: 0.9043 (tm-30) REVERT: F 85 MET cc_start: 0.8922 (tpt) cc_final: 0.8649 (tpp) REVERT: F 99 TYR cc_start: 0.9326 (m-10) cc_final: 0.8882 (m-10) REVERT: G 62 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8981 (mm-30) REVERT: G 91 ASP cc_start: 0.8805 (t0) cc_final: 0.8555 (t70) REVERT: H 94 GLU cc_start: 0.9422 (mp0) cc_final: 0.9190 (mp0) outliers start: 2 outliers final: 0 residues processed: 205 average time/residue: 0.1661 time to fit residues: 58.3221 Evaluate side-chains 146 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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: 6.9990 chunk 118 optimal weight: 10.0000 chunk 270 optimal weight: 50.0000 chunk 231 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 230 optimal weight: 7.9990 chunk 173 optimal weight: 0.0060 chunk 110 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.090522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.053959 restraints weight = 293949.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.055010 restraints weight = 142957.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.056081 restraints weight = 94682.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.056249 restraints weight = 75541.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.056388 restraints weight = 68962.749| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4819 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= 0.152 Angle : 0.629 10.033 45992 Z= 0.367 Chirality : 0.041 0.270 5174 Planarity : 0.004 0.066 3704 Dihedral : 29.807 178.944 9158 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.88 % Favored : 98.03 % Rotamer: Outliers : 0.11 % Allowed : 0.79 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.18), residues: 2182 helix: 1.76 (0.14), residues: 1400 sheet: -0.23 (0.46), residues: 92 loop : -0.22 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG T 80 TYR 0.026 0.001 TYR G 40 PHE 0.030 0.002 PHE K 280 TRP 0.006 0.001 TRP L 455 HIS 0.008 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (32164) covalent geometry : angle 0.62777 / 0.37 (45986) hydrogen bonds : bond 0.04834 / 3.24 ( 1895) hydrogen bonds : angle 3.81402 / 2.81 ( 4825) metal coordination : bond 0.01497 / 0.73 ( 8) metal coordination : angle 3.84267 / 2.39 ( 6) Misc. bond : bond 0.00024 / 0.02 ( 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 227 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 225 time to evaluate : 0.893 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: 0.9412 (mm-30) cc_final: 0.8929 (mm-30) REVERT: A 52 ILE cc_start: 0.9523 (mt) cc_final: 0.9297 (mm) REVERT: A 94 GLN cc_start: 0.9360 (tt0) cc_final: 0.9124 (tp40) REVERT: A 107 ASP cc_start: 0.8781 (m-30) cc_final: 0.8449 (m-30) REVERT: C 39 ASN cc_start: 0.8368 (m110) cc_final: 0.8165 (m110) REVERT: D 60 MET cc_start: 0.9139 (tpp) cc_final: 0.8860 (tpp) REVERT: D 77 GLU cc_start: 0.9318 (mm-30) cc_final: 0.9108 (tp30) REVERT: D 101 LEU cc_start: 0.9453 (mm) cc_final: 0.8899 (tp) REVERT: E 51 GLU cc_start: 0.9246 (mp0) cc_final: 0.8938 (mp0) REVERT: E 61 LEU cc_start: 0.9391 (mt) cc_final: 0.9158 (mt) REVERT: E 106 GLU cc_start: 0.9585 (tt0) cc_final: 0.8997 (tm-30) REVERT: E 107 ASP cc_start: 0.9464 (m-30) cc_final: 0.9258 (m-30) REVERT: F 69 ASP cc_start: 0.8984 (m-30) cc_final: 0.8689 (m-30) REVERT: F 85 MET cc_start: 0.8946 (tpt) cc_final: 0.8679 (tpp) REVERT: F 99 TYR cc_start: 0.9296 (m-10) cc_final: 0.8843 (m-10) REVERT: G 62 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8842 (mm-30) REVERT: G 91 ASP cc_start: 0.8760 (t0) cc_final: 0.8464 (t70) outliers start: 2 outliers final: 0 residues processed: 226 average time/residue: 0.1720 time to fit residues: 66.6166 Evaluate side-chains 157 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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: 0.6980 chunk 85 optimal weight: 50.0000 chunk 168 optimal weight: 10.0000 chunk 174 optimal weight: 80.0000 chunk 209 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 188 optimal weight: 30.0000 chunk 205 optimal weight: 0.0000 chunk 73 optimal weight: 50.0000 chunk 86 optimal weight: 50.0000 overall best weight: 3.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.080144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.057818 restraints weight = 264967.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.058755 restraints weight = 113830.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.059476 restraints weight = 68466.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.059762 restraints weight = 51043.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.060195 restraints weight = 44552.764| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32190 Z= 0.153 Angle : 0.621 10.412 45992 Z= 0.363 Chirality : 0.040 0.266 5174 Planarity : 0.004 0.049 3704 Dihedral : 29.700 178.902 9158 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.88 % Favored : 98.03 % Rotamer: Outliers : 0.05 % Allowed : 0.63 % Favored : 99.32 % 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: 1.57 (0.18), residues: 2182 helix: 1.79 (0.14), residues: 1391 sheet: -0.32 (0.46), residues: 88 loop : -0.21 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG S 89 TYR 0.022 0.001 TYR O 51 PHE 0.027 0.002 PHE K 433 TRP 0.006 0.001 TRP L 455 HIS 0.005 0.001 HIS T 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (32164) covalent geometry : angle 0.61798 / 0.36 (45986) hydrogen bonds : bond 0.05049 / 3.38 ( 1895) hydrogen bonds : angle 3.81891 / 2.82 ( 4825) metal coordination : bond 0.01418 / 0.66 ( 8) metal coordination : angle 5.00107 / 3.50 ( 6) Misc. bond : bond 0.00380 / 0.33 ( 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 218 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.535 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: A 51 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9073 (mm-30) REVERT: A 94 GLN cc_start: 0.9471 (tt0) cc_final: 0.9135 (tp40) REVERT: A 107 ASP cc_start: 0.8861 (m-30) cc_final: 0.8526 (m-30) REVERT: D 60 MET cc_start: 0.9295 (tpp) cc_final: 0.9091 (tpp) REVERT: D 77 GLU cc_start: 0.9532 (mm-30) cc_final: 0.9219 (tp30) REVERT: D 101 LEU cc_start: 0.9494 (mm) cc_final: 0.9037 (tp) REVERT: E 61 LEU cc_start: 0.9409 (mt) cc_final: 0.9160 (mt) REVERT: E 106 GLU cc_start: 0.9669 (tt0) cc_final: 0.9017 (tm-30) REVERT: E 121 MET cc_start: 0.9195 (tpp) cc_final: 0.8872 (mmm) REVERT: F 69 ASP cc_start: 0.9072 (m-30) cc_final: 0.8849 (m-30) REVERT: F 99 TYR cc_start: 0.9459 (m-10) cc_final: 0.8821 (m-10) REVERT: G 57 GLU cc_start: 0.8779 (tt0) cc_final: 0.8235 (tt0) REVERT: G 62 GLU cc_start: 0.9270 (mm-30) cc_final: 0.9002 (mm-30) REVERT: G 91 ASP cc_start: 0.8871 (t0) cc_final: 0.8561 (t70) REVERT: H 94 GLU cc_start: 0.9503 (mp0) cc_final: 0.9144 (mp0) REVERT: R 85 MET cc_start: 0.9511 (pmm) cc_final: 0.9304 (pmm) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.1671 time to fit residues: 61.6956 Evaluate side-chains 149 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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: 8.9990 chunk 72 optimal weight: 50.0000 chunk 263 optimal weight: 50.0000 chunk 1 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 247 optimal weight: 50.0000 chunk 225 optimal weight: 0.7980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4222 r_free = 0.4222 target = 0.090304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.056800 restraints weight = 294707.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.056577 restraints weight = 157204.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.056510 restraints weight = 130895.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.056591 restraints weight = 89737.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.056479 restraints weight = 90044.012| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32190 Z= 0.160 Angle : 0.622 11.457 45992 Z= 0.364 Chirality : 0.040 0.267 5174 Planarity : 0.004 0.054 3704 Dihedral : 29.698 178.554 9158 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.20 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: 1.67 (0.18), residues: 2182 helix: 1.88 (0.14), residues: 1380 sheet: -0.28 (0.46), residues: 88 loop : -0.17 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG N 68 TYR 0.020 0.001 TYR G 40 PHE 0.043 0.002 PHE M 105 TRP 0.006 0.001 TRP L 455 HIS 0.005 0.001 HIS T 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 (32164) covalent geometry : angle 0.62016 / 0.36 (45986) hydrogen bonds : bond 0.05056 / 3.39 ( 1895) hydrogen bonds : angle 3.80628 / 2.82 ( 4825) metal coordination : bond 0.01858 / 0.89 ( 8) metal coordination : angle 4.63172 / 3.12 ( 6) Misc. bond : bond 0.00365 / 0.33 ( 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 215 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.937 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: 0.9443 (mm-30) cc_final: 0.8984 (mm-30) REVERT: A 52 ILE cc_start: 0.9542 (mt) cc_final: 0.9317 (mm) REVERT: A 94 GLN cc_start: 0.9364 (tt0) cc_final: 0.9080 (tp40) REVERT: A 107 ASP cc_start: 0.8681 (m-30) cc_final: 0.8355 (m-30) REVERT: D 77 GLU cc_start: 0.9386 (mm-30) cc_final: 0.9158 (tp30) REVERT: E 51 GLU cc_start: 0.9267 (mp0) cc_final: 0.8825 (mp0) REVERT: E 56 GLN cc_start: 0.8830 (mt0) cc_final: 0.8506 (tt0) REVERT: E 61 LEU cc_start: 0.9429 (mt) cc_final: 0.9208 (mt) REVERT: E 106 GLU cc_start: 0.9547 (tt0) cc_final: 0.8982 (tm-30) REVERT: E 121 MET cc_start: 0.9291 (tpp) cc_final: 0.8864 (mmm) REVERT: F 69 ASP cc_start: 0.8870 (m-30) cc_final: 0.8644 (m-30) REVERT: F 99 TYR cc_start: 0.9330 (m-10) cc_final: 0.8893 (m-10) REVERT: G 57 GLU cc_start: 0.8766 (tt0) cc_final: 0.8223 (tt0) REVERT: G 62 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8888 (mm-30) REVERT: G 91 ASP cc_start: 0.8716 (t0) cc_final: 0.8498 (t70) REVERT: H 94 GLU cc_start: 0.9431 (mp0) cc_final: 0.9193 (mp0) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1821 time to fit residues: 66.3495 Evaluate side-chains 153 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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: 0.0870 chunk 234 optimal weight: 7.9990 chunk 151 optimal weight: 0.0970 chunk 190 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 98 optimal weight: 30.0000 chunk 57 optimal weight: 8.9990 chunk 118 optimal weight: 30.0000 chunk 256 optimal weight: 50.0000 chunk 184 optimal weight: 30.0000 overall best weight: 2.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.090744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.057221 restraints weight = 290722.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.057346 restraints weight = 149111.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.056896 restraints weight = 117704.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.057029 restraints weight = 90419.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.056926 restraints weight = 82364.339| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 32190 Z= 0.140 Angle : 0.615 11.706 45992 Z= 0.359 Chirality : 0.040 0.267 5174 Planarity : 0.004 0.050 3704 Dihedral : 29.616 178.094 9158 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.06 % Favored : 97.85 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % 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: 1.62 (0.18), residues: 2182 helix: 1.83 (0.14), residues: 1393 sheet: -0.23 (0.47), residues: 86 loop : -0.23 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 93 TYR 0.018 0.001 TYR O 51 PHE 0.037 0.002 PHE M 105 TRP 0.007 0.001 TRP K 455 HIS 0.005 0.001 HIS T 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (32164) covalent geometry : angle 0.61041 / 0.36 (45986) hydrogen bonds : bond 0.04460 / 2.99 ( 1895) hydrogen bonds : angle 3.73977 / 2.77 ( 4825) metal coordination : bond 0.02346 / 1.27 ( 8) metal coordination : angle 6.57141 / 4.18 ( 6) Misc. bond : bond 0.00058 / 0.05 ( 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 220 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.921 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: A 51 GLU cc_start: 0.9427 (mm-30) cc_final: 0.8942 (mm-30) REVERT: A 94 GLN cc_start: 0.9315 (tt0) cc_final: 0.9106 (tp40) REVERT: A 107 ASP cc_start: 0.8614 (m-30) cc_final: 0.8295 (m-30) REVERT: D 77 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9137 (tp30) REVERT: D 101 LEU cc_start: 0.9456 (mm) cc_final: 0.9133 (tp) REVERT: E 51 GLU cc_start: 0.9220 (mp0) cc_final: 0.8779 (mp0) REVERT: E 61 LEU cc_start: 0.9402 (mt) cc_final: 0.9192 (mt) REVERT: E 106 GLU cc_start: 0.9566 (tt0) cc_final: 0.9033 (tm-30) REVERT: E 121 MET cc_start: 0.9257 (tpp) cc_final: 0.8854 (mmm) REVERT: F 99 TYR cc_start: 0.9449 (m-10) cc_final: 0.8862 (m-10) REVERT: G 57 GLU cc_start: 0.8772 (tt0) cc_final: 0.8218 (tt0) REVERT: G 62 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8840 (mm-30) REVERT: G 91 ASP cc_start: 0.8641 (t0) cc_final: 0.8430 (t70) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.1742 time to fit residues: 65.1073 Evaluate side-chains 160 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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: 3.9990 chunk 73 optimal weight: 50.0000 chunk 271 optimal weight: 50.0000 chunk 70 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 141 optimal weight: 30.0000 chunk 134 optimal weight: 4.9990 chunk 104 optimal weight: 30.0000 chunk 130 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.089807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.052897 restraints weight = 296275.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.053883 restraints weight = 146249.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.054072 restraints weight = 97811.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.055270 restraints weight = 84238.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.055390 restraints weight = 73029.571| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32190 Z= 0.182 Angle : 0.639 14.755 45992 Z= 0.373 Chirality : 0.040 0.270 5174 Planarity : 0.004 0.050 3704 Dihedral : 29.668 178.164 9158 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.15 % Favored : 97.75 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % 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: 1.63 (0.18), residues: 2182 helix: 1.84 (0.14), residues: 1379 sheet: -0.26 (0.47), residues: 86 loop : -0.18 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 33 TYR 0.019 0.001 TYR G 40 PHE 0.032 0.002 PHE M 105 TRP 0.006 0.001 TRP K 330 HIS 0.010 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 (32164) covalent geometry : angle 0.63607 / 0.37 (45986) hydrogen bonds : bond 0.05701 / 3.81 ( 1895) hydrogen bonds : angle 3.85059 / 2.85 ( 4825) metal coordination : bond 0.01747 / 0.85 ( 8) metal coordination : angle 5.76321 / 3.63 ( 6) Misc. bond : bond 0.00223 / 0.20 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7585.99 seconds wall clock time: 129 minutes 54.26 seconds (7794.26 seconds total)