Starting phenix.real_space_refine on Sat Mar 7 04:52:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xkt_33270/03_2026/7xkt_33270_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xkt_33270/03_2026/7xkt_33270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xkt_33270/03_2026/7xkt_33270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xkt_33270/03_2026/7xkt_33270.map" model { file = "/net/cci-nas-00/data/ceres_data/7xkt_33270/03_2026/7xkt_33270_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xkt_33270/03_2026/7xkt_33270_trim.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.155 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 156 5.16 5 C 12444 2.51 5 N 2544 2.21 5 O 3336 1.98 5 H 16008 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34488 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 173 Unusual residues: {'LHG': 1, 'MC3': 6, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "F" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "H" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "I" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "J" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "K" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "L" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 3.92, per 1000 atoms: 0.11 Number of scatterers: 34488 At special positions: 0 Unit cell: (97.875, 100.575, 147.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 O 3336 8.00 N 2544 7.00 C 12444 6.00 H 16008 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.04 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.04 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.04 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.04 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.04 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.04 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.04 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.04 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.04 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.04 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.04 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.04 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.04 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.04 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.04 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.04 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.04 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.04 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.04 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.04 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.04 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.04 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.04 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.04 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.04 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.04 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.04 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.04 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.04 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.04 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 76.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.689A pdb=" N GLY A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 46' Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 246 through 276 Processing helix chain 'B' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 222 Processing helix chain 'B' and resid 246 through 276 Processing helix chain 'C' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 46' Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU C 91 " --> pdb=" O CYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 222 Processing helix chain 'C' and resid 246 through 276 Processing helix chain 'D' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 41 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 74 through 86 Processing helix chain 'D' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 222 Processing helix chain 'D' and resid 246 through 276 Processing helix chain 'E' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL E 41 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 41 through 46' Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU E 91 " --> pdb=" O CYS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 222 Processing helix chain 'E' and resid 246 through 276 Processing helix chain 'F' and resid 20 through 41 removed outlier: 4.099A pdb=" N ARG F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 61 through 71 Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU F 91 " --> pdb=" O CYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 222 Processing helix chain 'F' and resid 246 through 276 Processing helix chain 'G' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 41 through 46' Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 74 through 86 Processing helix chain 'G' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU G 91 " --> pdb=" O CYS G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 222 Processing helix chain 'G' and resid 246 through 276 Processing helix chain 'H' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG H 24 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE H 25 " --> pdb=" O MET H 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 41 through 46' Processing helix chain 'H' and resid 61 through 71 Processing helix chain 'H' and resid 74 through 86 Processing helix chain 'H' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU H 91 " --> pdb=" O CYS H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 222 Processing helix chain 'H' and resid 246 through 276 Processing helix chain 'I' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG I 24 " --> pdb=" O THR I 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE I 25 " --> pdb=" O MET I 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 41 through 46' Processing helix chain 'I' and resid 61 through 71 Processing helix chain 'I' and resid 74 through 86 Processing helix chain 'I' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU I 91 " --> pdb=" O CYS I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 222 Processing helix chain 'I' and resid 246 through 276 Processing helix chain 'J' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG J 24 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE J 25 " --> pdb=" O MET J 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 41 through 46' Processing helix chain 'J' and resid 61 through 71 Processing helix chain 'J' and resid 74 through 86 Processing helix chain 'J' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU J 91 " --> pdb=" O CYS J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 222 Processing helix chain 'J' and resid 246 through 276 Processing helix chain 'K' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG K 24 " --> pdb=" O THR K 20 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 41 through 46' Processing helix chain 'K' and resid 61 through 71 Processing helix chain 'K' and resid 74 through 86 Processing helix chain 'K' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU K 91 " --> pdb=" O CYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 222 Processing helix chain 'K' and resid 246 through 276 Processing helix chain 'L' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG L 24 " --> pdb=" O THR L 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE L 25 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 41 through 46' Processing helix chain 'L' and resid 61 through 71 Processing helix chain 'L' and resid 74 through 86 Processing helix chain 'L' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU L 91 " --> pdb=" O CYS L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 222 Processing helix chain 'L' and resid 246 through 276 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'F' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 55 Processing sheet with id=AA8, first strand: chain 'H' and resid 54 through 55 Processing sheet with id=AA9, first strand: chain 'I' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'J' and resid 54 through 55 Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 55 Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 1176 hydrogen bonds defined for protein. 3456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.69 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 15972 1.03 - 1.23: 1013 1.23 - 1.44: 6583 1.44 - 1.64: 10548 1.64 - 1.85: 300 Bond restraints: 34416 Sorted by residual: bond pdb=" CAI Y01 E 405 " pdb=" CAZ Y01 E 405 " ideal model delta sigma weight residual 1.332 1.034 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" CAI Y01 L 405 " pdb=" CAZ Y01 L 405 " ideal model delta sigma weight residual 1.332 1.034 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" CAI Y01 C 405 " pdb=" CAZ Y01 C 405 " ideal model delta sigma weight residual 1.332 1.034 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" CAI Y01 J 405 " pdb=" CAZ Y01 J 405 " ideal model delta sigma weight residual 1.332 1.035 0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" CAI Y01 A 405 " pdb=" CAZ Y01 A 405 " ideal model delta sigma weight residual 1.332 1.035 0.297 2.00e-02 2.50e+03 2.21e+02 ... (remaining 34411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 55887 2.50 - 5.01: 4131 5.01 - 7.51: 461 7.51 - 10.02: 253 10.02 - 12.52: 48 Bond angle restraints: 60780 Sorted by residual: angle pdb=" CAM Y01 L 406 " pdb=" CAY Y01 L 406 " pdb=" OAW Y01 L 406 " ideal model delta sigma weight residual 111.19 123.59 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CAM Y01 I 406 " pdb=" CAY Y01 I 406 " pdb=" OAW Y01 I 406 " ideal model delta sigma weight residual 111.19 123.59 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CAM Y01 C 406 " pdb=" CAY Y01 C 406 " pdb=" OAW Y01 C 406 " ideal model delta sigma weight residual 111.19 123.59 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CAM Y01 K 406 " pdb=" CAY Y01 K 406 " pdb=" OAW Y01 K 406 " ideal model delta sigma weight residual 111.19 123.59 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CAM Y01 B 406 " pdb=" CAY Y01 B 406 " pdb=" OAW Y01 B 406 " ideal model delta sigma weight residual 111.19 123.59 -12.40 3.00e+00 1.11e-01 1.71e+01 ... (remaining 60775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 15048 21.99 - 43.97: 2165 43.97 - 65.96: 715 65.96 - 87.94: 96 87.94 - 109.93: 48 Dihedral angle restraints: 18072 sinusoidal: 10800 harmonic: 7272 Sorted by residual: dihedral pdb=" CAT Y01 I 405 " pdb=" CAR Y01 I 405 " pdb=" CBC Y01 I 405 " pdb=" CAV Y01 I 405 " ideal model delta sinusoidal sigma weight residual 58.10 -51.83 109.93 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" CAT Y01 C 405 " pdb=" CAR Y01 C 405 " pdb=" CBC Y01 C 405 " pdb=" CAV Y01 C 405 " ideal model delta sinusoidal sigma weight residual 58.10 -51.78 109.88 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" CAT Y01 G 405 " pdb=" CAR Y01 G 405 " pdb=" CBC Y01 G 405 " pdb=" CAV Y01 G 405 " ideal model delta sinusoidal sigma weight residual 58.10 -51.76 109.86 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 18069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1886 0.099 - 0.197: 714 0.197 - 0.295: 124 0.295 - 0.394: 36 0.394 - 0.492: 48 Chirality restraints: 2808 Sorted by residual: chirality pdb=" CBF Y01 D 405 " pdb=" CAS Y01 D 405 " pdb=" CBD Y01 D 405 " pdb=" CBH Y01 D 405 " both_signs ideal model delta sigma weight residual False -2.45 -2.94 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CBF Y01 A 405 " pdb=" CAS Y01 A 405 " pdb=" CBD Y01 A 405 " pdb=" CBH Y01 A 405 " both_signs ideal model delta sigma weight residual False -2.45 -2.94 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CBF Y01 G 405 " pdb=" CAS Y01 G 405 " pdb=" CBD Y01 G 405 " pdb=" CBH Y01 G 405 " both_signs ideal model delta sigma weight residual False -2.45 -2.94 0.49 2.00e-01 2.50e+01 6.06e+00 ... (remaining 2805 not shown) Planarity restraints: 4716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 238 " -0.033 2.00e-02 2.50e+03 6.36e-02 4.04e+01 pdb=" N GLU E 239 " 0.109 2.00e-02 2.50e+03 pdb=" CA GLU E 239 " -0.028 2.00e-02 2.50e+03 pdb=" H GLU E 239 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS G 238 " 0.033 2.00e-02 2.50e+03 6.35e-02 4.03e+01 pdb=" N GLU G 239 " -0.109 2.00e-02 2.50e+03 pdb=" CA GLU G 239 " 0.028 2.00e-02 2.50e+03 pdb=" H GLU G 239 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 238 " -0.033 2.00e-02 2.50e+03 6.35e-02 4.03e+01 pdb=" N GLU F 239 " 0.109 2.00e-02 2.50e+03 pdb=" CA GLU F 239 " -0.028 2.00e-02 2.50e+03 pdb=" H GLU F 239 " -0.049 2.00e-02 2.50e+03 ... (remaining 4713 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.41: 13842 2.41 - 2.95: 66547 2.95 - 3.50: 83967 3.50 - 4.05: 110286 4.05 - 4.60: 164240 Nonbonded interactions: 438882 Sorted by model distance: nonbonded pdb=" OE1 GLN L 64 " pdb=" H GLN L 64 " model vdw 1.858 2.450 nonbonded pdb=" OE1 GLN I 64 " pdb=" H GLN I 64 " model vdw 1.858 2.450 nonbonded pdb=" OE1 GLN F 64 " pdb=" H GLN F 64 " model vdw 1.858 2.450 nonbonded pdb=" OE1 GLN A 64 " pdb=" H GLN A 64 " model vdw 1.858 2.450 nonbonded pdb=" OE1 GLN G 64 " pdb=" H GLN G 64 " model vdw 1.858 2.450 ... (remaining 438877 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.280 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: 0.220 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.830 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.029 0.298 18444 Z= 1.302 Angle : 1.851 12.521 24768 Z= 0.838 Chirality : 0.117 0.492 2808 Planarity : 0.008 0.051 2820 Dihedral : 20.882 109.928 8412 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.33 % Allowed : 14.67 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.53 (0.17), residues: 1944 helix: 1.92 (0.13), residues: 1320 sheet: 0.26 (0.36), residues: 144 loop : -1.32 (0.23), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 34 TYR 0.030 0.006 TYR F 67 PHE 0.035 0.005 PHE L 53 TRP 0.006 0.003 TRP F 79 HIS 0.007 0.003 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.02856 (18408) covalent geometry : angle 1.84763 (24696) SS BOND : bond 0.00851 ( 36) SS BOND : angle 2.74120 ( 72) hydrogen bonds : bond 0.18318 ( 1176) hydrogen bonds : angle 4.85357 ( 3456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 0.981 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 252 average time/residue: 1.4067 time to fit residues: 394.9606 Evaluate side-chains 200 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 100 GLN C 100 GLN D 100 GLN E 100 GLN F 100 GLN G 100 GLN H 100 GLN I 100 GLN J 100 GLN K 100 GLN L 100 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.178186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.125086 restraints weight = 42158.263| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.34 r_work: 0.3334 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18444 Z= 0.202 Angle : 0.789 8.105 24768 Z= 0.387 Chirality : 0.046 0.156 2808 Planarity : 0.005 0.031 2820 Dihedral : 16.826 66.079 4848 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.67 % Allowed : 15.89 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.18), residues: 1944 helix: 2.77 (0.13), residues: 1356 sheet: 1.45 (0.40), residues: 120 loop : -0.70 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 246 TYR 0.014 0.002 TYR E 67 PHE 0.014 0.001 PHE E 53 TRP 0.004 0.001 TRP H 79 HIS 0.002 0.001 HIS L 274 Details of bonding type rmsd covalent geometry : bond 0.00366 (18408) covalent geometry : angle 0.78809 (24696) SS BOND : bond 0.00328 ( 36) SS BOND : angle 1.07812 ( 72) hydrogen bonds : bond 0.10374 ( 1176) hydrogen bonds : angle 4.17649 ( 3456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.931 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 200 average time/residue: 1.5578 time to fit residues: 344.8971 Evaluate side-chains 172 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.172306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119568 restraints weight = 42282.159| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.30 r_work: 0.3255 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 18444 Z= 0.229 Angle : 0.806 7.945 24768 Z= 0.402 Chirality : 0.046 0.146 2808 Planarity : 0.005 0.028 2820 Dihedral : 15.088 58.680 4848 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.83 % Allowed : 15.11 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.18), residues: 1944 helix: 2.84 (0.13), residues: 1356 sheet: 1.83 (0.42), residues: 120 loop : -1.24 (0.23), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 206 TYR 0.020 0.003 TYR J 67 PHE 0.023 0.002 PHE E 53 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.001 HIS I 274 Details of bonding type rmsd covalent geometry : bond 0.00454 (18408) covalent geometry : angle 0.79985 (24696) SS BOND : bond 0.00817 ( 36) SS BOND : angle 1.99492 ( 72) hydrogen bonds : bond 0.10965 ( 1176) hydrogen bonds : angle 3.95228 ( 3456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.910 Fit side-chains REVERT: A 195 ILE cc_start: 0.4271 (OUTLIER) cc_final: 0.3919 (tt) REVERT: C 195 ILE cc_start: 0.4214 (OUTLIER) cc_final: 0.3873 (tt) REVERT: C 198 PHE cc_start: 0.5861 (OUTLIER) cc_final: 0.5005 (m-80) REVERT: D 195 ILE cc_start: 0.4262 (OUTLIER) cc_final: 0.3912 (tt) REVERT: F 195 ILE cc_start: 0.4215 (OUTLIER) cc_final: 0.3873 (tt) REVERT: F 198 PHE cc_start: 0.5862 (OUTLIER) cc_final: 0.5010 (m-80) REVERT: G 195 ILE cc_start: 0.4262 (OUTLIER) cc_final: 0.3910 (tt) REVERT: I 195 ILE cc_start: 0.4220 (OUTLIER) cc_final: 0.3877 (tt) REVERT: I 198 PHE cc_start: 0.5856 (OUTLIER) cc_final: 0.5000 (m-80) REVERT: J 195 ILE cc_start: 0.4282 (OUTLIER) cc_final: 0.3925 (tt) REVERT: L 195 ILE cc_start: 0.4218 (OUTLIER) cc_final: 0.3873 (tt) REVERT: L 198 PHE cc_start: 0.5863 (OUTLIER) cc_final: 0.5010 (m-80) outliers start: 33 outliers final: 0 residues processed: 197 average time/residue: 1.6862 time to fit residues: 365.5642 Evaluate side-chains 175 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain I residue 198 PHE Chi-restraints excluded: chain J residue 195 ILE Chi-restraints excluded: chain L residue 195 ILE Chi-restraints excluded: chain L residue 198 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 127 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.171360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.117584 restraints weight = 42349.176| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.32 r_work: 0.3247 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18444 Z= 0.227 Angle : 0.754 5.519 24768 Z= 0.388 Chirality : 0.045 0.155 2808 Planarity : 0.005 0.028 2820 Dihedral : 15.049 59.967 4848 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.44 % Allowed : 15.50 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.18), residues: 1944 helix: 2.91 (0.13), residues: 1356 sheet: 1.66 (0.42), residues: 120 loop : -1.23 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 34 TYR 0.020 0.004 TYR G 67 PHE 0.020 0.002 PHE A 53 TRP 0.005 0.002 TRP J 79 HIS 0.004 0.001 HIS L 274 Details of bonding type rmsd covalent geometry : bond 0.00448 (18408) covalent geometry : angle 0.74760 (24696) SS BOND : bond 0.00808 ( 36) SS BOND : angle 1.98799 ( 72) hydrogen bonds : bond 0.10811 ( 1176) hydrogen bonds : angle 3.86797 ( 3456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.905 Fit side-chains REVERT: A 195 ILE cc_start: 0.4324 (OUTLIER) cc_final: 0.3960 (tt) REVERT: A 198 PHE cc_start: 0.5846 (OUTLIER) cc_final: 0.5131 (m-80) REVERT: B 202 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.7150 (pt0) REVERT: C 195 ILE cc_start: 0.4203 (OUTLIER) cc_final: 0.3864 (tt) REVERT: C 198 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.5179 (m-80) REVERT: D 195 ILE cc_start: 0.4318 (OUTLIER) cc_final: 0.3954 (tt) REVERT: D 198 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.5132 (m-80) REVERT: E 195 ILE cc_start: 0.4247 (OUTLIER) cc_final: 0.3860 (tt) REVERT: E 202 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.7151 (pt0) REVERT: F 195 ILE cc_start: 0.4203 (OUTLIER) cc_final: 0.3864 (tt) REVERT: F 198 PHE cc_start: 0.5991 (OUTLIER) cc_final: 0.5168 (m-80) REVERT: G 195 ILE cc_start: 0.4314 (OUTLIER) cc_final: 0.3950 (tt) REVERT: G 198 PHE cc_start: 0.5846 (OUTLIER) cc_final: 0.5134 (m-80) REVERT: H 202 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7146 (pt0) REVERT: I 195 ILE cc_start: 0.4216 (OUTLIER) cc_final: 0.3874 (tt) REVERT: I 198 PHE cc_start: 0.6006 (OUTLIER) cc_final: 0.5174 (m-80) REVERT: J 195 ILE cc_start: 0.4317 (OUTLIER) cc_final: 0.3959 (tt) REVERT: J 198 PHE cc_start: 0.5840 (OUTLIER) cc_final: 0.5131 (m-80) REVERT: K 202 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.7147 (pt0) REVERT: L 195 ILE cc_start: 0.4200 (OUTLIER) cc_final: 0.3860 (tt) REVERT: L 198 PHE cc_start: 0.5993 (OUTLIER) cc_final: 0.5166 (m-80) outliers start: 44 outliers final: 8 residues processed: 192 average time/residue: 1.5323 time to fit residues: 324.0824 Evaluate side-chains 177 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain I residue 198 PHE Chi-restraints excluded: chain J residue 195 ILE Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 202 GLN Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 195 ILE Chi-restraints excluded: chain L residue 198 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.170849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116889 restraints weight = 42638.107| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.31 r_work: 0.3238 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18444 Z= 0.235 Angle : 0.770 5.786 24768 Z= 0.396 Chirality : 0.046 0.154 2808 Planarity : 0.005 0.029 2820 Dihedral : 15.254 58.570 4848 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.56 % Allowed : 14.83 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.18), residues: 1944 helix: 2.89 (0.13), residues: 1356 sheet: 1.68 (0.43), residues: 120 loop : -1.18 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 34 TYR 0.021 0.004 TYR D 67 PHE 0.022 0.002 PHE D 53 TRP 0.005 0.002 TRP G 79 HIS 0.003 0.001 HIS L 274 Details of bonding type rmsd covalent geometry : bond 0.00479 (18408) covalent geometry : angle 0.76219 (24696) SS BOND : bond 0.00871 ( 36) SS BOND : angle 2.10692 ( 72) hydrogen bonds : bond 0.11035 ( 1176) hydrogen bonds : angle 3.84000 ( 3456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 1.052 Fit side-chains REVERT: A 198 PHE cc_start: 0.6043 (OUTLIER) cc_final: 0.5322 (m-80) REVERT: C 198 PHE cc_start: 0.6060 (OUTLIER) cc_final: 0.5257 (m-80) REVERT: D 198 PHE cc_start: 0.6037 (OUTLIER) cc_final: 0.5316 (m-80) REVERT: E 195 ILE cc_start: 0.4188 (OUTLIER) cc_final: 0.3820 (tt) REVERT: F 198 PHE cc_start: 0.6057 (OUTLIER) cc_final: 0.5250 (m-80) REVERT: G 198 PHE cc_start: 0.6034 (OUTLIER) cc_final: 0.5314 (m-80) REVERT: I 198 PHE cc_start: 0.6060 (OUTLIER) cc_final: 0.5252 (m-80) REVERT: J 198 PHE cc_start: 0.6039 (OUTLIER) cc_final: 0.5321 (m-80) REVERT: L 198 PHE cc_start: 0.6055 (OUTLIER) cc_final: 0.5251 (m-80) outliers start: 64 outliers final: 21 residues processed: 219 average time/residue: 1.4021 time to fit residues: 342.2557 Evaluate side-chains 186 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain I residue 198 PHE Chi-restraints excluded: chain I residue 202 GLN Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 198 PHE Chi-restraints excluded: chain L residue 202 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 28 optimal weight: 0.0970 chunk 160 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.175051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.122369 restraints weight = 43095.013| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.32 r_work: 0.3309 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18444 Z= 0.155 Angle : 0.625 6.025 24768 Z= 0.321 Chirality : 0.042 0.151 2808 Planarity : 0.004 0.024 2820 Dihedral : 14.186 59.806 4848 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.78 % Allowed : 17.44 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.44 (0.18), residues: 1944 helix: 3.35 (0.13), residues: 1356 sheet: 1.85 (0.42), residues: 120 loop : -1.11 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 233 TYR 0.014 0.002 TYR G 67 PHE 0.014 0.001 PHE E 53 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00282 (18408) covalent geometry : angle 0.62322 (24696) SS BOND : bond 0.00316 ( 36) SS BOND : angle 0.99889 ( 72) hydrogen bonds : bond 0.08625 ( 1176) hydrogen bonds : angle 3.56933 ( 3456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.829 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 0 residues processed: 170 average time/residue: 1.6587 time to fit residues: 310.0794 Evaluate side-chains 156 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 157 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.173163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119719 restraints weight = 42912.651| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.32 r_work: 0.3274 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18444 Z= 0.184 Angle : 0.664 5.854 24768 Z= 0.342 Chirality : 0.043 0.152 2808 Planarity : 0.004 0.026 2820 Dihedral : 14.346 59.491 4848 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.61 % Allowed : 16.61 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.42 (0.18), residues: 1944 helix: 3.32 (0.13), residues: 1356 sheet: 1.85 (0.43), residues: 120 loop : -1.06 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 34 TYR 0.016 0.003 TYR G 67 PHE 0.018 0.002 PHE G 53 TRP 0.003 0.001 TRP J 79 HIS 0.003 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00351 (18408) covalent geometry : angle 0.65968 (24696) SS BOND : bond 0.00607 ( 36) SS BOND : angle 1.50734 ( 72) hydrogen bonds : bond 0.09423 ( 1176) hydrogen bonds : angle 3.59324 ( 3456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 198 PHE cc_start: 0.5793 (OUTLIER) cc_final: 0.5038 (m-80) REVERT: C 198 PHE cc_start: 0.5955 (OUTLIER) cc_final: 0.5161 (m-80) REVERT: D 198 PHE cc_start: 0.5797 (OUTLIER) cc_final: 0.5034 (m-80) REVERT: F 198 PHE cc_start: 0.5943 (OUTLIER) cc_final: 0.5153 (m-80) REVERT: G 198 PHE cc_start: 0.5798 (OUTLIER) cc_final: 0.5036 (m-80) REVERT: I 198 PHE cc_start: 0.5963 (OUTLIER) cc_final: 0.5168 (m-80) REVERT: J 198 PHE cc_start: 0.5791 (OUTLIER) cc_final: 0.5028 (m-80) REVERT: L 198 PHE cc_start: 0.5946 (OUTLIER) cc_final: 0.5157 (m-80) outliers start: 29 outliers final: 8 residues processed: 184 average time/residue: 1.5783 time to fit residues: 320.0296 Evaluate side-chains 172 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 198 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 198 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.171221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117314 restraints weight = 42623.569| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.38 r_work: 0.3238 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 18444 Z= 0.224 Angle : 0.734 5.367 24768 Z= 0.381 Chirality : 0.045 0.156 2808 Planarity : 0.005 0.028 2820 Dihedral : 14.937 59.522 4848 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.06 % Allowed : 16.39 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.17 (0.18), residues: 1944 helix: 3.11 (0.13), residues: 1356 sheet: 1.88 (0.44), residues: 120 loop : -1.15 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 34 TYR 0.020 0.004 TYR I 67 PHE 0.020 0.002 PHE J 53 TRP 0.005 0.002 TRP G 79 HIS 0.002 0.001 HIS F 274 Details of bonding type rmsd covalent geometry : bond 0.00449 (18408) covalent geometry : angle 0.72712 (24696) SS BOND : bond 0.00842 ( 36) SS BOND : angle 1.98628 ( 72) hydrogen bonds : bond 0.10576 ( 1176) hydrogen bonds : angle 3.69554 ( 3456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.5908 (OUTLIER) cc_final: 0.5186 (m-80) REVERT: C 195 ILE cc_start: 0.4168 (OUTLIER) cc_final: 0.3804 (tt) REVERT: D 198 PHE cc_start: 0.5908 (OUTLIER) cc_final: 0.5185 (m-80) REVERT: F 195 ILE cc_start: 0.4172 (OUTLIER) cc_final: 0.3807 (tt) REVERT: G 198 PHE cc_start: 0.5908 (OUTLIER) cc_final: 0.5188 (m-80) REVERT: I 195 ILE cc_start: 0.4174 (OUTLIER) cc_final: 0.3809 (tt) REVERT: J 198 PHE cc_start: 0.5909 (OUTLIER) cc_final: 0.5187 (m-80) REVERT: L 195 ILE cc_start: 0.4165 (OUTLIER) cc_final: 0.3802 (tt) outliers start: 37 outliers final: 21 residues processed: 201 average time/residue: 1.5375 time to fit residues: 342.1555 Evaluate side-chains 193 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 202 GLN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain I residue 195 ILE Chi-restraints excluded: chain I residue 202 GLN Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 195 ILE Chi-restraints excluded: chain L residue 202 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 124 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 128 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 268 ASN I 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.174855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.121828 restraints weight = 43058.761| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.31 r_work: 0.3305 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18444 Z= 0.158 Angle : 0.610 4.524 24768 Z= 0.317 Chirality : 0.042 0.155 2808 Planarity : 0.004 0.024 2820 Dihedral : 13.940 59.625 4848 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.44 % Allowed : 18.11 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.62 (0.18), residues: 1944 helix: 3.50 (0.13), residues: 1356 sheet: 1.85 (0.43), residues: 120 loop : -1.11 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 233 TYR 0.014 0.002 TYR G 67 PHE 0.014 0.001 PHE H 53 TRP 0.003 0.001 TRP E 79 HIS 0.002 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00283 (18408) covalent geometry : angle 0.60728 (24696) SS BOND : bond 0.00386 ( 36) SS BOND : angle 1.18641 ( 72) hydrogen bonds : bond 0.08427 ( 1176) hydrogen bonds : angle 3.45988 ( 3456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 198 PHE cc_start: 0.5741 (OUTLIER) cc_final: 0.4947 (m-80) REVERT: D 198 PHE cc_start: 0.5737 (OUTLIER) cc_final: 0.4946 (m-80) REVERT: G 198 PHE cc_start: 0.5735 (OUTLIER) cc_final: 0.4947 (m-80) REVERT: J 198 PHE cc_start: 0.5735 (OUTLIER) cc_final: 0.4941 (m-80) REVERT: L 239 GLU cc_start: 0.8472 (tt0) cc_final: 0.8253 (tt0) outliers start: 8 outliers final: 4 residues processed: 164 average time/residue: 1.7705 time to fit residues: 318.2763 Evaluate side-chains 164 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 198 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 HIS ** 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 = 0.4083 r_free = 0.4083 target = 0.176693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.123767 restraints weight = 43199.010| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.32 r_work: 0.3332 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18444 Z= 0.141 Angle : 0.574 4.215 24768 Z= 0.297 Chirality : 0.041 0.151 2808 Planarity : 0.003 0.023 2820 Dihedral : 13.297 59.417 4848 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.44 % Allowed : 17.67 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.95 (0.18), residues: 1944 helix: 3.77 (0.13), residues: 1356 sheet: 2.13 (0.42), residues: 120 loop : -1.07 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 233 TYR 0.012 0.002 TYR C 67 PHE 0.013 0.001 PHE B 53 TRP 0.002 0.001 TRP G 79 HIS 0.002 0.001 HIS F 274 Details of bonding type rmsd covalent geometry : bond 0.00258 (18408) covalent geometry : angle 0.57231 (24696) SS BOND : bond 0.00325 ( 36) SS BOND : angle 0.96308 ( 72) hydrogen bonds : bond 0.07602 ( 1176) hydrogen bonds : angle 3.27766 ( 3456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.5650 (OUTLIER) cc_final: 0.4870 (m-80) REVERT: D 198 PHE cc_start: 0.5649 (OUTLIER) cc_final: 0.4873 (m-80) REVERT: G 198 PHE cc_start: 0.5643 (OUTLIER) cc_final: 0.4871 (m-80) REVERT: J 198 PHE cc_start: 0.5648 (OUTLIER) cc_final: 0.4869 (m-80) outliers start: 8 outliers final: 4 residues processed: 168 average time/residue: 1.7135 time to fit residues: 315.5155 Evaluate side-chains 164 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 198 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 11 optimal weight: 0.3980 chunk 137 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 162 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 165 optimal weight: 0.2980 chunk 161 optimal weight: 0.0570 chunk 115 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 274 HIS ** 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 = 0.4092 r_free = 0.4092 target = 0.180078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127104 restraints weight = 42896.310| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.36 r_work: 0.3388 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18444 Z= 0.115 Angle : 0.518 4.263 24768 Z= 0.268 Chirality : 0.040 0.155 2808 Planarity : 0.003 0.022 2820 Dihedral : 12.381 58.645 4848 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.50 % Allowed : 17.89 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.40 (0.19), residues: 1944 helix: 4.06 (0.13), residues: 1356 sheet: 2.70 (0.42), residues: 120 loop : -0.90 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 233 TYR 0.009 0.001 TYR F 67 PHE 0.007 0.001 PHE J 53 TRP 0.002 0.001 TRP E 79 HIS 0.002 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00215 (18408) covalent geometry : angle 0.51775 (24696) SS BOND : bond 0.00130 ( 36) SS BOND : angle 0.67343 ( 72) hydrogen bonds : bond 0.06126 ( 1176) hydrogen bonds : angle 3.05433 ( 3456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13229.85 seconds wall clock time: 223 minutes 58.02 seconds (13438.02 seconds total)