Starting phenix.real_space_refine on Tue Aug 26 01:03:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xh9_38345/08_2025/8xh9_38345_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xh9_38345/08_2025/8xh9_38345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xh9_38345/08_2025/8xh9_38345_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xh9_38345/08_2025/8xh9_38345_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xh9_38345/08_2025/8xh9_38345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xh9_38345/08_2025/8xh9_38345.map" } resolution = 2.58 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= 0.003 sd= 0.059 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 11040 2.51 5 N 2508 2.21 5 O 2688 1.98 5 H 15864 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32256 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 2636 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {'MC3': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'MC3:plan-1': 5, 'MC3:plan-2': 5} Unresolved non-hydrogen planarities: 35 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 3.07, per 1000 atoms: 0.10 Number of scatterers: 32256 At special positions: 0 Unit cell: (97.8, 100.2, 149.4, 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 2688 8.00 N 2508 7.00 C 11040 6.00 H 15864 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: 2.52 Conformation dependent library (CDL) restraints added in 917.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 75.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 20 through 41 removed outlier: 4.315A pdb=" N ARG A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 removed outlier: 3.840A pdb=" N VAL A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.048A 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 100 Processing helix chain 'A' and resid 196 through 222 Processing helix chain 'A' and resid 246 through 276 Processing helix chain 'B' and resid 21 through 41 removed outlier: 3.950A pdb=" N ILE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.840A pdb=" N VAL B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 4.049A 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 100 removed outlier: 3.500A pdb=" N LEU B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 222 Processing helix chain 'B' and resid 246 through 276 Processing helix chain 'C' and resid 21 through 41 removed outlier: 3.950A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.839A pdb=" N VAL C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.049A 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 100 Processing helix chain 'C' and resid 196 through 222 Processing helix chain 'C' and resid 246 through 276 Processing helix chain 'D' and resid 21 through 41 removed outlier: 3.950A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 41 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.840A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 4.048A 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 100 Processing helix chain 'D' and resid 196 through 222 Processing helix chain 'D' and resid 246 through 276 Processing helix chain 'E' and resid 21 through 41 removed outlier: 3.950A pdb=" N ILE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL E 41 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.840A pdb=" N VAL E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.048A 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 100 Processing helix chain 'E' and resid 196 through 222 Processing helix chain 'E' and resid 246 through 276 Processing helix chain 'F' and resid 21 through 41 removed outlier: 3.951A pdb=" N ILE F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.840A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 4.048A 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 100 Processing helix chain 'F' and resid 196 through 222 Processing helix chain 'F' and resid 246 through 276 Processing helix chain 'G' and resid 21 through 41 removed outlier: 3.950A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 removed outlier: 3.840A pdb=" N VAL G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.048A 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 100 Processing helix chain 'G' and resid 196 through 222 Processing helix chain 'G' and resid 246 through 276 Processing helix chain 'H' and resid 21 through 41 removed outlier: 3.951A pdb=" N ILE H 25 " --> pdb=" O MET H 21 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 46 removed outlier: 3.840A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 4.048A 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 100 Processing helix chain 'H' and resid 196 through 222 Processing helix chain 'H' and resid 246 through 276 Processing helix chain 'I' and resid 21 through 41 removed outlier: 3.950A pdb=" N ILE I 25 " --> pdb=" O MET I 21 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 46 removed outlier: 3.839A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 4.048A 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 100 Processing helix chain 'I' and resid 196 through 222 Processing helix chain 'I' and resid 246 through 276 Processing helix chain 'J' and resid 21 through 41 removed outlier: 3.950A pdb=" N ILE J 25 " --> pdb=" O MET J 21 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 46 removed outlier: 3.840A pdb=" N VAL J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 4.047A 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 100 Processing helix chain 'J' and resid 196 through 222 Processing helix chain 'J' and resid 246 through 276 Processing helix chain 'K' and resid 21 through 41 removed outlier: 3.950A pdb=" N ILE K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 46 removed outlier: 3.839A pdb=" N VAL K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 4.048A 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 100 Processing helix chain 'K' and resid 196 through 222 Processing helix chain 'K' and resid 246 through 276 Processing helix chain 'L' and resid 21 through 41 removed outlier: 3.950A pdb=" N ILE L 25 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 removed outlier: 3.840A pdb=" N VAL L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 4.049A 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 100 Processing helix chain 'L' and resid 196 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 removed outlier: 3.635A pdb=" N VAL A 54 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.635A pdb=" N VAL B 54 " --> pdb=" O TYR B 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.635A pdb=" N VAL C 54 " --> pdb=" O TYR C 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.634A pdb=" N VAL D 54 " --> pdb=" O TYR D 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.635A pdb=" N VAL E 54 " --> pdb=" O TYR E 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 54 through 55 removed outlier: 3.635A pdb=" N VAL F 54 " --> pdb=" O TYR F 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.635A pdb=" N VAL G 54 " --> pdb=" O TYR G 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 54 through 55 removed outlier: 3.634A pdb=" N VAL H 54 " --> pdb=" O TYR H 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 54 through 55 removed outlier: 3.635A pdb=" N VAL I 54 " --> pdb=" O TYR I 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 54 through 55 removed outlier: 3.634A pdb=" N VAL J 54 " --> pdb=" O TYR J 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 55 removed outlier: 3.634A pdb=" N VAL K 54 " --> pdb=" O TYR K 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.635A pdb=" N VAL L 54 " --> pdb=" O TYR L 243 " (cutoff:3.500A) 1151 hydrogen bonds defined for protein. 3417 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: 6.39 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 15828 1.02 - 1.22: 36 1.22 - 1.42: 6900 1.42 - 1.62: 9612 1.62 - 1.83: 204 Bond restraints: 32580 Sorted by residual: bond pdb=" NE ARG K 24 " pdb=" HE ARG K 24 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" NE ARG A 24 " pdb=" HE ARG A 24 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" NE ARG C 24 " pdb=" HE ARG C 24 " ideal model delta sigma weight residual 0.860 0.969 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" NE ARG B 24 " pdb=" HE ARG B 24 " ideal model delta sigma weight residual 0.860 0.969 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" NE ARG J 24 " pdb=" HE ARG J 24 " ideal model delta sigma weight residual 0.860 0.969 -0.109 2.00e-02 2.50e+03 2.99e+01 ... (remaining 32575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 51539 1.13 - 2.26: 5896 2.26 - 3.39: 552 3.39 - 4.51: 164 4.51 - 5.64: 73 Bond angle restraints: 58224 Sorted by residual: angle pdb=" C VAL B 98 " pdb=" N HIS B 99 " pdb=" CA HIS B 99 " ideal model delta sigma weight residual 120.29 116.46 3.83 1.42e+00 4.96e-01 7.26e+00 angle pdb=" C VAL H 98 " pdb=" N HIS H 99 " pdb=" CA HIS H 99 " ideal model delta sigma weight residual 120.29 116.48 3.81 1.42e+00 4.96e-01 7.20e+00 angle pdb=" C VAL I 98 " pdb=" N HIS I 99 " pdb=" CA HIS I 99 " ideal model delta sigma weight residual 120.29 116.50 3.79 1.42e+00 4.96e-01 7.13e+00 angle pdb=" C VAL D 98 " pdb=" N HIS D 99 " pdb=" CA HIS D 99 " ideal model delta sigma weight residual 120.29 116.51 3.78 1.42e+00 4.96e-01 7.09e+00 angle pdb=" C VAL J 98 " pdb=" N HIS J 99 " pdb=" CA HIS J 99 " ideal model delta sigma weight residual 120.29 116.52 3.77 1.42e+00 4.96e-01 7.05e+00 ... (remaining 58219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 13136 16.86 - 33.72: 1516 33.72 - 50.58: 727 50.58 - 67.44: 281 67.44 - 84.29: 24 Dihedral angle restraints: 15684 sinusoidal: 8496 harmonic: 7188 Sorted by residual: dihedral pdb=" CB GLU I 241 " pdb=" CG GLU I 241 " pdb=" CD GLU I 241 " pdb=" OE1 GLU I 241 " ideal model delta sinusoidal sigma weight residual 0.00 84.29 -84.29 1 3.00e+01 1.11e-03 9.61e+00 dihedral pdb=" CB GLU C 241 " pdb=" CG GLU C 241 " pdb=" CD GLU C 241 " pdb=" OE1 GLU C 241 " ideal model delta sinusoidal sigma weight residual 0.00 84.23 -84.23 1 3.00e+01 1.11e-03 9.59e+00 dihedral pdb=" CB GLU E 241 " pdb=" CG GLU E 241 " pdb=" CD GLU E 241 " pdb=" OE1 GLU E 241 " ideal model delta sinusoidal sigma weight residual 0.00 84.23 -84.23 1 3.00e+01 1.11e-03 9.59e+00 ... (remaining 15681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1550 0.033 - 0.065: 641 0.065 - 0.098: 305 0.098 - 0.130: 60 0.130 - 0.163: 24 Chirality restraints: 2580 Sorted by residual: chirality pdb=" CA ARG H 246 " pdb=" N ARG H 246 " pdb=" C ARG H 246 " pdb=" CB ARG H 246 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CA ARG G 246 " pdb=" N ARG G 246 " pdb=" C ARG G 246 " pdb=" CB ARG G 246 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA ARG K 246 " pdb=" N ARG K 246 " pdb=" C ARG K 246 " pdb=" CB ARG K 246 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.56e-01 ... (remaining 2577 not shown) Planarity restraints: 4572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 20 " -0.018 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" N MET C 21 " 0.057 2.00e-02 2.50e+03 pdb=" CA MET C 21 " -0.015 2.00e-02 2.50e+03 pdb=" H MET C 21 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 20 " -0.018 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" N MET D 21 " 0.057 2.00e-02 2.50e+03 pdb=" CA MET D 21 " -0.015 2.00e-02 2.50e+03 pdb=" H MET D 21 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 20 " -0.018 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" N MET F 21 " 0.057 2.00e-02 2.50e+03 pdb=" CA MET F 21 " -0.015 2.00e-02 2.50e+03 pdb=" H MET F 21 " -0.025 2.00e-02 2.50e+03 ... (remaining 4569 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 5385 2.29 - 2.87: 65839 2.87 - 3.44: 77764 3.44 - 4.02: 104107 4.02 - 4.60: 158959 Nonbonded interactions: 412054 Sorted by model distance: nonbonded pdb=" O SER K 245 " pdb=" HZ2 LYS K 250 " model vdw 1.712 2.450 nonbonded pdb=" O SER B 245 " pdb=" HZ2 LYS B 250 " model vdw 1.712 2.450 nonbonded pdb=" O SER H 245 " pdb=" HZ2 LYS H 250 " model vdw 1.713 2.450 nonbonded pdb=" O SER I 245 " pdb=" HZ2 LYS I 250 " model vdw 1.713 2.450 nonbonded pdb=" O SER E 245 " pdb=" HZ2 LYS E 250 " model vdw 1.713 2.450 ... (remaining 412049 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: 0.07 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: 3.170 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: 0.160 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 24.240 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.004 0.028 16752 Z= 0.222 Angle : 0.860 5.643 22548 Z= 0.463 Chirality : 0.044 0.163 2580 Planarity : 0.006 0.043 2712 Dihedral : 15.039 84.294 6132 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 14.86 % Favored : 85.14 % 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 aren not related in a simple way. whole: 1.63 (0.17), residues: 1908 helix: 1.98 (0.13), residues: 1332 sheet: 1.10 (0.36), residues: 120 loop : -1.73 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 34 TYR 0.015 0.002 TYR I 67 PHE 0.019 0.002 PHE D 53 TRP 0.003 0.001 TRP G 79 HIS 0.009 0.003 HIS I 274 Details of bonding type rmsd covalent geometry : bond 0.00400 (16716) covalent geometry : angle 0.85910 (22476) SS BOND : bond 0.00736 ( 36) SS BOND : angle 1.18826 ( 72) hydrogen bonds : bond 0.11271 ( 1151) hydrogen bonds : angle 3.95775 ( 3417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7461 (t70) cc_final: 0.7246 (t0) REVERT: A 69 ARG cc_start: 0.7633 (tpt170) cc_final: 0.7384 (tpt90) REVERT: A 232 ASN cc_start: 0.8025 (p0) cc_final: 0.7815 (p0) REVERT: A 239 GLU cc_start: 0.7882 (tt0) cc_final: 0.7606 (tt0) REVERT: B 232 ASN cc_start: 0.7951 (p0) cc_final: 0.7718 (p0) REVERT: B 239 GLU cc_start: 0.7945 (tt0) cc_final: 0.7659 (tt0) REVERT: C 47 ASP cc_start: 0.7503 (t70) cc_final: 0.7299 (t0) REVERT: C 232 ASN cc_start: 0.8090 (p0) cc_final: 0.7862 (p0) REVERT: C 239 GLU cc_start: 0.7868 (tt0) cc_final: 0.7612 (tt0) REVERT: D 69 ARG cc_start: 0.7760 (tpt170) cc_final: 0.7464 (tpt90) REVERT: D 232 ASN cc_start: 0.8027 (p0) cc_final: 0.7737 (p0) REVERT: D 239 GLU cc_start: 0.7994 (tt0) cc_final: 0.7733 (tt0) REVERT: E 232 ASN cc_start: 0.8076 (p0) cc_final: 0.7793 (p0) REVERT: E 239 GLU cc_start: 0.7955 (tt0) cc_final: 0.7675 (tt0) REVERT: F 232 ASN cc_start: 0.7952 (p0) cc_final: 0.7651 (p0) REVERT: F 239 GLU cc_start: 0.7965 (tt0) cc_final: 0.7639 (tt0) REVERT: G 47 ASP cc_start: 0.7477 (t70) cc_final: 0.7255 (t0) REVERT: G 69 ARG cc_start: 0.7656 (tpt170) cc_final: 0.7377 (tpt90) REVERT: H 47 ASP cc_start: 0.7528 (t70) cc_final: 0.7321 (t0) REVERT: H 232 ASN cc_start: 0.8053 (p0) cc_final: 0.7846 (p0) REVERT: H 239 GLU cc_start: 0.7808 (tt0) cc_final: 0.7572 (tt0) REVERT: I 232 ASN cc_start: 0.8122 (p0) cc_final: 0.7872 (p0) REVERT: J 69 ARG cc_start: 0.7720 (tpt170) cc_final: 0.7438 (tpt90) REVERT: J 232 ASN cc_start: 0.8030 (p0) cc_final: 0.7749 (p0) REVERT: J 239 GLU cc_start: 0.8031 (tt0) cc_final: 0.7774 (tt0) REVERT: K 52 MET cc_start: 0.8320 (mmt) cc_final: 0.8067 (mmt) REVERT: K 69 ARG cc_start: 0.7781 (tpt170) cc_final: 0.7499 (tpt90) REVERT: K 232 ASN cc_start: 0.7909 (p0) cc_final: 0.7654 (p0) REVERT: K 239 GLU cc_start: 0.8169 (tt0) cc_final: 0.7912 (tt0) REVERT: L 232 ASN cc_start: 0.7998 (p0) cc_final: 0.7733 (p0) REVERT: L 239 GLU cc_start: 0.7944 (tt0) cc_final: 0.7654 (tt0) outliers start: 0 outliers final: 6 residues processed: 312 average time/residue: 0.7805 time to fit residues: 286.1491 Evaluate side-chains 234 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 228 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain E residue 273 ASN Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain I residue 273 ASN Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 273 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 207 ASN C 207 ASN C 268 ASN D 207 ASN E 207 ASN F 207 ASN F 268 ASN G 207 ASN H 207 ASN I 207 ASN I 268 ASN J 207 ASN K 207 ASN L 207 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.193074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138724 restraints weight = 46658.285| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.78 r_work: 0.3527 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16752 Z= 0.157 Angle : 0.561 4.778 22548 Z= 0.305 Chirality : 0.041 0.126 2580 Planarity : 0.004 0.028 2712 Dihedral : 5.509 27.884 2604 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.80 % Allowed : 15.93 % Favored : 82.26 % 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 aren not related in a simple way. whole: 3.50 (0.18), residues: 1908 helix: 3.33 (0.12), residues: 1344 sheet: 2.34 (0.43), residues: 120 loop : -1.17 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 197 TYR 0.012 0.002 TYR F 67 PHE 0.007 0.001 PHE I 33 TRP 0.004 0.002 TRP I 79 HIS 0.004 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00328 (16716) covalent geometry : angle 0.55987 (22476) SS BOND : bond 0.00439 ( 36) SS BOND : angle 0.83513 ( 72) hydrogen bonds : bond 0.07881 ( 1151) hydrogen bonds : angle 3.57904 ( 3417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7728 (tpt170) cc_final: 0.7434 (tpt90) REVERT: A 232 ASN cc_start: 0.8186 (p0) cc_final: 0.7871 (p0) REVERT: A 239 GLU cc_start: 0.7947 (tt0) cc_final: 0.7641 (tt0) REVERT: B 43 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6973 (tp30) REVERT: B 232 ASN cc_start: 0.8107 (p0) cc_final: 0.7871 (p0) REVERT: B 239 GLU cc_start: 0.8037 (tt0) cc_final: 0.7791 (tt0) REVERT: C 21 MET cc_start: 0.5847 (OUTLIER) cc_final: 0.5403 (mpt) REVERT: D 69 ARG cc_start: 0.7798 (tpt170) cc_final: 0.7481 (tpt90) REVERT: D 239 GLU cc_start: 0.8069 (tt0) cc_final: 0.7817 (tt0) REVERT: E 239 GLU cc_start: 0.8042 (tt0) cc_final: 0.7814 (tt0) REVERT: F 239 GLU cc_start: 0.7973 (tt0) cc_final: 0.7699 (tt0) REVERT: G 47 ASP cc_start: 0.7595 (t70) cc_final: 0.7345 (t0) REVERT: G 69 ARG cc_start: 0.7756 (tpt170) cc_final: 0.7445 (tpt90) REVERT: G 232 ASN cc_start: 0.8192 (p0) cc_final: 0.7977 (p0) REVERT: J 69 ARG cc_start: 0.7791 (tpt170) cc_final: 0.7484 (tpt90) REVERT: J 239 GLU cc_start: 0.8138 (tt0) cc_final: 0.7906 (tt0) REVERT: K 232 ASN cc_start: 0.8115 (p0) cc_final: 0.7866 (p0) REVERT: K 239 GLU cc_start: 0.8261 (tt0) cc_final: 0.8033 (tt0) outliers start: 32 outliers final: 18 residues processed: 222 average time/residue: 0.9114 time to fit residues: 233.8669 Evaluate side-chains 223 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 224 SER Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 224 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 164 optimal weight: 0.0980 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 207 ASN C 207 ASN D 207 ASN E 207 ASN F 207 ASN G 207 ASN H 207 ASN I 207 ASN J 207 ASN K 207 ASN L 207 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.194084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.138646 restraints weight = 46583.069| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.84 r_work: 0.3534 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16752 Z= 0.136 Angle : 0.511 4.301 22548 Z= 0.275 Chirality : 0.041 0.146 2580 Planarity : 0.003 0.028 2712 Dihedral : 4.826 24.722 2592 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.73 % Allowed : 17.62 % Favored : 81.64 % 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 aren not related in a simple way. whole: 4.09 (0.18), residues: 1908 helix: 3.93 (0.12), residues: 1344 sheet: 2.38 (0.41), residues: 120 loop : -1.51 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 69 TYR 0.010 0.001 TYR I 67 PHE 0.007 0.001 PHE E 71 TRP 0.003 0.001 TRP H 79 HIS 0.004 0.001 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00272 (16716) covalent geometry : angle 0.50926 (22476) SS BOND : bond 0.00341 ( 36) SS BOND : angle 0.89249 ( 72) hydrogen bonds : bond 0.06781 ( 1151) hydrogen bonds : angle 3.32796 ( 3417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7700 (tpt170) cc_final: 0.7400 (tpt90) REVERT: A 232 ASN cc_start: 0.8250 (p0) cc_final: 0.7959 (p0) REVERT: A 239 GLU cc_start: 0.7929 (tt0) cc_final: 0.7661 (tt0) REVERT: C 21 MET cc_start: 0.5962 (OUTLIER) cc_final: 0.5605 (mpt) REVERT: D 69 ARG cc_start: 0.7713 (tpt170) cc_final: 0.7401 (tpt90) REVERT: D 232 ASN cc_start: 0.8146 (p0) cc_final: 0.7856 (p0) REVERT: D 239 GLU cc_start: 0.8019 (tt0) cc_final: 0.7735 (tt0) REVERT: E 239 GLU cc_start: 0.8030 (tt0) cc_final: 0.7757 (tt0) REVERT: G 232 ASN cc_start: 0.8181 (p0) cc_final: 0.7897 (p0) REVERT: H 69 ARG cc_start: 0.7822 (tpt170) cc_final: 0.7493 (tpt90) REVERT: H 239 GLU cc_start: 0.8067 (tt0) cc_final: 0.7805 (tt0) REVERT: J 69 ARG cc_start: 0.7707 (tpt170) cc_final: 0.7401 (tpt90) REVERT: J 232 ASN cc_start: 0.8153 (p0) cc_final: 0.7853 (p0) REVERT: J 239 GLU cc_start: 0.8071 (tt0) cc_final: 0.7783 (tt0) outliers start: 13 outliers final: 9 residues processed: 210 average time/residue: 1.0046 time to fit residues: 242.2932 Evaluate side-chains 219 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 209 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain K residue 224 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 190 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 207 ASN C 207 ASN D 207 ASN E 207 ASN F 207 ASN G 207 ASN H 207 ASN I 207 ASN J 207 ASN K 207 ASN L 207 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.191006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.134816 restraints weight = 46374.169| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.84 r_work: 0.3490 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16752 Z= 0.157 Angle : 0.548 5.034 22548 Z= 0.292 Chirality : 0.042 0.136 2580 Planarity : 0.003 0.032 2712 Dihedral : 5.719 30.544 2592 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.75 % Allowed : 17.17 % Favored : 81.08 % 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 aren not related in a simple way. whole: 4.19 (0.18), residues: 1908 helix: 4.02 (0.12), residues: 1344 sheet: 2.38 (0.42), residues: 120 loop : -1.51 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 69 TYR 0.010 0.002 TYR L 67 PHE 0.008 0.001 PHE G 33 TRP 0.005 0.002 TRP G 79 HIS 0.004 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00349 (16716) covalent geometry : angle 0.54452 (22476) SS BOND : bond 0.00533 ( 36) SS BOND : angle 1.16140 ( 72) hydrogen bonds : bond 0.07378 ( 1151) hydrogen bonds : angle 3.31419 ( 3417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7806 (tpt170) cc_final: 0.7531 (tpt90) REVERT: A 232 ASN cc_start: 0.8365 (p0) cc_final: 0.8003 (p0) REVERT: C 21 MET cc_start: 0.5976 (OUTLIER) cc_final: 0.5625 (mpt) REVERT: D 69 ARG cc_start: 0.7817 (tpt170) cc_final: 0.7537 (tpt90) REVERT: D 232 ASN cc_start: 0.8257 (p0) cc_final: 0.7904 (p0) REVERT: E 69 ARG cc_start: 0.7894 (tpt170) cc_final: 0.7584 (tpt90) REVERT: G 232 ASN cc_start: 0.8295 (p0) cc_final: 0.7940 (p0) REVERT: J 69 ARG cc_start: 0.7817 (tpt170) cc_final: 0.7539 (tpt90) REVERT: K 69 ARG cc_start: 0.7945 (tpt170) cc_final: 0.7639 (tpt90) outliers start: 31 outliers final: 25 residues processed: 227 average time/residue: 0.9567 time to fit residues: 250.6887 Evaluate side-chains 236 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 224 SER Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain J residue 273 ASN Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 224 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 112 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 67 optimal weight: 0.0870 chunk 69 optimal weight: 0.3980 chunk 75 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 overall best weight: 3.8964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 207 ASN C 207 ASN D 207 ASN E 207 ASN F 207 ASN G 207 ASN H 207 ASN I 207 ASN J 207 ASN K 207 ASN L 207 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.187379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.131783 restraints weight = 46585.833| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.77 r_work: 0.3450 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16752 Z= 0.197 Angle : 0.609 5.671 22548 Z= 0.325 Chirality : 0.044 0.150 2580 Planarity : 0.004 0.036 2712 Dihedral : 6.584 33.844 2592 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.55 % Allowed : 15.60 % Favored : 80.86 % 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 aren not related in a simple way. whole: 4.01 (0.19), residues: 1908 helix: 3.92 (0.12), residues: 1344 sheet: 2.20 (0.43), residues: 120 loop : -1.67 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 69 TYR 0.012 0.002 TYR G 67 PHE 0.011 0.002 PHE B 253 TRP 0.006 0.002 TRP J 79 HIS 0.004 0.002 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00455 (16716) covalent geometry : angle 0.60302 (22476) SS BOND : bond 0.00709 ( 36) SS BOND : angle 1.58478 ( 72) hydrogen bonds : bond 0.08367 ( 1151) hydrogen bonds : angle 3.41820 ( 3417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 221 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: C 21 MET cc_start: 0.6050 (OUTLIER) cc_final: 0.5725 (mpt) outliers start: 63 outliers final: 41 residues processed: 246 average time/residue: 0.8346 time to fit residues: 240.0129 Evaluate side-chains 257 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 224 SER Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain J residue 273 ASN Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 224 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 170 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 207 ASN C 207 ASN D 207 ASN E 207 ASN F 207 ASN G 207 ASN H 207 ASN I 207 ASN J 207 ASN K 207 ASN L 207 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.189916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.133560 restraints weight = 46026.889| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.82 r_work: 0.3480 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16752 Z= 0.154 Angle : 0.536 4.879 22548 Z= 0.289 Chirality : 0.042 0.132 2580 Planarity : 0.004 0.034 2712 Dihedral : 6.050 32.025 2592 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.08 % Allowed : 17.45 % Favored : 80.46 % 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 aren not related in a simple way. whole: 4.13 (0.19), residues: 1908 helix: 4.04 (0.12), residues: 1344 sheet: 2.31 (0.43), residues: 120 loop : -1.76 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 69 TYR 0.011 0.002 TYR G 67 PHE 0.008 0.001 PHE L 33 TRP 0.004 0.002 TRP E 79 HIS 0.004 0.001 HIS I 274 Details of bonding type rmsd covalent geometry : bond 0.00339 (16716) covalent geometry : angle 0.53297 (22476) SS BOND : bond 0.00453 ( 36) SS BOND : angle 1.19396 ( 72) hydrogen bonds : bond 0.07515 ( 1151) hydrogen bonds : angle 3.34263 ( 3417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: C 21 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5787 (mpt) outliers start: 37 outliers final: 36 residues processed: 229 average time/residue: 0.8589 time to fit residues: 228.2478 Evaluate side-chains 251 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 224 SER Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain J residue 273 ASN Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 224 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 172 optimal weight: 0.0470 chunk 116 optimal weight: 1.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 207 ASN C 207 ASN D 207 ASN E 207 ASN F 207 ASN G 207 ASN H 207 ASN I 207 ASN J 207 ASN K 207 ASN L 207 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.189234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132465 restraints weight = 45182.496| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.78 r_work: 0.3414 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16752 Z= 0.171 Angle : 0.564 5.395 22548 Z= 0.302 Chirality : 0.042 0.141 2580 Planarity : 0.004 0.036 2712 Dihedral : 6.319 33.217 2592 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.25 % Allowed : 17.51 % Favored : 80.24 % 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 aren not related in a simple way. whole: 4.12 (0.19), residues: 1908 helix: 4.03 (0.12), residues: 1344 sheet: 2.40 (0.45), residues: 120 loop : -1.79 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 69 TYR 0.011 0.002 TYR I 67 PHE 0.009 0.002 PHE I 33 TRP 0.005 0.002 TRP B 79 HIS 0.003 0.001 HIS I 274 Details of bonding type rmsd covalent geometry : bond 0.00389 (16716) covalent geometry : angle 0.55882 (22476) SS BOND : bond 0.00564 ( 36) SS BOND : angle 1.40099 ( 72) hydrogen bonds : bond 0.07765 ( 1151) hydrogen bonds : angle 3.34898 ( 3417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.939 Fit side-chains REVERT: C 21 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.5977 (mpt) outliers start: 40 outliers final: 41 residues processed: 231 average time/residue: 0.9002 time to fit residues: 241.6693 Evaluate side-chains 256 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 224 SER Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain J residue 273 ASN Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 224 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 44 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 207 ASN C 207 ASN D 207 ASN E 207 ASN F 207 ASN G 207 ASN H 207 ASN I 207 ASN J 207 ASN K 207 ASN L 207 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.192477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136415 restraints weight = 45434.126| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.77 r_work: 0.3458 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16752 Z= 0.121 Angle : 0.482 4.439 22548 Z= 0.260 Chirality : 0.040 0.124 2580 Planarity : 0.003 0.030 2712 Dihedral : 5.228 26.791 2592 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.69 % Allowed : 17.57 % Favored : 80.74 % 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 aren not related in a simple way. whole: 4.33 (0.19), residues: 1908 helix: 4.25 (0.12), residues: 1344 sheet: 2.37 (0.43), residues: 120 loop : -1.90 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 69 TYR 0.009 0.001 TYR C 67 PHE 0.006 0.001 PHE L 33 TRP 0.003 0.001 TRP G 79 HIS 0.004 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00243 (16716) covalent geometry : angle 0.48023 (22476) SS BOND : bond 0.00247 ( 36) SS BOND : angle 0.89513 ( 72) hydrogen bonds : bond 0.06417 ( 1151) hydrogen bonds : angle 3.22830 ( 3417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.894 Fit side-chains REVERT: A 232 ASN cc_start: 0.8391 (p0) cc_final: 0.8092 (p0) REVERT: C 21 MET cc_start: 0.6194 (OUTLIER) cc_final: 0.5927 (mpt) REVERT: D 232 ASN cc_start: 0.8381 (p0) cc_final: 0.8080 (p0) REVERT: G 232 ASN cc_start: 0.8388 (p0) cc_final: 0.8093 (p0) REVERT: J 232 ASN cc_start: 0.8380 (p0) cc_final: 0.8087 (p0) outliers start: 30 outliers final: 26 residues processed: 224 average time/residue: 0.8709 time to fit residues: 226.4495 Evaluate side-chains 239 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 224 SER Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 224 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 135 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 ASN E 207 ASN F 207 ASN H 207 ASN I 207 ASN L 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.187137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128237 restraints weight = 43930.570| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.75 r_work: 0.3440 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16752 Z= 0.148 Angle : 0.530 5.135 22548 Z= 0.282 Chirality : 0.041 0.136 2580 Planarity : 0.004 0.033 2712 Dihedral : 5.681 30.042 2592 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.03 % Allowed : 17.12 % Favored : 80.86 % 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 aren not related in a simple way. whole: 4.35 (0.19), residues: 1908 helix: 4.23 (0.12), residues: 1344 sheet: 2.59 (0.45), residues: 120 loop : -1.86 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 69 TYR 0.010 0.002 TYR I 67 PHE 0.008 0.001 PHE C 33 TRP 0.004 0.002 TRP B 79 HIS 0.003 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00332 (16716) covalent geometry : angle 0.52613 (22476) SS BOND : bond 0.00460 ( 36) SS BOND : angle 1.22514 ( 72) hydrogen bonds : bond 0.06986 ( 1151) hydrogen bonds : angle 3.24426 ( 3417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.974 Fit side-chains REVERT: C 21 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5892 (mpt) outliers start: 36 outliers final: 34 residues processed: 230 average time/residue: 0.9184 time to fit residues: 245.3283 Evaluate side-chains 250 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 224 SER Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 224 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 70 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 207 ASN H 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.187896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129169 restraints weight = 44327.108| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.75 r_work: 0.3454 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16752 Z= 0.131 Angle : 0.501 4.450 22548 Z= 0.268 Chirality : 0.041 0.131 2580 Planarity : 0.003 0.032 2712 Dihedral : 5.344 27.827 2592 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.69 % Allowed : 17.62 % Favored : 80.69 % 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 aren not related in a simple way. whole: 4.37 (0.19), residues: 1908 helix: 4.27 (0.12), residues: 1344 sheet: 2.59 (0.45), residues: 120 loop : -1.94 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 69 TYR 0.010 0.002 TYR C 67 PHE 0.007 0.001 PHE I 33 TRP 0.003 0.001 TRP A 79 HIS 0.003 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00277 (16716) covalent geometry : angle 0.49787 (22476) SS BOND : bond 0.00356 ( 36) SS BOND : angle 1.05894 ( 72) hydrogen bonds : bond 0.06572 ( 1151) hydrogen bonds : angle 3.21169 ( 3417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.930 Fit side-chains REVERT: A 232 ASN cc_start: 0.8359 (p0) cc_final: 0.8079 (p0) REVERT: C 21 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5887 (mpt) REVERT: D 232 ASN cc_start: 0.8372 (p0) cc_final: 0.8093 (p0) outliers start: 30 outliers final: 30 residues processed: 226 average time/residue: 0.9284 time to fit residues: 242.8834 Evaluate side-chains 244 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 273 ASN Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain H residue 21 MET Chi-restraints excluded: chain H residue 224 SER Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain J residue 21 MET Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain K residue 21 MET Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 224 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 28 optimal weight: 0.8980 chunk 172 optimal weight: 0.4980 chunk 189 optimal weight: 0.3980 chunk 131 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 132 optimal weight: 0.5980 chunk 111 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4265 r_free = 0.4265 target = 0.195903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.140452 restraints weight = 45601.125| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.76 r_work: 0.3508 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16752 Z= 0.100 Angle : 0.438 4.461 22548 Z= 0.236 Chirality : 0.039 0.120 2580 Planarity : 0.003 0.022 2712 Dihedral : 4.184 20.586 2592 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.96 % Allowed : 18.52 % Favored : 80.52 % 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 aren not related in a simple way. whole: 4.62 (0.19), residues: 1908 helix: 4.50 (0.12), residues: 1344 sheet: 2.54 (0.43), residues: 120 loop : -1.97 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 24 TYR 0.007 0.001 TYR K 243 PHE 0.005 0.001 PHE B 33 TRP 0.002 0.001 TRP F 79 HIS 0.003 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00195 (16716) covalent geometry : angle 0.43736 (22476) SS BOND : bond 0.00070 ( 36) SS BOND : angle 0.68112 ( 72) hydrogen bonds : bond 0.05064 ( 1151) hydrogen bonds : angle 3.10780 ( 3417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12504.34 seconds wall clock time: 211 minutes 46.09 seconds (12706.09 seconds total)