Starting phenix.real_space_refine on Fri Jun 27 19:29:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xh9_38345/06_2025/8xh9_38345_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xh9_38345/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xh9_38345/06_2025/8xh9_38345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xh9_38345/06_2025/8xh9_38345.map" model { file = "/net/cci-nas-00/data/ceres_data/8xh9_38345/06_2025/8xh9_38345_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xh9_38345/06_2025/8xh9_38345_trim.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-2': 5, 'MC3:plan-1': 5} Unresolved non-hydrogen planarities: 35 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 10.30, per 1000 atoms: 0.32 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 C 55 " - pdb=" SG CYS C 242 " distance=2.04 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.04 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.04 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.04 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.04 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.04 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.04 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.04 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.04 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.04 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.04 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.04 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.04 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.04 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.04 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.04 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.04 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.04 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.04 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.04 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.04 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.04 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.04 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.04 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.04 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.04 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.04 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 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: 8.95 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.62 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: 11.60 Time building geometry restraints manager: 10.79 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 3.380 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: 0.590 Extract box with map and model: 1.510 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 62.760 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.001 TRP G 79 HIS 0.009 0.003 HIS I 274 PHE 0.019 0.002 PHE D 53 TYR 0.015 0.002 TYR I 67 ARG 0.004 0.001 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.11271 ( 1151) hydrogen bonds : angle 3.95775 ( 3417) SS BOND : bond 0.00736 ( 36) SS BOND : angle 1.18826 ( 72) covalent geometry : bond 0.00400 (16716) covalent geometry : angle 0.85910 (22476) *********************** 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 : 2.438 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: 1.6346 time to fit residues: 602.8654 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 : 2.604 ------------------------------------------------------------------------------- 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 162 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.191527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136927 restraints weight = 46302.687| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.76 r_work: 0.3507 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1628 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= 0.176 Angle : 0.590 4.889 22548 Z= 0.321 Chirality : 0.042 0.130 2580 Planarity : 0.004 0.030 2712 Dihedral : 5.910 29.789 2604 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.03 % Allowed : 15.65 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.18), residues: 1908 helix: 3.29 (0.12), residues: 1344 sheet: 2.28 (0.43), residues: 120 loop : -1.27 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP G 79 HIS 0.004 0.001 HIS C 274 PHE 0.007 0.001 PHE I 33 TYR 0.013 0.002 TYR L 67 ARG 0.002 0.000 ARG G 197 Details of bonding type rmsd hydrogen bonds : bond 0.08214 ( 1151) hydrogen bonds : angle 3.60797 ( 3417) SS BOND : bond 0.00587 ( 36) SS BOND : angle 1.13734 ( 72) covalent geometry : bond 0.00388 (16716) covalent geometry : angle 0.58776 (22476) *********************** 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 247 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7806 (tpt170) cc_final: 0.7511 (tpt90) REVERT: A 232 ASN cc_start: 0.8270 (p0) cc_final: 0.7980 (p0) REVERT: B 43 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6953 (tp30) REVERT: B 69 ARG cc_start: 0.7839 (tpt170) cc_final: 0.7492 (tpt90) REVERT: B 239 GLU cc_start: 0.8113 (tt0) cc_final: 0.7895 (tt0) REVERT: C 21 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.5398 (mpt) REVERT: D 69 ARG cc_start: 0.7848 (tpt170) cc_final: 0.7534 (tpt90) REVERT: D 232 ASN cc_start: 0.8247 (p0) cc_final: 0.7922 (p0) REVERT: F 239 GLU cc_start: 0.8058 (tt0) cc_final: 0.7815 (tt0) REVERT: G 69 ARG cc_start: 0.7825 (tpt170) cc_final: 0.7511 (tpt90) REVERT: G 232 ASN cc_start: 0.8246 (p0) cc_final: 0.8010 (p0) REVERT: J 69 ARG cc_start: 0.7846 (tpt170) cc_final: 0.7540 (tpt90) REVERT: J 232 ASN cc_start: 0.8232 (p0) cc_final: 0.7891 (p0) REVERT: K 69 ARG cc_start: 0.7845 (tpt170) cc_final: 0.7547 (tpt90) REVERT: K 232 ASN cc_start: 0.8176 (p0) cc_final: 0.7949 (p0) REVERT: K 239 GLU cc_start: 0.8289 (tt0) cc_final: 0.8050 (tt0) outliers start: 36 outliers final: 19 residues processed: 223 average time/residue: 1.8434 time to fit residues: 476.5512 Evaluate side-chains 227 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 2.399 ------------------------------------------------------------------------------- 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 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 21 MET 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 224 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 157 optimal weight: 0.3980 chunk 176 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.190757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135435 restraints weight = 46787.391| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.80 r_work: 0.3513 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16752 Z= 0.164 Angle : 0.558 4.923 22548 Z= 0.301 Chirality : 0.042 0.136 2580 Planarity : 0.004 0.032 2712 Dihedral : 5.670 28.796 2594 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.86 % Allowed : 16.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.18), residues: 1908 helix: 3.81 (0.12), residues: 1344 sheet: 2.25 (0.42), residues: 120 loop : -1.55 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP C 79 HIS 0.004 0.001 HIS C 274 PHE 0.008 0.001 PHE K 253 TYR 0.011 0.002 TYR L 243 ARG 0.002 0.000 ARG B 246 Details of bonding type rmsd hydrogen bonds : bond 0.07792 ( 1151) hydrogen bonds : angle 3.41567 ( 3417) SS BOND : bond 0.00521 ( 36) SS BOND : angle 1.16027 ( 72) covalent geometry : bond 0.00345 (16716) covalent geometry : angle 0.55507 (22476) *********************** 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 247 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7771 (tpt170) cc_final: 0.7457 (tpt90) REVERT: A 232 ASN cc_start: 0.8327 (p0) cc_final: 0.8007 (p0) REVERT: C 21 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.5615 (mpt) REVERT: D 69 ARG cc_start: 0.7794 (tpt170) cc_final: 0.7473 (tpt90) REVERT: D 232 ASN cc_start: 0.8336 (p0) cc_final: 0.8003 (p0) REVERT: G 69 ARG cc_start: 0.7786 (tpt170) cc_final: 0.7516 (tpt90) REVERT: G 232 ASN cc_start: 0.8293 (p0) cc_final: 0.7975 (p0) REVERT: J 69 ARG cc_start: 0.7781 (tpt170) cc_final: 0.7464 (tpt90) REVERT: J 232 ASN cc_start: 0.8352 (p0) cc_final: 0.8017 (p0) outliers start: 33 outliers final: 33 residues processed: 230 average time/residue: 1.8267 time to fit residues: 490.0521 Evaluate side-chains 249 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 3.314 ------------------------------------------------------------------------------- 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 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 90 SER Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain D residue 21 MET 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 90 SER Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 90 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 21 MET Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain J residue 21 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 76 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 148 optimal weight: 0.0980 chunk 91 optimal weight: 0.0670 chunk 111 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 155 optimal weight: 0.1980 chunk 159 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.195564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140885 restraints weight = 46774.784| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.83 r_work: 0.3560 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16752 Z= 0.113 Angle : 0.460 4.419 22548 Z= 0.249 Chirality : 0.039 0.119 2580 Planarity : 0.003 0.024 2712 Dihedral : 4.474 20.937 2594 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.28 % Allowed : 18.52 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.36 (0.18), residues: 1908 helix: 4.16 (0.12), residues: 1344 sheet: 2.33 (0.40), residues: 120 loop : -1.49 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 79 HIS 0.004 0.001 HIS D 274 PHE 0.006 0.001 PHE J 33 TYR 0.007 0.001 TYR C 67 ARG 0.001 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.05859 ( 1151) hydrogen bonds : angle 3.28621 ( 3417) SS BOND : bond 0.00066 ( 36) SS BOND : angle 0.62999 ( 72) covalent geometry : bond 0.00210 (16716) covalent geometry : angle 0.45924 (22476) *********************** 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 213 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 208 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7696 (tpt170) cc_final: 0.7392 (tpt90) REVERT: A 232 ASN cc_start: 0.8204 (p0) cc_final: 0.7931 (p0) REVERT: B 69 ARG cc_start: 0.7818 (tpt170) cc_final: 0.7510 (tpt90) REVERT: D 69 ARG cc_start: 0.7715 (tpt170) cc_final: 0.7406 (tpt90) REVERT: D 232 ASN cc_start: 0.8221 (p0) cc_final: 0.7948 (p0) REVERT: E 69 ARG cc_start: 0.7819 (tpt170) cc_final: 0.7510 (tpt90) REVERT: G 69 ARG cc_start: 0.7713 (tpt170) cc_final: 0.7410 (tpt90) REVERT: G 232 ASN cc_start: 0.8175 (p0) cc_final: 0.7874 (p0) REVERT: J 69 ARG cc_start: 0.7696 (tpt170) cc_final: 0.7391 (tpt90) REVERT: J 232 ASN cc_start: 0.8205 (p0) cc_final: 0.7935 (p0) outliers start: 5 outliers final: 4 residues processed: 208 average time/residue: 2.0920 time to fit residues: 505.3374 Evaluate side-chains 210 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 206 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 21 MET Chi-restraints excluded: chain J residue 273 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 88 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.191657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.135604 restraints weight = 46473.928| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.83 r_work: 0.3481 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2421 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= 0.144 Angle : 0.535 5.036 22548 Z= 0.282 Chirality : 0.041 0.135 2580 Planarity : 0.003 0.030 2712 Dihedral : 5.466 30.119 2592 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.25 % Allowed : 16.55 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.42 (0.19), residues: 1908 helix: 4.20 (0.12), residues: 1344 sheet: 2.49 (0.43), residues: 120 loop : -1.47 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP G 79 HIS 0.004 0.001 HIS E 274 PHE 0.008 0.001 PHE K 53 TYR 0.010 0.002 TYR G 243 ARG 0.003 0.000 ARG L 69 Details of bonding type rmsd hydrogen bonds : bond 0.06904 ( 1151) hydrogen bonds : angle 3.24362 ( 3417) SS BOND : bond 0.00481 ( 36) SS BOND : angle 1.11739 ( 72) covalent geometry : bond 0.00313 (16716) covalent geometry : angle 0.53198 (22476) *********************** 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 254 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7728 (tpt170) cc_final: 0.7393 (tpt90) REVERT: A 232 ASN cc_start: 0.8336 (p0) cc_final: 0.7967 (p0) REVERT: C 21 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.5666 (mpt) REVERT: D 69 ARG cc_start: 0.7755 (tpt170) cc_final: 0.7413 (tpt90) REVERT: D 232 ASN cc_start: 0.8362 (p0) cc_final: 0.8000 (p0) REVERT: G 69 ARG cc_start: 0.7757 (tpt170) cc_final: 0.7421 (tpt90) REVERT: G 232 ASN cc_start: 0.8257 (p0) cc_final: 0.7889 (p0) REVERT: J 69 ARG cc_start: 0.7745 (tpt170) cc_final: 0.7407 (tpt90) REVERT: J 232 ASN cc_start: 0.8348 (p0) cc_final: 0.7979 (p0) outliers start: 40 outliers final: 25 residues processed: 238 average time/residue: 1.8227 time to fit residues: 507.6969 Evaluate side-chains 235 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 SER 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 224 SER Chi-restraints excluded: chain F residue 41 VAL 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 157 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.189511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132876 restraints weight = 46147.589| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.82 r_work: 0.3472 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2682 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= 0.176 Angle : 0.570 5.441 22548 Z= 0.306 Chirality : 0.043 0.144 2580 Planarity : 0.004 0.036 2712 Dihedral : 6.118 31.130 2592 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.97 % Allowed : 17.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.12 (0.19), residues: 1908 helix: 3.99 (0.12), residues: 1344 sheet: 2.32 (0.43), residues: 120 loop : -1.64 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP I 79 HIS 0.005 0.002 HIS C 274 PHE 0.009 0.002 PHE B 253 TYR 0.011 0.002 TYR G 67 ARG 0.003 0.000 ARG L 69 Details of bonding type rmsd hydrogen bonds : bond 0.07747 ( 1151) hydrogen bonds : angle 3.30447 ( 3417) SS BOND : bond 0.00634 ( 36) SS BOND : angle 1.35711 ( 72) covalent geometry : bond 0.00406 (16716) covalent geometry : angle 0.56585 (22476) *********************** 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 253 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 2.726 Fit side-chains revert: symmetry clash REVERT: C 21 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5781 (mpt) outliers start: 35 outliers final: 32 residues processed: 231 average time/residue: 1.7950 time to fit residues: 483.5921 Evaluate side-chains 246 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 2.527 ------------------------------------------------------------------------------- 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 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 47 ASP Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 273 ASN 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 F residue 275 LEU 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 21 MET 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 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 2 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.191587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135329 restraints weight = 45744.142| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.77 r_work: 0.3437 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2782 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= 0.146 Angle : 0.523 4.787 22548 Z= 0.281 Chirality : 0.041 0.134 2580 Planarity : 0.004 0.035 2712 Dihedral : 5.737 28.821 2592 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.80 % Allowed : 17.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.28 (0.19), residues: 1908 helix: 4.16 (0.12), residues: 1344 sheet: 2.40 (0.43), residues: 120 loop : -1.76 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP B 79 HIS 0.004 0.001 HIS B 274 PHE 0.008 0.001 PHE H 33 TYR 0.011 0.002 TYR L 67 ARG 0.002 0.000 ARG K 69 Details of bonding type rmsd hydrogen bonds : bond 0.07143 ( 1151) hydrogen bonds : angle 3.28413 ( 3417) SS BOND : bond 0.00437 ( 36) SS BOND : angle 1.12530 ( 72) covalent geometry : bond 0.00317 (16716) covalent geometry : angle 0.52005 (22476) *********************** 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 245 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 2.655 Fit side-chains revert: symmetry clash REVERT: C 21 MET cc_start: 0.6197 (OUTLIER) cc_final: 0.5916 (mpt) outliers start: 32 outliers final: 32 residues processed: 226 average time/residue: 1.8285 time to fit residues: 481.1625 Evaluate side-chains 246 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 2.645 ------------------------------------------------------------------------------- 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 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 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 41 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 54 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.190333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133808 restraints weight = 45655.852| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.77 r_work: 0.3420 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2878 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= 0.165 Angle : 0.554 5.273 22548 Z= 0.297 Chirality : 0.042 0.140 2580 Planarity : 0.004 0.036 2712 Dihedral : 6.073 31.138 2592 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.03 % Allowed : 17.34 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.21 (0.19), residues: 1908 helix: 4.11 (0.12), residues: 1344 sheet: 2.46 (0.45), residues: 120 loop : -1.83 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 79 HIS 0.003 0.001 HIS L 274 PHE 0.009 0.002 PHE J 253 TYR 0.011 0.002 TYR C 67 ARG 0.003 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.07496 ( 1151) hydrogen bonds : angle 3.29714 ( 3417) SS BOND : bond 0.00549 ( 36) SS BOND : angle 1.31621 ( 72) covalent geometry : bond 0.00378 (16716) covalent geometry : angle 0.54956 (22476) *********************** 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 253 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 2.650 Fit side-chains REVERT: C 21 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5908 (mpt) outliers start: 36 outliers final: 38 residues processed: 231 average time/residue: 1.8567 time to fit residues: 501.1787 Evaluate side-chains 254 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 2.821 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 170 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 207 ASN C 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.187557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130326 restraints weight = 45354.462| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.78 r_work: 0.3387 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16752 Z= 0.220 Angle : 0.636 6.299 22548 Z= 0.341 Chirality : 0.045 0.163 2580 Planarity : 0.004 0.039 2712 Dihedral : 7.135 36.786 2592 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.82 % Allowed : 16.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.01 (0.19), residues: 1908 helix: 3.91 (0.12), residues: 1344 sheet: 2.60 (0.47), residues: 120 loop : -1.75 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP B 79 HIS 0.004 0.001 HIS E 274 PHE 0.012 0.002 PHE G 253 TYR 0.014 0.003 TYR G 67 ARG 0.003 0.001 ARG I 24 Details of bonding type rmsd hydrogen bonds : bond 0.08675 ( 1151) hydrogen bonds : angle 3.41842 ( 3417) SS BOND : bond 0.00806 ( 36) SS BOND : angle 1.74663 ( 72) covalent geometry : bond 0.00532 (16716) covalent geometry : angle 0.62929 (22476) *********************** 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 267 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 2.696 Fit side-chains REVERT: C 21 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.5914 (mpt) outliers start: 50 outliers final: 38 residues processed: 232 average time/residue: 1.8154 time to fit residues: 490.8773 Evaluate side-chains 255 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 2.591 ------------------------------------------------------------------------------- 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 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 C residue 266 VAL 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 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 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 41 VAL Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 266 VAL 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 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 58 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.190451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133941 restraints weight = 45396.865| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.77 r_work: 0.3429 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3000 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= 0.146 Angle : 0.526 4.518 22548 Z= 0.285 Chirality : 0.041 0.131 2580 Planarity : 0.004 0.038 2712 Dihedral : 6.089 33.379 2592 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.86 % Allowed : 17.00 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.19), residues: 1908 helix: 4.11 (0.12), residues: 1344 sheet: 2.70 (0.47), residues: 120 loop : -1.85 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.003 0.001 HIS B 274 PHE 0.008 0.001 PHE I 33 TYR 0.011 0.002 TYR C 67 ARG 0.002 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.07267 ( 1151) hydrogen bonds : angle 3.30725 ( 3417) SS BOND : bond 0.00414 ( 36) SS BOND : angle 1.12088 ( 72) covalent geometry : bond 0.00315 (16716) covalent geometry : angle 0.52309 (22476) ********************** 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 250 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 2.456 Fit side-chains REVERT: C 21 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5981 (mpt) REVERT: E 207 ASN cc_start: 0.6921 (m-40) cc_final: 0.6693 (m-40) REVERT: H 207 ASN cc_start: 0.6904 (m-40) cc_final: 0.6682 (m-40) outliers start: 33 outliers final: 35 residues processed: 229 average time/residue: 1.8087 time to fit residues: 481.9893 Evaluate side-chains 253 residues out of total 1776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 2.388 ------------------------------------------------------------------------------- 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 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 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 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 41 VAL 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 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 67 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 77 optimal weight: 0.0970 chunk 169 optimal weight: 8.9990 chunk 179 optimal weight: 0.0870 chunk 162 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN C 207 ASN F 207 ASN I 207 ASN K 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 = 0.4257 r_free = 0.4257 target = 0.195108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139458 restraints weight = 45451.587| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.77 r_work: 0.3497 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3084 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= 0.106 Angle : 0.447 4.454 22548 Z= 0.243 Chirality : 0.039 0.120 2580 Planarity : 0.003 0.025 2712 Dihedral : 4.525 21.432 2592 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.73 % Allowed : 18.13 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.56 (0.19), residues: 1908 helix: 4.45 (0.12), residues: 1344 sheet: 2.50 (0.43), residues: 120 loop : -1.96 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 79 HIS 0.003 0.001 HIS A 274 PHE 0.005 0.001 PHE A 33 TYR 0.007 0.001 TYR F 243 ARG 0.002 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.05419 ( 1151) hydrogen bonds : angle 3.15614 ( 3417) SS BOND : bond 0.00055 ( 36) SS BOND : angle 0.67967 ( 72) covalent geometry : bond 0.00205 (16716) covalent geometry : angle 0.44624 (22476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25704.90 seconds wall clock time: 440 minutes 40.32 seconds (26440.32 seconds total)