Starting phenix.real_space_refine on Mon Oct 13 10:43:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgj_38327/10_2025/8xgj_38327_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgj_38327/10_2025/8xgj_38327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xgj_38327/10_2025/8xgj_38327_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgj_38327/10_2025/8xgj_38327_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xgj_38327/10_2025/8xgj_38327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgj_38327/10_2025/8xgj_38327.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 156 5.16 5 C 11580 2.51 5 N 2568 2.21 5 O 2760 1.98 5 F 72 1.80 5 H 16008 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33144 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 98 Unusual residues: {'MC3': 7, 'YMZ': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 51 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 4.47, per 1000 atoms: 0.13 Number of scatterers: 33144 At special positions: 0 Unit cell: (98.9, 100.62, 148.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 156 16.00 F 72 9.00 O 2760 8.00 N 2568 7.00 C 11580 6.00 H 16008 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.04 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.04 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.04 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.04 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.04 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.04 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.04 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.04 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.04 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.04 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.04 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.04 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.04 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.04 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.04 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.04 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.04 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.04 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.04 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.04 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.04 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.04 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.04 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.04 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.04 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.04 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.04 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.04 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.04 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.04 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 238.4 nanoseconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 76.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.728A pdb=" N GLY A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 removed outlier: 3.822A pdb=" N VAL A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 46' Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.513A pdb=" N SER A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 246 through 276 Processing helix chain 'B' and resid 20 through 41 removed outlier: 4.033A pdb=" N ARG B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.822A pdb=" N VAL B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.512A pdb=" N SER B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 222 Processing helix chain 'B' and resid 246 through 276 Processing helix chain 'C' and resid 20 through 41 removed outlier: 4.033A pdb=" N ARG C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.822A pdb=" N VAL C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 46' Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 87 through 101 removed outlier: 3.513A pdb=" N SER C 101 " --> pdb=" O SER C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 222 Processing helix chain 'C' and resid 246 through 276 Processing helix chain 'D' and resid 20 through 41 removed outlier: 4.033A pdb=" N ARG D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL D 41 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.822A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 74 through 86 Processing helix chain 'D' and resid 87 through 101 removed outlier: 3.513A pdb=" N SER D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 222 Processing helix chain 'D' and resid 246 through 276 Processing helix chain 'E' and resid 20 through 41 removed outlier: 4.032A pdb=" N ARG E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL E 41 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.822A pdb=" N VAL E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 41 through 46' Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 87 through 101 removed outlier: 3.513A pdb=" N SER E 101 " --> pdb=" O SER E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 222 Processing helix chain 'E' and resid 246 through 276 Processing helix chain 'F' and resid 20 through 41 removed outlier: 4.033A pdb=" N ARG F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.821A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 61 through 71 Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 87 through 101 removed outlier: 3.513A pdb=" N SER F 101 " --> pdb=" O SER F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 222 Processing helix chain 'F' and resid 246 through 276 Processing helix chain 'G' and resid 20 through 41 removed outlier: 4.032A pdb=" N ARG G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 removed outlier: 3.822A pdb=" N VAL G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 41 through 46' Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 74 through 86 Processing helix chain 'G' and resid 87 through 101 removed outlier: 3.513A pdb=" N SER G 101 " --> pdb=" O SER G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 222 Processing helix chain 'G' and resid 246 through 276 Processing helix chain 'H' and resid 20 through 41 removed outlier: 4.032A pdb=" N ARG H 24 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE H 25 " --> pdb=" O MET H 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 46 removed outlier: 3.822A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 41 through 46' Processing helix chain 'H' and resid 61 through 71 Processing helix chain 'H' and resid 74 through 86 Processing helix chain 'H' and resid 87 through 101 removed outlier: 3.513A pdb=" N SER H 101 " --> pdb=" O SER H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 222 Processing helix chain 'H' and resid 246 through 276 Processing helix chain 'I' and resid 20 through 41 removed outlier: 4.033A pdb=" N ARG I 24 " --> pdb=" O THR I 20 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE I 25 " --> pdb=" O MET I 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 46 removed outlier: 3.822A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 41 through 46' Processing helix chain 'I' and resid 61 through 71 Processing helix chain 'I' and resid 74 through 86 Processing helix chain 'I' and resid 87 through 101 removed outlier: 3.513A pdb=" N SER I 101 " --> pdb=" O SER I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 222 Processing helix chain 'I' and resid 246 through 276 Processing helix chain 'J' and resid 20 through 41 removed outlier: 4.033A pdb=" N ARG J 24 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE J 25 " --> pdb=" O MET J 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 46 removed outlier: 3.822A pdb=" N VAL J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 41 through 46' Processing helix chain 'J' and resid 61 through 71 Processing helix chain 'J' and resid 74 through 86 Processing helix chain 'J' and resid 87 through 101 removed outlier: 3.513A pdb=" N SER J 101 " --> pdb=" O SER J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 222 Processing helix chain 'J' and resid 246 through 276 Processing helix chain 'K' and resid 20 through 41 removed outlier: 4.032A pdb=" N ARG K 24 " --> pdb=" O THR K 20 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 46 removed outlier: 3.822A pdb=" N VAL K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 41 through 46' Processing helix chain 'K' and resid 61 through 71 Processing helix chain 'K' and resid 74 through 86 Processing helix chain 'K' and resid 87 through 101 removed outlier: 3.513A pdb=" N SER K 101 " --> pdb=" O SER K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 222 Processing helix chain 'K' and resid 246 through 276 Processing helix chain 'L' and resid 20 through 41 removed outlier: 4.032A pdb=" N ARG L 24 " --> pdb=" O THR L 20 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE L 25 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 removed outlier: 3.822A pdb=" N VAL L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 41 through 46' Processing helix chain 'L' and resid 61 through 71 Processing helix chain 'L' and resid 74 through 86 Processing helix chain 'L' and resid 87 through 101 removed outlier: 3.513A pdb=" N SER L 101 " --> pdb=" O SER L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 222 Processing helix chain 'L' and resid 246 through 276 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.605A 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: 3.605A 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: 3.605A 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: 3.605A 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: 3.604A 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: 3.604A 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: 3.605A 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: 3.604A 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: 3.604A 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: 3.605A 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: 3.604A 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: 3.605A pdb=" N VAL L 54 " --> pdb=" O TYR L 243 " (cutoff:3.500A) 1164 hydrogen bonds defined for protein. 3456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.95 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15972 1.04 - 1.23: 700 1.23 - 1.43: 6620 1.43 - 1.63: 9972 1.63 - 1.83: 204 Bond restraints: 33468 Sorted by residual: bond pdb=" CAL YMZ I 401 " pdb=" CAM YMZ I 401 " ideal model delta sigma weight residual 1.525 1.437 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CAL YMZ H 401 " pdb=" CAM YMZ H 401 " ideal model delta sigma weight residual 1.525 1.437 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CAL YMZ A 401 " pdb=" CAM YMZ A 401 " ideal model delta sigma weight residual 1.525 1.437 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" CAL YMZ J 401 " pdb=" CAM YMZ J 401 " ideal model delta sigma weight residual 1.525 1.437 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CAL YMZ E 401 " pdb=" CAM YMZ E 401 " ideal model delta sigma weight residual 1.525 1.437 0.088 2.00e-02 2.50e+03 1.92e+01 ... (remaining 33463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 52752 1.15 - 2.29: 5764 2.29 - 3.44: 610 3.44 - 4.58: 332 4.58 - 5.73: 62 Bond angle restraints: 59520 Sorted by residual: angle pdb=" N GLU B 43 " pdb=" CA GLU B 43 " pdb=" CB GLU B 43 " ideal model delta sigma weight residual 110.39 105.77 4.62 1.75e+00 3.27e-01 6.98e+00 angle pdb=" N GLU C 43 " pdb=" CA GLU C 43 " pdb=" CB GLU C 43 " ideal model delta sigma weight residual 110.39 105.77 4.62 1.75e+00 3.27e-01 6.97e+00 angle pdb=" N GLU G 43 " pdb=" CA GLU G 43 " pdb=" CB GLU G 43 " ideal model delta sigma weight residual 110.39 105.77 4.62 1.75e+00 3.27e-01 6.97e+00 angle pdb=" N GLU D 43 " pdb=" CA GLU D 43 " pdb=" CB GLU D 43 " ideal model delta sigma weight residual 110.39 105.78 4.61 1.75e+00 3.27e-01 6.95e+00 angle pdb=" N GLU I 43 " pdb=" CA GLU I 43 " pdb=" CB GLU I 43 " ideal model delta sigma weight residual 110.39 105.78 4.61 1.75e+00 3.27e-01 6.95e+00 ... (remaining 59515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 14244 16.83 - 33.67: 1400 33.67 - 50.50: 448 50.50 - 67.33: 132 67.33 - 84.16: 12 Dihedral angle restraints: 16236 sinusoidal: 8964 harmonic: 7272 Sorted by residual: dihedral pdb=" CB CYS H 62 " pdb=" SG CYS H 62 " pdb=" SG CYS H 236 " pdb=" CB CYS H 236 " ideal model delta sinusoidal sigma weight residual 93.00 120.03 -27.03 1 1.00e+01 1.00e-02 1.05e+01 dihedral pdb=" CB CYS F 62 " pdb=" SG CYS F 62 " pdb=" SG CYS F 236 " pdb=" CB CYS F 236 " ideal model delta sinusoidal sigma weight residual 93.00 120.02 -27.02 1 1.00e+01 1.00e-02 1.05e+01 dihedral pdb=" CB CYS I 62 " pdb=" SG CYS I 62 " pdb=" SG CYS I 236 " pdb=" CB CYS I 236 " ideal model delta sinusoidal sigma weight residual 93.00 120.01 -27.01 1 1.00e+01 1.00e-02 1.05e+01 ... (remaining 16233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1964 0.052 - 0.104: 580 0.104 - 0.156: 48 0.156 - 0.208: 12 0.208 - 0.260: 24 Chirality restraints: 2628 Sorted by residual: chirality pdb=" CAW YMZ C 401 " pdb=" CAS YMZ C 401 " pdb=" CAX YMZ C 401 " pdb=" OAA YMZ C 401 " both_signs ideal model delta sigma weight residual False 2.34 2.60 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CAW YMZ A 401 " pdb=" CAS YMZ A 401 " pdb=" CAX YMZ A 401 " pdb=" OAA YMZ A 401 " both_signs ideal model delta sigma weight residual False 2.34 2.60 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CAW YMZ D 401 " pdb=" CAS YMZ D 401 " pdb=" CAX YMZ D 401 " pdb=" OAA YMZ D 401 " both_signs ideal model delta sigma weight residual False 2.34 2.60 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 2625 not shown) Planarity restraints: 4656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU I 43 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" N THR I 44 " 0.037 2.00e-02 2.50e+03 pdb=" CA THR I 44 " -0.009 2.00e-02 2.50e+03 pdb=" H THR I 44 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU G 43 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" N THR G 44 " -0.036 2.00e-02 2.50e+03 pdb=" CA THR G 44 " 0.009 2.00e-02 2.50e+03 pdb=" H THR G 44 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 43 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" N THR C 44 " -0.036 2.00e-02 2.50e+03 pdb=" CA THR C 44 " 0.009 2.00e-02 2.50e+03 pdb=" H THR C 44 " 0.016 2.00e-02 2.50e+03 ... (remaining 4653 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.44: 15262 2.44 - 2.98: 69146 2.98 - 3.52: 79467 3.52 - 4.06: 104126 4.06 - 4.60: 155643 Nonbonded interactions: 423644 Sorted by model distance: nonbonded pdb=" O SER K 245 " pdb=" HZ1 LYS K 250 " model vdw 1.896 2.450 nonbonded pdb=" O SER F 245 " pdb=" HZ1 LYS F 250 " model vdw 1.896 2.450 nonbonded pdb=" O SER C 245 " pdb=" HZ1 LYS C 250 " model vdw 1.896 2.450 nonbonded pdb=" O SER L 245 " pdb=" HZ1 LYS L 250 " model vdw 1.896 2.450 nonbonded pdb=" O SER H 245 " pdb=" HZ1 LYS H 250 " model vdw 1.896 2.450 ... (remaining 423639 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.430 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: 0.190 Extract box with map and model: 0.500 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 32.450 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.007 0.088 17496 Z= 0.330 Angle : 0.910 5.727 23508 Z= 0.465 Chirality : 0.051 0.260 2628 Planarity : 0.006 0.046 2760 Dihedral : 15.263 84.162 6576 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.00 % Allowed : 15.33 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.17), residues: 1944 helix: 2.12 (0.13), residues: 1320 sheet: 1.12 (0.36), residues: 120 loop : -1.29 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 233 TYR 0.010 0.002 TYR I 67 PHE 0.013 0.002 PHE L 253 TRP 0.005 0.002 TRP K 79 HIS 0.003 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00652 (17460) covalent geometry : angle 0.90693 (23436) SS BOND : bond 0.00957 ( 36) SS BOND : angle 1.68744 ( 72) hydrogen bonds : bond 0.14492 ( 1164) hydrogen bonds : angle 4.42081 ( 3456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.734 Fit side-chains REVERT: C 85 MET cc_start: 0.8043 (tpp) cc_final: 0.7828 (tpt) REVERT: C 94 ILE cc_start: 0.6059 (mm) cc_final: 0.5729 (mt) REVERT: F 85 MET cc_start: 0.8042 (tpp) cc_final: 0.7823 (tpt) REVERT: F 94 ILE cc_start: 0.6058 (mm) cc_final: 0.5728 (mt) REVERT: I 85 MET cc_start: 0.8042 (tpp) cc_final: 0.7827 (tpt) REVERT: I 94 ILE cc_start: 0.6059 (mm) cc_final: 0.5728 (mt) REVERT: L 85 MET cc_start: 0.8047 (tpp) cc_final: 0.7832 (tpt) REVERT: L 94 ILE cc_start: 0.6061 (mm) cc_final: 0.5732 (mt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.9746 time to fit residues: 230.0998 Evaluate side-chains 144 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN C 63 ASN C 268 ASN D 232 ASN F 63 ASN F 268 ASN G 232 ASN I 63 ASN I 268 ASN J 232 ASN L 63 ASN L 268 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.192578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.143382 restraints weight = 42270.593| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.52 r_work: 0.3565 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17496 Z= 0.139 Angle : 0.534 4.571 23508 Z= 0.288 Chirality : 0.040 0.123 2628 Planarity : 0.004 0.031 2760 Dihedral : 6.869 29.181 3012 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.11 % Allowed : 14.89 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.23 (0.18), residues: 1944 helix: 3.11 (0.13), residues: 1368 sheet: 2.18 (0.41), residues: 120 loop : -1.14 (0.24), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 246 TYR 0.008 0.001 TYR L 67 PHE 0.006 0.001 PHE F 53 TRP 0.002 0.001 TRP J 79 HIS 0.001 0.000 HIS I 274 Details of bonding type rmsd covalent geometry : bond 0.00259 (17460) covalent geometry : angle 0.53277 (23436) SS BOND : bond 0.00173 ( 36) SS BOND : angle 0.73623 ( 72) hydrogen bonds : bond 0.07333 ( 1164) hydrogen bonds : angle 3.47868 ( 3456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.957 Fit side-chains REVERT: C 85 MET cc_start: 0.7944 (tpp) cc_final: 0.7514 (tpt) REVERT: C 94 ILE cc_start: 0.5838 (mm) cc_final: 0.5554 (mt) REVERT: F 85 MET cc_start: 0.7921 (tpp) cc_final: 0.7478 (tpt) REVERT: F 94 ILE cc_start: 0.5832 (mm) cc_final: 0.5549 (mt) REVERT: I 85 MET cc_start: 0.7913 (tpp) cc_final: 0.7473 (tpt) REVERT: I 94 ILE cc_start: 0.5820 (mm) cc_final: 0.5536 (mt) REVERT: L 85 MET cc_start: 0.7949 (tpp) cc_final: 0.7522 (tpt) REVERT: L 94 ILE cc_start: 0.5863 (mm) cc_final: 0.5577 (mt) outliers start: 20 outliers final: 12 residues processed: 156 average time/residue: 0.9232 time to fit residues: 169.0313 Evaluate side-chains 156 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN B 232 ASN B 268 ASN C 63 ASN D 268 ASN E 232 ASN E 268 ASN F 63 ASN G 268 ASN H 232 ASN H 268 ASN I 63 ASN J 268 ASN K 232 ASN K 268 ASN L 63 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.192512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.141642 restraints weight = 40609.821| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.30 r_work: 0.3471 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17496 Z= 0.157 Angle : 0.572 4.451 23508 Z= 0.307 Chirality : 0.041 0.145 2628 Planarity : 0.004 0.039 2760 Dihedral : 7.347 30.238 3012 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.89 % Allowed : 14.28 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.39 (0.18), residues: 1944 helix: 3.35 (0.13), residues: 1368 sheet: 2.53 (0.44), residues: 120 loop : -1.67 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 69 TYR 0.014 0.002 TYR E 243 PHE 0.011 0.001 PHE B 53 TRP 0.004 0.002 TRP J 79 HIS 0.002 0.001 HIS I 274 Details of bonding type rmsd covalent geometry : bond 0.00338 (17460) covalent geometry : angle 0.56797 (23436) SS BOND : bond 0.00545 ( 36) SS BOND : angle 1.34199 ( 72) hydrogen bonds : bond 0.07879 ( 1164) hydrogen bonds : angle 3.28463 ( 3456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.821 Fit side-chains REVERT: C 94 ILE cc_start: 0.5800 (mm) cc_final: 0.5529 (mt) REVERT: F 94 ILE cc_start: 0.5802 (mm) cc_final: 0.5531 (mt) REVERT: I 94 ILE cc_start: 0.5789 (mm) cc_final: 0.5518 (mt) REVERT: L 94 ILE cc_start: 0.5785 (mm) cc_final: 0.5516 (mt) outliers start: 16 outliers final: 12 residues processed: 137 average time/residue: 1.1684 time to fit residues: 182.3921 Evaluate side-chains 137 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 ASN E 232 ASN H 232 ASN K 232 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.188970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137032 restraints weight = 40382.120| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.31 r_work: 0.3407 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17496 Z= 0.221 Angle : 0.679 5.006 23508 Z= 0.363 Chirality : 0.045 0.158 2628 Planarity : 0.006 0.045 2760 Dihedral : 8.957 43.873 3012 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.00 % Allowed : 14.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.22 (0.19), residues: 1944 helix: 3.21 (0.13), residues: 1368 sheet: 2.82 (0.48), residues: 120 loop : -1.76 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 246 TYR 0.017 0.003 TYR B 243 PHE 0.015 0.002 PHE A 53 TRP 0.007 0.003 TRP C 79 HIS 0.003 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00527 (17460) covalent geometry : angle 0.67223 (23436) SS BOND : bond 0.00849 ( 36) SS BOND : angle 1.85117 ( 72) hydrogen bonds : bond 0.09397 ( 1164) hydrogen bonds : angle 3.21495 ( 3456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.934 Fit side-chains outliers start: 36 outliers final: 12 residues processed: 150 average time/residue: 1.4544 time to fit residues: 242.3688 Evaluate side-chains 128 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 19 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 101 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN B 232 ASN D 232 ASN E 232 ASN G 232 ASN H 232 ASN J 232 ASN K 232 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.190757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139576 restraints weight = 40431.738| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.29 r_work: 0.3449 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17496 Z= 0.147 Angle : 0.550 3.936 23508 Z= 0.296 Chirality : 0.041 0.136 2628 Planarity : 0.005 0.043 2760 Dihedral : 7.699 35.412 3012 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.67 % Allowed : 13.78 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.47 (0.19), residues: 1944 helix: 3.41 (0.13), residues: 1368 sheet: 2.82 (0.47), residues: 120 loop : -1.68 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 246 TYR 0.014 0.002 TYR K 243 PHE 0.009 0.001 PHE A 53 TRP 0.004 0.002 TRP C 79 HIS 0.002 0.001 HIS J 274 Details of bonding type rmsd covalent geometry : bond 0.00309 (17460) covalent geometry : angle 0.54687 (23436) SS BOND : bond 0.00431 ( 36) SS BOND : angle 1.19490 ( 72) hydrogen bonds : bond 0.07780 ( 1164) hydrogen bonds : angle 3.16223 ( 3456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 0.989 Fit side-chains REVERT: C 94 ILE cc_start: 0.5915 (mm) cc_final: 0.5638 (mt) REVERT: F 94 ILE cc_start: 0.5919 (mm) cc_final: 0.5644 (mt) REVERT: I 94 ILE cc_start: 0.5905 (mm) cc_final: 0.5630 (mt) REVERT: L 94 ILE cc_start: 0.5905 (mm) cc_final: 0.5632 (mt) outliers start: 48 outliers final: 24 residues processed: 160 average time/residue: 1.2856 time to fit residues: 231.5460 Evaluate side-chains 138 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 63 ASN Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 83 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 88 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN B 232 ASN D 232 ASN E 232 ASN G 232 ASN H 232 ASN J 232 ASN K 232 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.187362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.135388 restraints weight = 40401.033| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.30 r_work: 0.3395 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17496 Z= 0.214 Angle : 0.665 5.079 23508 Z= 0.354 Chirality : 0.044 0.158 2628 Planarity : 0.006 0.048 2760 Dihedral : 8.974 43.826 3012 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.33 % Allowed : 12.67 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.29 (0.19), residues: 1944 helix: 3.27 (0.13), residues: 1368 sheet: 3.09 (0.49), residues: 120 loop : -1.87 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 246 TYR 0.018 0.002 TYR E 243 PHE 0.014 0.002 PHE A 256 TRP 0.007 0.003 TRP H 79 HIS 0.003 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00512 (17460) covalent geometry : angle 0.65831 (23436) SS BOND : bond 0.00819 ( 36) SS BOND : angle 1.81153 ( 72) hydrogen bonds : bond 0.09161 ( 1164) hydrogen bonds : angle 3.15715 ( 3456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 110 time to evaluate : 0.839 Fit side-chains outliers start: 60 outliers final: 32 residues processed: 166 average time/residue: 1.2910 time to fit residues: 241.2538 Evaluate side-chains 140 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 202 GLN Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 202 GLN Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 275 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 2.9990 chunk 172 optimal weight: 0.2980 chunk 110 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 176 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN B 232 ASN D 232 ASN E 232 ASN G 232 ASN H 232 ASN J 232 ASN K 232 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.192198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141103 restraints weight = 40375.620| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.29 r_work: 0.3461 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17496 Z= 0.127 Angle : 0.512 3.783 23508 Z= 0.276 Chirality : 0.040 0.128 2628 Planarity : 0.004 0.040 2760 Dihedral : 7.185 34.487 3012 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.22 % Allowed : 13.22 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.19), residues: 1944 helix: 3.53 (0.13), residues: 1368 sheet: 3.24 (0.48), residues: 120 loop : -1.66 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 233 TYR 0.013 0.001 TYR K 243 PHE 0.007 0.001 PHE J 53 TRP 0.003 0.001 TRP H 79 HIS 0.004 0.001 HIS I 274 Details of bonding type rmsd covalent geometry : bond 0.00253 (17460) covalent geometry : angle 0.50943 (23436) SS BOND : bond 0.00265 ( 36) SS BOND : angle 1.00284 ( 72) hydrogen bonds : bond 0.07082 ( 1164) hydrogen bonds : angle 3.11228 ( 3456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.995 Fit side-chains REVERT: C 94 ILE cc_start: 0.5826 (mm) cc_final: 0.5563 (mt) REVERT: F 94 ILE cc_start: 0.5837 (mm) cc_final: 0.5573 (mt) REVERT: I 94 ILE cc_start: 0.5820 (mm) cc_final: 0.5557 (mt) REVERT: L 94 ILE cc_start: 0.5838 (mm) cc_final: 0.5573 (mt) outliers start: 40 outliers final: 28 residues processed: 165 average time/residue: 1.2220 time to fit residues: 228.5216 Evaluate side-chains 151 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 275 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 45 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN B 232 ASN D 232 ASN E 232 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 ASN H 232 ASN ** I 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 ASN K 232 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.188544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.136455 restraints weight = 40345.634| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.30 r_work: 0.3419 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17496 Z= 0.196 Angle : 0.631 4.904 23508 Z= 0.336 Chirality : 0.043 0.157 2628 Planarity : 0.005 0.046 2760 Dihedral : 8.448 41.105 3012 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.44 % Allowed : 13.00 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.44 (0.19), residues: 1944 helix: 3.41 (0.13), residues: 1368 sheet: 3.31 (0.50), residues: 120 loop : -1.95 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 246 TYR 0.016 0.002 TYR B 243 PHE 0.013 0.002 PHE J 53 TRP 0.006 0.002 TRP H 79 HIS 0.003 0.001 HIS G 274 Details of bonding type rmsd covalent geometry : bond 0.00467 (17460) covalent geometry : angle 0.62501 (23436) SS BOND : bond 0.00733 ( 36) SS BOND : angle 1.69686 ( 72) hydrogen bonds : bond 0.08605 ( 1164) hydrogen bonds : angle 3.08907 ( 3456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 0.896 Fit side-chains REVERT: C 94 ILE cc_start: 0.5880 (mm) cc_final: 0.5609 (OUTLIER) REVERT: F 94 ILE cc_start: 0.5897 (mm) cc_final: 0.5624 (OUTLIER) REVERT: I 94 ILE cc_start: 0.5867 (mm) cc_final: 0.5595 (OUTLIER) REVERT: L 94 ILE cc_start: 0.5879 (mm) cc_final: 0.5608 (OUTLIER) outliers start: 44 outliers final: 32 residues processed: 144 average time/residue: 1.3461 time to fit residues: 217.7661 Evaluate side-chains 140 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 275 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN B 232 ASN D 232 ASN E 232 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 ASN H 232 ASN ** I 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 ASN K 232 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.191774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.140412 restraints weight = 40128.325| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.28 r_work: 0.3483 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17496 Z= 0.134 Angle : 0.522 3.796 23508 Z= 0.281 Chirality : 0.040 0.134 2628 Planarity : 0.005 0.042 2760 Dihedral : 7.260 34.803 3012 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.22 % Allowed : 13.22 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.65 (0.19), residues: 1944 helix: 3.56 (0.13), residues: 1368 sheet: 3.45 (0.50), residues: 120 loop : -1.87 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 246 TYR 0.013 0.002 TYR K 243 PHE 0.007 0.001 PHE A 53 TRP 0.003 0.001 TRP F 79 HIS 0.002 0.001 HIS G 274 Details of bonding type rmsd covalent geometry : bond 0.00279 (17460) covalent geometry : angle 0.51931 (23436) SS BOND : bond 0.00372 ( 36) SS BOND : angle 1.13083 ( 72) hydrogen bonds : bond 0.07189 ( 1164) hydrogen bonds : angle 3.05886 ( 3456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.926 Fit side-chains REVERT: B 94 ILE cc_start: 0.5839 (mm) cc_final: 0.5587 (mt) REVERT: C 94 ILE cc_start: 0.5874 (mm) cc_final: 0.5602 (mt) REVERT: E 94 ILE cc_start: 0.5838 (mm) cc_final: 0.5587 (mt) REVERT: F 94 ILE cc_start: 0.5866 (mm) cc_final: 0.5610 (mt) REVERT: H 94 ILE cc_start: 0.5826 (mm) cc_final: 0.5575 (mt) REVERT: I 94 ILE cc_start: 0.5858 (mm) cc_final: 0.5587 (mt) REVERT: K 94 ILE cc_start: 0.5835 (mm) cc_final: 0.5584 (mt) REVERT: L 94 ILE cc_start: 0.5858 (mm) cc_final: 0.5603 (mt) outliers start: 40 outliers final: 32 residues processed: 164 average time/residue: 1.1775 time to fit residues: 219.4547 Evaluate side-chains 155 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 63 ASN Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN B 232 ASN D 232 ASN E 232 ASN G 232 ASN H 232 ASN J 232 ASN K 232 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.191739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140264 restraints weight = 40408.836| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.29 r_work: 0.3480 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17496 Z= 0.137 Angle : 0.532 3.967 23508 Z= 0.285 Chirality : 0.040 0.140 2628 Planarity : 0.005 0.042 2760 Dihedral : 7.056 33.613 3012 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.44 % Allowed : 13.44 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.19), residues: 1944 helix: 3.57 (0.13), residues: 1368 sheet: 3.33 (0.50), residues: 120 loop : -1.84 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 246 TYR 0.014 0.002 TYR B 243 PHE 0.009 0.001 PHE J 53 TRP 0.004 0.002 TRP B 79 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00296 (17460) covalent geometry : angle 0.52855 (23436) SS BOND : bond 0.00388 ( 36) SS BOND : angle 1.21053 ( 72) hydrogen bonds : bond 0.07150 ( 1164) hydrogen bonds : angle 3.04030 ( 3456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 0.961 Fit side-chains REVERT: A 94 ILE cc_start: 0.5665 (mm) cc_final: 0.5429 (mt) REVERT: C 94 ILE cc_start: 0.5791 (mm) cc_final: 0.5546 (mt) REVERT: D 94 ILE cc_start: 0.5650 (mm) cc_final: 0.5415 (mt) REVERT: F 94 ILE cc_start: 0.5801 (mm) cc_final: 0.5556 (mt) REVERT: G 94 ILE cc_start: 0.5656 (mm) cc_final: 0.5416 (OUTLIER) REVERT: I 94 ILE cc_start: 0.5769 (mm) cc_final: 0.5525 (mt) REVERT: L 94 ILE cc_start: 0.5786 (mm) cc_final: 0.5542 (mt) outliers start: 44 outliers final: 33 residues processed: 148 average time/residue: 1.1686 time to fit residues: 196.3531 Evaluate side-chains 144 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 275 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 63 ASN Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 117 optimal weight: 0.0980 chunk 113 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 85 optimal weight: 0.0980 chunk 77 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN B 232 ASN D 232 ASN E 232 ASN G 232 ASN H 232 ASN J 232 ASN K 232 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.193251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142355 restraints weight = 40300.047| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.27 r_work: 0.3481 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17496 Z= 0.117 Angle : 0.488 3.800 23508 Z= 0.262 Chirality : 0.039 0.131 2628 Planarity : 0.004 0.038 2760 Dihedral : 6.176 29.775 3012 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.44 % Allowed : 13.39 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.80 (0.19), residues: 1944 helix: 3.71 (0.13), residues: 1368 sheet: 3.23 (0.49), residues: 120 loop : -1.86 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 34 TYR 0.012 0.001 TYR B 243 PHE 0.006 0.001 PHE G 53 TRP 0.003 0.001 TRP F 79 HIS 0.002 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00240 (17460) covalent geometry : angle 0.48517 (23436) SS BOND : bond 0.00264 ( 36) SS BOND : angle 0.98962 ( 72) hydrogen bonds : bond 0.06341 ( 1164) hydrogen bonds : angle 2.98060 ( 3456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10131.27 seconds wall clock time: 171 minutes 59.85 seconds (10319.85 seconds total)