Starting phenix.real_space_refine on Sat Jun 28 11:01:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xgj_38327/06_2025/8xgj_38327_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xgj_38327/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xgj_38327/06_2025/8xgj_38327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xgj_38327/06_2025/8xgj_38327.map" model { file = "/net/cci-nas-00/data/ceres_data/8xgj_38327/06_2025/8xgj_38327_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xgj_38327/06_2025/8xgj_38327_trim.cif" } resolution = 2.7 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= 0.004 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 51 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 10.70, per 1000 atoms: 0.32 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 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: 8.32 Conformation dependent library (CDL) restraints added in 2.5 seconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 76.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 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: 13.04 Time building geometry restraints manager: 10.07 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: 0.19 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.600 Extract box with map and model: 1.430 Check model and map are aligned: 0.230 Set scattering table: 0.330 Process input model: 65.290 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.100 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:15.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.920 ------------------------------------------------------------------------------- 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 (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: 1.83 (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 TRP 0.005 0.002 TRP K 79 HIS 0.003 0.001 HIS E 99 PHE 0.013 0.002 PHE L 253 TYR 0.010 0.002 TYR I 67 ARG 0.003 0.001 ARG I 233 Details of bonding type rmsd hydrogen bonds : bond 0.14492 ( 1164) hydrogen bonds : angle 4.42081 ( 3456) SS BOND : bond 0.00957 ( 36) SS BOND : angle 1.68744 ( 72) covalent geometry : bond 0.00652 (17460) covalent geometry : angle 0.90693 (23436) *********************** 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 : 2.584 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: 0.5730 (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: 1.9385 time to fit residues: 461.5516 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 : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN C 268 ASN D 232 ASN F 268 ASN G 232 ASN I 268 ASN J 232 ASN L 268 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.189640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.140042 restraints weight = 42351.555| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.52 r_work: 0.3529 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 17496 Z= 0.151 Angle : 0.565 4.511 23508 Z= 0.306 Chirality : 0.041 0.128 2628 Planarity : 0.004 0.034 2760 Dihedral : 7.414 29.958 3012 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 (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: 3.06 (0.18), residues: 1944 helix: 2.98 (0.13), residues: 1368 sheet: 2.23 (0.41), residues: 120 loop : -1.24 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.001 0.000 HIS K 274 PHE 0.008 0.001 PHE F 53 TYR 0.010 0.001 TYR L 67 ARG 0.002 0.000 ARG L 69 Details of bonding type rmsd hydrogen bonds : bond 0.08122 ( 1164) hydrogen bonds : angle 3.49448 ( 3456) SS BOND : bond 0.00373 ( 36) SS BOND : angle 1.00653 ( 72) covalent geometry : bond 0.00299 (17460) covalent geometry : angle 0.56346 (23436) *********************** 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 168 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 2.819 Fit side-chains REVERT: A 63 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8353 (m-40) REVERT: C 85 MET cc_start: 0.8035 (tpp) cc_final: 0.7644 (tpt) REVERT: C 94 ILE cc_start: 0.5873 (mm) cc_final: 0.5565 (mt) REVERT: D 63 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8348 (m-40) REVERT: F 85 MET cc_start: 0.8003 (tpp) cc_final: 0.7592 (tpt) REVERT: F 94 ILE cc_start: 0.5868 (mm) cc_final: 0.5558 (mt) REVERT: G 63 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8344 (m-40) REVERT: I 85 MET cc_start: 0.8014 (tpp) cc_final: 0.7620 (tpt) REVERT: I 94 ILE cc_start: 0.5858 (mm) cc_final: 0.5548 (mt) REVERT: L 85 MET cc_start: 0.8022 (tpp) cc_final: 0.7627 (tpt) REVERT: L 94 ILE cc_start: 0.5902 (mm) cc_final: 0.5591 (mt) outliers start: 20 outliers final: 12 residues processed: 152 average time/residue: 1.8277 time to fit residues: 327.4349 Evaluate side-chains 148 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 63 ASN 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 D residue 63 ASN 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 G residue 63 ASN 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 138 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 268 ASN B 232 ASN B 268 ASN D 232 ASN D 268 ASN E 232 ASN E 268 ASN G 232 ASN G 268 ASN H 232 ASN H 268 ASN J 232 ASN J 268 ASN K 232 ASN K 268 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.192390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141114 restraints weight = 40942.037| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.30 r_work: 0.3467 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1262 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= 0.155 Angle : 0.567 4.204 23508 Z= 0.304 Chirality : 0.041 0.140 2628 Planarity : 0.004 0.039 2760 Dihedral : 7.326 30.879 3012 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.28 % Allowed : 14.06 % 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 (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: 3.34 (0.18), residues: 1944 helix: 3.32 (0.13), residues: 1368 sheet: 2.54 (0.44), residues: 120 loop : -1.69 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP D 79 HIS 0.002 0.001 HIS G 99 PHE 0.011 0.001 PHE C 53 TYR 0.014 0.002 TYR B 243 ARG 0.002 0.000 ARG F 77 Details of bonding type rmsd hydrogen bonds : bond 0.07950 ( 1164) hydrogen bonds : angle 3.28702 ( 3456) SS BOND : bond 0.00504 ( 36) SS BOND : angle 1.30822 ( 72) covalent geometry : bond 0.00332 (17460) covalent geometry : angle 0.56317 (23436) *********************** 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 156 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 2.793 Fit side-chains REVERT: A 63 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8490 (m-40) REVERT: C 94 ILE cc_start: 0.5837 (mm) cc_final: 0.5561 (mt) REVERT: D 63 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8502 (m-40) REVERT: F 94 ILE cc_start: 0.5858 (mm) cc_final: 0.5578 (mt) REVERT: G 63 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8485 (m-40) REVERT: I 94 ILE cc_start: 0.5841 (mm) cc_final: 0.5565 (mt) REVERT: L 94 ILE cc_start: 0.5829 (mm) cc_final: 0.5554 (mt) outliers start: 23 outliers final: 12 residues processed: 140 average time/residue: 2.2332 time to fit residues: 358.8824 Evaluate side-chains 136 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 63 ASN 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 D residue 63 ASN 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 G residue 63 ASN 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 127 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.0170 chunk 16 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 overall best weight: 1.3424 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.193811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142816 restraints weight = 40518.281| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.29 r_work: 0.3486 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17496 Z= 0.131 Angle : 0.516 4.033 23508 Z= 0.277 Chirality : 0.040 0.133 2628 Planarity : 0.004 0.039 2760 Dihedral : 6.638 27.889 3012 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.33 % Allowed : 14.67 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.56 (0.19), residues: 1944 helix: 3.52 (0.13), residues: 1368 sheet: 2.56 (0.44), residues: 120 loop : -1.71 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 79 HIS 0.002 0.001 HIS B 274 PHE 0.009 0.001 PHE D 53 TYR 0.013 0.002 TYR E 243 ARG 0.002 0.000 ARG B 246 Details of bonding type rmsd hydrogen bonds : bond 0.07119 ( 1164) hydrogen bonds : angle 3.15085 ( 3456) SS BOND : bond 0.00374 ( 36) SS BOND : angle 1.04030 ( 72) covalent geometry : bond 0.00265 (17460) covalent geometry : angle 0.51353 (23436) *********************** 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 153 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 2.734 Fit side-chains REVERT: A 63 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8501 (m-40) REVERT: C 94 ILE cc_start: 0.5758 (mm) cc_final: 0.5503 (mt) REVERT: D 63 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8495 (m-40) REVERT: F 94 ILE cc_start: 0.5778 (mm) cc_final: 0.5520 (mt) REVERT: G 63 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8492 (m-40) REVERT: I 94 ILE cc_start: 0.5760 (mm) cc_final: 0.5506 (mt) REVERT: L 94 ILE cc_start: 0.5760 (mm) cc_final: 0.5506 (mt) outliers start: 24 outliers final: 12 residues processed: 140 average time/residue: 3.0388 time to fit residues: 487.4208 Evaluate side-chains 123 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 63 ASN 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 D residue 63 ASN 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 G residue 63 ASN 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 62 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.193721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142679 restraints weight = 40358.709| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.54 r_work: 0.3475 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1724 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= 0.124 Angle : 0.499 3.987 23508 Z= 0.267 Chirality : 0.040 0.135 2628 Planarity : 0.004 0.038 2760 Dihedral : 6.247 26.421 3012 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.72 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 (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: 3.70 (0.19), residues: 1944 helix: 3.63 (0.13), residues: 1368 sheet: 2.60 (0.44), residues: 120 loop : -1.71 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 79 HIS 0.002 0.001 HIS A 274 PHE 0.008 0.001 PHE G 53 TYR 0.012 0.001 TYR K 243 ARG 0.001 0.000 ARG L 69 Details of bonding type rmsd hydrogen bonds : bond 0.06700 ( 1164) hydrogen bonds : angle 3.05877 ( 3456) SS BOND : bond 0.00328 ( 36) SS BOND : angle 0.98619 ( 72) covalent geometry : bond 0.00256 (17460) covalent geometry : angle 0.49679 (23436) *********************** 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 172 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 2.690 Fit side-chains REVERT: A 63 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8483 (m-40) REVERT: C 94 ILE cc_start: 0.5681 (mm) cc_final: 0.5448 (mt) REVERT: D 63 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8473 (m-40) REVERT: F 94 ILE cc_start: 0.5689 (mm) cc_final: 0.5456 (mt) REVERT: G 63 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8475 (m-40) REVERT: I 94 ILE cc_start: 0.5672 (mm) cc_final: 0.5441 (mt) REVERT: L 94 ILE cc_start: 0.5674 (mm) cc_final: 0.5448 (mt) outliers start: 48 outliers final: 12 residues processed: 155 average time/residue: 1.9527 time to fit residues: 353.2995 Evaluate side-chains 124 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 63 ASN 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 D residue 63 ASN 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 G residue 63 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 27 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 105 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: 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 = 0.4137 r_free = 0.4137 target = 0.188919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.136947 restraints weight = 40351.477| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.28 r_work: 0.3426 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17496 Z= 0.188 Angle : 0.625 4.875 23508 Z= 0.331 Chirality : 0.043 0.157 2628 Planarity : 0.005 0.045 2760 Dihedral : 8.049 40.396 3012 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.11 % Allowed : 13.44 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.56 (0.19), residues: 1944 helix: 3.50 (0.13), residues: 1368 sheet: 2.86 (0.48), residues: 120 loop : -1.75 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP J 79 HIS 0.004 0.002 HIS F 274 PHE 0.013 0.002 PHE A 53 TYR 0.018 0.002 TYR H 243 ARG 0.003 0.001 ARG I 246 Details of bonding type rmsd hydrogen bonds : bond 0.08340 ( 1164) hydrogen bonds : angle 3.07964 ( 3456) SS BOND : bond 0.00701 ( 36) SS BOND : angle 1.58994 ( 72) covalent geometry : bond 0.00435 (17460) covalent geometry : angle 0.61931 (23436) *********************** 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 176 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 120 time to evaluate : 4.670 Fit side-chains REVERT: A 63 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8579 (m-40) REVERT: C 94 ILE cc_start: 0.5864 (mm) cc_final: 0.5611 (mt) REVERT: D 63 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8581 (m-40) REVERT: F 94 ILE cc_start: 0.5875 (mm) cc_final: 0.5622 (mt) REVERT: G 63 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8578 (m-40) REVERT: I 94 ILE cc_start: 0.5851 (mm) cc_final: 0.5601 (mt) REVERT: L 94 ILE cc_start: 0.5854 (mm) cc_final: 0.5606 (mt) outliers start: 56 outliers final: 28 residues processed: 164 average time/residue: 3.1912 time to fit residues: 594.7934 Evaluate side-chains 148 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 63 ASN 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 63 ASN Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 63 ASN 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 63 ASN Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 63 ASN 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 63 ASN 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 63 ASN 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 183 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.191703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139435 restraints weight = 40383.496| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.31 r_work: 0.3450 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1916 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= 0.146 Angle : 0.547 4.040 23508 Z= 0.292 Chirality : 0.041 0.141 2628 Planarity : 0.005 0.043 2760 Dihedral : 7.357 34.772 3012 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.78 % Allowed : 12.61 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.63 (0.19), residues: 1944 helix: 3.54 (0.13), residues: 1368 sheet: 2.97 (0.48), residues: 120 loop : -1.73 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP K 79 HIS 0.002 0.001 HIS C 274 PHE 0.010 0.001 PHE G 53 TYR 0.014 0.002 TYR E 243 ARG 0.002 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.07520 ( 1164) hydrogen bonds : angle 3.06403 ( 3456) SS BOND : bond 0.00469 ( 36) SS BOND : angle 1.22154 ( 72) covalent geometry : bond 0.00317 (17460) covalent geometry : angle 0.54378 (23436) *********************** 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 181 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 2.718 Fit side-chains REVERT: A 63 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8542 (m-40) REVERT: A 94 ILE cc_start: 0.5686 (mm) cc_final: 0.5455 (mt) REVERT: C 94 ILE cc_start: 0.5776 (mm) cc_final: 0.5534 (mt) REVERT: D 63 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8546 (m-40) REVERT: D 94 ILE cc_start: 0.5646 (mm) cc_final: 0.5417 (mt) REVERT: F 94 ILE cc_start: 0.5789 (mm) cc_final: 0.5546 (mt) REVERT: G 63 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8550 (m-40) REVERT: G 94 ILE cc_start: 0.5658 (mm) cc_final: 0.5428 (mt) REVERT: I 94 ILE cc_start: 0.5762 (mm) cc_final: 0.5521 (mt) REVERT: J 94 ILE cc_start: 0.5642 (mm) cc_final: 0.5414 (mt) REVERT: L 94 ILE cc_start: 0.5773 (mm) cc_final: 0.5533 (mt) outliers start: 50 outliers final: 32 residues processed: 170 average time/residue: 2.3675 time to fit residues: 458.5854 Evaluate side-chains 160 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 202 GLN 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 63 ASN Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 63 ASN Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 202 GLN Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 202 GLN 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 275 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 34 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 128 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 189 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.195120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144319 restraints weight = 40225.146| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.28 r_work: 0.3515 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 : 0.002 0.022 17496 Z= 0.111 Angle : 0.470 3.923 23508 Z= 0.253 Chirality : 0.039 0.123 2628 Planarity : 0.004 0.034 2760 Dihedral : 5.590 26.486 3012 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.33 % Allowed : 13.33 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.90 (0.19), residues: 1944 helix: 3.79 (0.13), residues: 1368 sheet: 2.86 (0.45), residues: 120 loop : -1.72 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 79 HIS 0.005 0.001 HIS A 274 PHE 0.005 0.001 PHE C 71 TYR 0.011 0.001 TYR K 243 ARG 0.001 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.05906 ( 1164) hydrogen bonds : angle 2.93616 ( 3456) SS BOND : bond 0.00234 ( 36) SS BOND : angle 0.81187 ( 72) covalent geometry : bond 0.00222 (17460) covalent geometry : angle 0.46894 (23436) *********************** 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 164 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 2.879 Fit side-chains REVERT: A 63 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8497 (m-40) REVERT: C 94 ILE cc_start: 0.5610 (mm) cc_final: 0.5390 (mt) REVERT: D 63 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8492 (m-40) REVERT: F 94 ILE cc_start: 0.5622 (mm) cc_final: 0.5402 (mt) REVERT: G 63 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8498 (m-40) REVERT: I 94 ILE cc_start: 0.5598 (mm) cc_final: 0.5380 (mt) REVERT: L 94 ILE cc_start: 0.5603 (mm) cc_final: 0.5386 (mt) outliers start: 42 outliers final: 22 residues processed: 155 average time/residue: 2.0554 time to fit residues: 369.3423 Evaluate side-chains 136 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 63 ASN 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 275 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain J residue 41 VAL 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 275 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.194005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142504 restraints weight = 40188.540| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.28 r_work: 0.3485 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17496 Z= 0.129 Angle : 0.510 3.940 23508 Z= 0.271 Chirality : 0.040 0.140 2628 Planarity : 0.004 0.038 2760 Dihedral : 6.052 26.725 3012 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.67 % Allowed : 14.22 % 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 (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: 3.82 (0.19), residues: 1944 helix: 3.73 (0.13), residues: 1368 sheet: 2.90 (0.47), residues: 120 loop : -1.79 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.003 0.001 HIS J 274 PHE 0.007 0.001 PHE G 53 TYR 0.012 0.002 TYR J 243 ARG 0.001 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.06435 ( 1164) hydrogen bonds : angle 2.90773 ( 3456) SS BOND : bond 0.00380 ( 36) SS BOND : angle 1.07278 ( 72) covalent geometry : bond 0.00290 (17460) covalent geometry : angle 0.50742 (23436) *********************** 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 151 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 2.725 Fit side-chains REVERT: A 63 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8528 (m-40) REVERT: C 94 ILE cc_start: 0.5635 (mm) cc_final: 0.5413 (mt) REVERT: D 63 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8529 (m-40) REVERT: F 94 ILE cc_start: 0.5641 (mm) cc_final: 0.5420 (mt) REVERT: G 63 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8526 (m-40) REVERT: I 94 ILE cc_start: 0.5628 (mm) cc_final: 0.5408 (mt) REVERT: L 94 ILE cc_start: 0.5631 (mm) cc_final: 0.5413 (mt) outliers start: 30 outliers final: 19 residues processed: 142 average time/residue: 2.3247 time to fit residues: 378.3685 Evaluate side-chains 139 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 232 ASN Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 232 ASN Chi-restraints excluded: chain L residue 41 VAL 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 71 optimal weight: 0.5980 chunk 112 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN D 232 ASN G 232 ASN H 232 ASN J 232 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.193981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142437 restraints weight = 40121.512| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.29 r_work: 0.3483 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 17496 Z= 0.200 Angle : 0.976 59.193 23508 Z= 0.597 Chirality : 0.043 0.442 2628 Planarity : 0.004 0.045 2760 Dihedral : 6.063 26.775 3012 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.56 % Allowed : 14.17 % Favored : 84.28 % Cbeta Deviations : 0.16 % 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: 3.83 (0.19), residues: 1944 helix: 3.73 (0.13), residues: 1368 sheet: 3.06 (0.47), residues: 120 loop : -1.80 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 79 HIS 0.003 0.001 HIS D 274 PHE 0.007 0.001 PHE G 53 TYR 0.013 0.002 TYR J 243 ARG 0.001 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.06552 ( 1164) hydrogen bonds : angle 2.90323 ( 3456) SS BOND : bond 0.00453 ( 36) SS BOND : angle 1.13013 ( 72) covalent geometry : bond 0.00427 (17460) covalent geometry : angle 0.97533 (23436) ********************** 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 145 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 2.569 Fit side-chains REVERT: A 63 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8533 (m-40) REVERT: C 94 ILE cc_start: 0.5722 (mm) cc_final: 0.5496 (mt) REVERT: D 63 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8533 (m-40) REVERT: F 94 ILE cc_start: 0.5730 (mm) cc_final: 0.5503 (mt) REVERT: G 63 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8534 (m-40) REVERT: I 94 ILE cc_start: 0.5716 (mm) cc_final: 0.5492 (mt) REVERT: L 94 ILE cc_start: 0.5719 (mm) cc_final: 0.5496 (mt) outliers start: 28 outliers final: 16 residues processed: 137 average time/residue: 2.3894 time to fit residues: 374.5205 Evaluate side-chains 136 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain L residue 41 VAL 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 184 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN D 232 ASN G 232 ASN H 232 ASN J 232 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.193947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142404 restraints weight = 40222.732| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.29 r_work: 0.3483 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 17496 Z= 0.200 Angle : 0.976 59.200 23508 Z= 0.597 Chirality : 0.043 0.442 2628 Planarity : 0.004 0.045 2760 Dihedral : 6.063 26.775 3012 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.33 % Allowed : 14.17 % Favored : 84.50 % Cbeta Deviations : 0.16 % 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: 3.83 (0.19), residues: 1944 helix: 3.73 (0.13), residues: 1368 sheet: 3.06 (0.47), residues: 120 loop : -1.80 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 79 HIS 0.003 0.001 HIS D 274 PHE 0.007 0.001 PHE G 53 TYR 0.013 0.002 TYR J 243 ARG 0.001 0.000 ARG C 69 Details of bonding type rmsd hydrogen bonds : bond 0.06552 ( 1164) hydrogen bonds : angle 2.90323 ( 3456) SS BOND : bond 0.00453 ( 36) SS BOND : angle 1.13014 ( 72) covalent geometry : bond 0.00427 (17460) covalent geometry : angle 0.97535 (23436) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19620.47 seconds wall clock time: 336 minutes 49.84 seconds (20209.84 seconds total)