Starting phenix.real_space_refine on Mon Nov 18 19:07:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxc_35076/11_2024/8hxc_35076.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxc_35076/11_2024/8hxc_35076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxc_35076/11_2024/8hxc_35076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxc_35076/11_2024/8hxc_35076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxc_35076/11_2024/8hxc_35076.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxc_35076/11_2024/8hxc_35076.cif" } resolution = 3.12 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= 0.001 sd= 0.037 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: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 10941 2.51 5 N 2933 2.21 5 O 3360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17374 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Restraints were copied for chains: H, K, J, M, L, N, C, B, E, D, G, F Time building chain proxies: 5.93, per 1000 atoms: 0.34 Number of scatterers: 17374 At special positions: 0 Unit cell: (185.25, 183.35, 67.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3360 8.00 N 2933 7.00 C 10941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 205 " distance=2.02 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: 4.09 Conformation dependent library (CDL) restraints added in 2.2 seconds 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4102 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 28 sheets defined 4.9% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.649A pdb=" N MET A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.648A pdb=" N MET B 190 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.649A pdb=" N MET C 190 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.649A pdb=" N MET D 190 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 3.649A pdb=" N MET E 190 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.647A pdb=" N MET F 190 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 191 removed outlier: 3.648A pdb=" N MET G 190 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU H 52 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU H 53 " --> pdb=" O LEU H 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 49 through 53' Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'I' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU I 52 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU I 53 " --> pdb=" O LEU I 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 49 through 53' Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 49 through 53 removed outlier: 3.711A pdb=" N GLU J 52 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 53 " --> pdb=" O LEU J 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 49 through 53' Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU K 52 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU K 53 " --> pdb=" O LEU K 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 49 through 53' Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU L 52 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU L 53 " --> pdb=" O LEU L 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 49 through 53' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU M 52 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU M 53 " --> pdb=" O LEU M 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 49 through 53' Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU N 52 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU N 53 " --> pdb=" O LEU N 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 49 through 53' Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 184 removed outlier: 5.531A pdb=" N PHE A 36 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR A 108 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 38 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS A 101 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 96 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER A 103 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU A 94 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 105 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA A 92 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE A 107 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 165 removed outlier: 9.443A pdb=" N SER A 193 " --> pdb=" O HIS H 124 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N HIS H 124 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY A 195 " --> pdb=" O ARG H 122 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE H 112 " --> pdb=" O ILE H 123 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN H 125 " --> pdb=" O CYS H 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS H 110 " --> pdb=" O GLN H 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN H 127 " --> pdb=" O TYR H 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR H 108 " --> pdb=" O ASN H 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL H 55 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU H 67 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP H 57 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 181 through 184 removed outlier: 5.530A pdb=" N PHE B 36 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR B 108 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 38 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 101 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL B 96 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER B 103 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU B 94 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 105 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 92 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE B 107 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 62 Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 165 removed outlier: 9.397A pdb=" N SER B 193 " --> pdb=" O HIS I 124 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS I 124 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLY B 195 " --> pdb=" O ARG I 122 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE I 112 " --> pdb=" O ILE I 123 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN I 125 " --> pdb=" O CYS I 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS I 110 " --> pdb=" O GLN I 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN I 127 " --> pdb=" O TYR I 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR I 108 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL I 55 " --> pdb=" O GLU I 67 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU I 67 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP I 57 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 181 through 184 removed outlier: 5.530A pdb=" N PHE C 36 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR C 108 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 38 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS C 101 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL C 96 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER C 103 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU C 94 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 105 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA C 92 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE C 107 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 57 through 62 Processing sheet with id=AA9, first strand: chain 'C' and resid 160 through 165 removed outlier: 9.444A pdb=" N SER C 193 " --> pdb=" O HIS J 124 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N HIS J 124 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLY C 195 " --> pdb=" O ARG J 122 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE J 112 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN J 125 " --> pdb=" O CYS J 110 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS J 110 " --> pdb=" O GLN J 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN J 127 " --> pdb=" O TYR J 108 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR J 108 " --> pdb=" O ASN J 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL J 55 " --> pdb=" O GLU J 67 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU J 67 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP J 57 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 181 through 184 removed outlier: 5.530A pdb=" N PHE D 36 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR D 108 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 38 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS D 101 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL D 96 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER D 103 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU D 94 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU D 105 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA D 92 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE D 107 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 57 through 62 Processing sheet with id=AB3, first strand: chain 'D' and resid 160 through 165 removed outlier: 9.240A pdb=" N SER D 193 " --> pdb=" O HIS K 124 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N HIS K 124 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLY D 195 " --> pdb=" O ARG K 122 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE K 112 " --> pdb=" O ILE K 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN K 125 " --> pdb=" O CYS K 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS K 110 " --> pdb=" O GLN K 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN K 127 " --> pdb=" O TYR K 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR K 108 " --> pdb=" O ASN K 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL K 55 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU K 67 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP K 57 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 181 through 184 removed outlier: 5.531A pdb=" N PHE E 36 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR E 108 " --> pdb=" O PHE E 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA E 38 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS E 101 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL E 96 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER E 103 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU E 94 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU E 105 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA E 92 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE E 107 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 57 through 62 Processing sheet with id=AB6, first strand: chain 'E' and resid 160 through 165 removed outlier: 9.501A pdb=" N SER E 193 " --> pdb=" O HIS L 124 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N HIS L 124 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY E 195 " --> pdb=" O ARG L 122 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE L 112 " --> pdb=" O ILE L 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN L 125 " --> pdb=" O CYS L 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS L 110 " --> pdb=" O GLN L 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN L 127 " --> pdb=" O TYR L 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR L 108 " --> pdb=" O ASN L 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL L 55 " --> pdb=" O GLU L 67 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU L 67 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP L 57 " --> pdb=" O LEU L 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 181 through 184 removed outlier: 5.531A pdb=" N PHE F 36 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR F 108 " --> pdb=" O PHE F 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA F 38 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS F 101 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL F 96 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER F 103 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU F 94 " --> pdb=" O SER F 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU F 105 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA F 92 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE F 107 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 57 through 62 Processing sheet with id=AB9, first strand: chain 'F' and resid 160 through 165 removed outlier: 9.487A pdb=" N SER F 193 " --> pdb=" O HIS M 124 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N HIS M 124 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLY F 195 " --> pdb=" O ARG M 122 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE M 112 " --> pdb=" O ILE M 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN M 125 " --> pdb=" O CYS M 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS M 110 " --> pdb=" O GLN M 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN M 127 " --> pdb=" O TYR M 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR M 108 " --> pdb=" O ASN M 127 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL M 55 " --> pdb=" O GLU M 67 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU M 67 " --> pdb=" O VAL M 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP M 57 " --> pdb=" O LEU M 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 181 through 184 removed outlier: 5.531A pdb=" N PHE G 36 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR G 108 " --> pdb=" O PHE G 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA G 38 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS G 101 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL G 96 " --> pdb=" O LYS G 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER G 103 " --> pdb=" O GLU G 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU G 94 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU G 105 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA G 92 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE G 107 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 57 through 62 Processing sheet with id=AC3, first strand: chain 'G' and resid 160 through 165 removed outlier: 9.503A pdb=" N SER G 193 " --> pdb=" O HIS N 124 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N HIS N 124 " --> pdb=" O SER G 193 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY G 195 " --> pdb=" O ARG N 122 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE N 112 " --> pdb=" O ILE N 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN N 125 " --> pdb=" O CYS N 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS N 110 " --> pdb=" O GLN N 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN N 127 " --> pdb=" O TYR N 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR N 108 " --> pdb=" O ASN N 127 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL N 55 " --> pdb=" O GLU N 67 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU N 67 " --> pdb=" O VAL N 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP N 57 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 35 through 39 Processing sheet with id=AC5, first strand: chain 'I' and resid 35 through 39 Processing sheet with id=AC6, first strand: chain 'J' and resid 35 through 39 Processing sheet with id=AC7, first strand: chain 'K' and resid 35 through 39 Processing sheet with id=AC8, first strand: chain 'L' and resid 35 through 39 Processing sheet with id=AC9, first strand: chain 'M' and resid 35 through 39 Processing sheet with id=AD1, first strand: chain 'N' and resid 35 through 39 504 hydrogen bonds defined for protein. 1260 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: 5.37 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5545 1.34 - 1.46: 4049 1.46 - 1.58: 7934 1.58 - 1.70: 7 1.70 - 1.83: 203 Bond restraints: 17738 Sorted by residual: bond pdb=" CA GLU L 52 " pdb=" CB GLU L 52 " ideal model delta sigma weight residual 1.527 1.630 -0.103 2.48e-02 1.63e+03 1.73e+01 bond pdb=" CA GLU M 52 " pdb=" CB GLU M 52 " ideal model delta sigma weight residual 1.527 1.630 -0.103 2.48e-02 1.63e+03 1.72e+01 bond pdb=" CA GLU J 52 " pdb=" CB GLU J 52 " ideal model delta sigma weight residual 1.527 1.630 -0.103 2.48e-02 1.63e+03 1.72e+01 bond pdb=" CA GLU H 52 " pdb=" CB GLU H 52 " ideal model delta sigma weight residual 1.527 1.630 -0.103 2.48e-02 1.63e+03 1.71e+01 bond pdb=" CA GLU N 52 " pdb=" CB GLU N 52 " ideal model delta sigma weight residual 1.527 1.630 -0.102 2.48e-02 1.63e+03 1.70e+01 ... (remaining 17733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 23417 3.08 - 6.17: 453 6.17 - 9.25: 91 9.25 - 12.34: 30 12.34 - 15.42: 19 Bond angle restraints: 24010 Sorted by residual: angle pdb=" C ASN F 203 " pdb=" N GLN F 204 " pdb=" CA GLN F 204 " ideal model delta sigma weight residual 124.31 134.19 -9.88 1.67e+00 3.59e-01 3.50e+01 angle pdb=" C ASN E 203 " pdb=" N GLN E 204 " pdb=" CA GLN E 204 " ideal model delta sigma weight residual 124.31 134.18 -9.87 1.67e+00 3.59e-01 3.49e+01 angle pdb=" C ASN A 203 " pdb=" N GLN A 204 " pdb=" CA GLN A 204 " ideal model delta sigma weight residual 124.31 134.16 -9.85 1.67e+00 3.59e-01 3.48e+01 angle pdb=" C ASN C 203 " pdb=" N GLN C 204 " pdb=" CA GLN C 204 " ideal model delta sigma weight residual 124.31 134.16 -9.85 1.67e+00 3.59e-01 3.48e+01 angle pdb=" CA GLU I 52 " pdb=" CB GLU I 52 " pdb=" CG GLU I 52 " ideal model delta sigma weight residual 114.10 125.85 -11.75 2.00e+00 2.50e-01 3.45e+01 ... (remaining 24005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 8898 15.67 - 31.34: 1313 31.34 - 47.00: 324 47.00 - 62.67: 106 62.67 - 78.34: 15 Dihedral angle restraints: 10656 sinusoidal: 4286 harmonic: 6370 Sorted by residual: dihedral pdb=" CB CYS A 160 " pdb=" SG CYS A 160 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual 93.00 165.15 -72.15 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CA PRO C 140 " pdb=" C PRO C 140 " pdb=" N GLU C 141 " pdb=" CA GLU C 141 " ideal model delta harmonic sigma weight residual 180.00 157.82 22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PRO G 140 " pdb=" C PRO G 140 " pdb=" N GLU G 141 " pdb=" CA GLU G 141 " ideal model delta harmonic sigma weight residual 180.00 157.83 22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 10653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1747 0.058 - 0.116: 714 0.116 - 0.175: 150 0.175 - 0.233: 35 0.233 - 0.291: 21 Chirality restraints: 2667 Sorted by residual: chirality pdb=" CG LEU L 63 " pdb=" CB LEU L 63 " pdb=" CD1 LEU L 63 " pdb=" CD2 LEU L 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU N 63 " pdb=" CB LEU N 63 " pdb=" CD1 LEU N 63 " pdb=" CD2 LEU N 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CG LEU M 63 " pdb=" CB LEU M 63 " pdb=" CD1 LEU M 63 " pdb=" CD2 LEU M 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 2664 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS M 124 " 0.015 2.00e-02 2.50e+03 2.11e-02 6.71e+00 pdb=" CG HIS M 124 " -0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS M 124 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS M 124 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS M 124 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS M 124 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 124 " 0.015 2.00e-02 2.50e+03 2.11e-02 6.67e+00 pdb=" CG HIS K 124 " -0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS K 124 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS K 124 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS K 124 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS K 124 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS L 124 " 0.015 2.00e-02 2.50e+03 2.10e-02 6.63e+00 pdb=" CG HIS L 124 " -0.044 2.00e-02 2.50e+03 pdb=" ND1 HIS L 124 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS L 124 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS L 124 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS L 124 " 0.000 2.00e-02 2.50e+03 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 173 2.57 - 3.15: 12552 3.15 - 3.73: 25821 3.73 - 4.32: 36661 4.32 - 4.90: 63296 Nonbonded interactions: 138503 Sorted by model distance: nonbonded pdb=" SG CYS B 25 " pdb=" SG CYS C 130 " model vdw 1.987 3.760 nonbonded pdb=" SG CYS E 25 " pdb=" SG CYS F 130 " model vdw 2.012 3.760 nonbonded pdb=" SG CYS F 25 " pdb=" SG CYS G 130 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS D 160 " pdb=" SG CYS D 205 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS B 160 " pdb=" SG CYS B 205 " model vdw 2.024 3.760 ... (remaining 138498 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: 0.00 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' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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=0.00 max=1.00 mean=0.93 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: 2.020 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 33.750 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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 0.103 17738 Z= 0.457 Angle : 1.204 15.424 24010 Z= 0.608 Chirality : 0.068 0.291 2667 Planarity : 0.006 0.039 3066 Dihedral : 16.375 78.339 6545 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.05 % Allowed : 27.02 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.17), residues: 2121 helix: None (None), residues: 0 sheet: -0.35 (0.16), residues: 903 loop : -1.48 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.005 TRP D 34 HIS 0.027 0.003 HIS M 124 PHE 0.030 0.003 PHE N 56 TYR 0.025 0.003 TYR G 74 ARG 0.008 0.001 ARG N 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 392 time to evaluate : 2.089 Fit side-chains REVERT: B 83 MET cc_start: 0.8012 (mmt) cc_final: 0.7597 (mpp) REVERT: B 88 ARG cc_start: 0.8734 (ptp-170) cc_final: 0.8494 (ptp90) REVERT: B 173 HIS cc_start: 0.8316 (m-70) cc_final: 0.7925 (m90) REVERT: D 83 MET cc_start: 0.8013 (mmt) cc_final: 0.7559 (mpp) REVERT: E 83 MET cc_start: 0.7906 (mmt) cc_final: 0.7433 (mpp) REVERT: F 83 MET cc_start: 0.7980 (mmt) cc_final: 0.7531 (mpp) REVERT: F 126 MET cc_start: 0.8532 (mmp) cc_final: 0.8316 (mmm) REVERT: F 213 SER cc_start: 0.8648 (p) cc_final: 0.8434 (m) REVERT: G 83 MET cc_start: 0.7999 (mmt) cc_final: 0.7611 (mpp) REVERT: H 50 LEU cc_start: 0.7873 (tt) cc_final: 0.7496 (tt) REVERT: H 74 LYS cc_start: 0.6836 (mtpp) cc_final: 0.6322 (mmtp) REVERT: I 50 LEU cc_start: 0.8022 (tt) cc_final: 0.7815 (tt) REVERT: L 50 LEU cc_start: 0.7414 (tt) cc_final: 0.7139 (tt) REVERT: L 63 LEU cc_start: 0.8093 (mm) cc_final: 0.7593 (mp) REVERT: N 50 LEU cc_start: 0.7929 (tt) cc_final: 0.7637 (tt) REVERT: N 63 LEU cc_start: 0.8531 (mm) cc_final: 0.8030 (mp) outliers start: 21 outliers final: 7 residues processed: 406 average time/residue: 0.3380 time to fit residues: 198.7022 Evaluate side-chains 273 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 266 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain G residue 143 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 63 optimal weight: 0.0170 chunk 100 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 190 optimal weight: 20.0000 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 162 ASN A 173 HIS B 79 ASN B 162 ASN B 179 ASN B 204 GLN C 79 ASN C 162 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN D 79 ASN D 162 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN E 162 ASN E 204 GLN F 79 ASN F 162 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN G 79 ASN G 162 ASN ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 ASN G 204 GLN H 124 HIS I 124 HIS J 124 HIS K 41 GLN K 124 HIS ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 HIS M 124 HIS ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17738 Z= 0.215 Angle : 0.650 8.396 24010 Z= 0.336 Chirality : 0.047 0.165 2667 Planarity : 0.004 0.027 3066 Dihedral : 5.040 24.306 2352 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.56 % Allowed : 22.31 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.17), residues: 2121 helix: None (None), residues: 0 sheet: -0.57 (0.16), residues: 973 loop : -1.34 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 34 HIS 0.010 0.001 HIS L 124 PHE 0.016 0.001 PHE H 56 TYR 0.012 0.001 TYR D 46 ARG 0.008 0.001 ARG N 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 275 time to evaluate : 2.183 Fit side-chains REVERT: A 28 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7538 (ptm160) REVERT: A 41 THR cc_start: 0.8507 (p) cc_final: 0.8296 (m) REVERT: A 113 ASP cc_start: 0.8372 (p0) cc_final: 0.7922 (p0) REVERT: B 83 MET cc_start: 0.8107 (mmt) cc_final: 0.7589 (mpp) REVERT: B 113 ASP cc_start: 0.8237 (p0) cc_final: 0.7796 (p0) REVERT: C 64 ASP cc_start: 0.8034 (t0) cc_final: 0.7783 (t0) REVERT: C 113 ASP cc_start: 0.8245 (p0) cc_final: 0.7891 (p0) REVERT: E 83 MET cc_start: 0.8101 (mmt) cc_final: 0.7536 (mpp) REVERT: E 113 ASP cc_start: 0.8258 (p0) cc_final: 0.7867 (p0) REVERT: E 185 ASN cc_start: 0.8607 (t0) cc_final: 0.8132 (t0) REVERT: F 28 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7038 (ptm160) REVERT: F 64 ASP cc_start: 0.7715 (t0) cc_final: 0.7446 (t0) REVERT: F 113 ASP cc_start: 0.8302 (p0) cc_final: 0.7916 (p0) REVERT: F 213 SER cc_start: 0.8680 (p) cc_final: 0.8471 (m) REVERT: G 83 MET cc_start: 0.8148 (mmt) cc_final: 0.7667 (mpp) REVERT: I 50 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7918 (tt) REVERT: J 65 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7900 (mp) REVERT: K 126 MET cc_start: 0.6912 (ptm) cc_final: 0.6706 (ptm) REVERT: L 50 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6886 (tt) REVERT: N 50 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7306 (tt) outliers start: 111 outliers final: 51 residues processed: 352 average time/residue: 0.3264 time to fit residues: 171.4186 Evaluate side-chains 307 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 250 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 191 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 170 optimal weight: 0.0030 chunk 189 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 HIS ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17738 Z= 0.283 Angle : 0.652 7.846 24010 Z= 0.335 Chirality : 0.048 0.187 2667 Planarity : 0.003 0.026 3066 Dihedral : 4.870 27.208 2352 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.06 % Allowed : 21.95 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.44 (0.17), residues: 2121 helix: None (None), residues: 0 sheet: -0.68 (0.16), residues: 980 loop : -1.15 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 93 HIS 0.003 0.001 HIS E 184 PHE 0.013 0.001 PHE K 56 TYR 0.015 0.001 TYR D 46 ARG 0.009 0.001 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 303 time to evaluate : 2.049 Fit side-chains REVERT: A 28 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7946 (ptm160) REVERT: A 113 ASP cc_start: 0.8286 (p0) cc_final: 0.7819 (p0) REVERT: B 113 ASP cc_start: 0.8288 (p0) cc_final: 0.7804 (p0) REVERT: B 157 CYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8556 (p) REVERT: B 219 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6894 (mtp180) REVERT: C 64 ASP cc_start: 0.8053 (t0) cc_final: 0.7747 (t0) REVERT: C 113 ASP cc_start: 0.8187 (p0) cc_final: 0.7785 (p0) REVERT: C 157 CYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8586 (p) REVERT: D 64 ASP cc_start: 0.8138 (t0) cc_final: 0.7800 (t0) REVERT: D 134 LYS cc_start: 0.8325 (tttt) cc_final: 0.8032 (ttpt) REVERT: D 157 CYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8504 (p) REVERT: E 113 ASP cc_start: 0.8260 (p0) cc_final: 0.7833 (p0) REVERT: E 134 LYS cc_start: 0.8190 (tttt) cc_final: 0.7813 (ttpt) REVERT: E 190 MET cc_start: 0.8409 (tpp) cc_final: 0.8041 (ttm) REVERT: F 28 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.6846 (ptm160) REVERT: F 30 ASP cc_start: 0.7180 (p0) cc_final: 0.6431 (p0) REVERT: F 64 ASP cc_start: 0.7872 (t0) cc_final: 0.7621 (t0) REVERT: F 85 THR cc_start: 0.9374 (p) cc_final: 0.9142 (p) REVERT: F 113 ASP cc_start: 0.8321 (p0) cc_final: 0.7901 (p0) REVERT: F 157 CYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8598 (p) REVERT: F 190 MET cc_start: 0.8389 (tpp) cc_final: 0.8057 (ttm) REVERT: G 64 ASP cc_start: 0.7855 (t0) cc_final: 0.7539 (t0) REVERT: I 50 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8070 (tt) REVERT: J 126 MET cc_start: 0.7587 (ptm) cc_final: 0.7291 (ptm) REVERT: K 124 HIS cc_start: 0.9084 (t70) cc_final: 0.8783 (t-90) REVERT: K 126 MET cc_start: 0.7008 (ptm) cc_final: 0.6739 (ptm) REVERT: L 50 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7175 (tt) REVERT: M 50 LEU cc_start: 0.7805 (tt) cc_final: 0.7524 (tt) REVERT: N 50 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7534 (tt) outliers start: 101 outliers final: 69 residues processed: 369 average time/residue: 0.2980 time to fit residues: 165.1436 Evaluate side-chains 354 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 276 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.1980 chunk 143 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 202 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 54 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN C 185 ASN F 79 ASN G 173 HIS ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17738 Z= 0.178 Angle : 0.599 7.363 24010 Z= 0.301 Chirality : 0.046 0.184 2667 Planarity : 0.003 0.027 3066 Dihedral : 4.617 24.524 2352 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.31 % Allowed : 23.71 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.17), residues: 2121 helix: None (None), residues: 0 sheet: -0.73 (0.16), residues: 980 loop : -1.13 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 57 HIS 0.004 0.000 HIS K 124 PHE 0.011 0.001 PHE H 56 TYR 0.012 0.001 TYR D 46 ARG 0.005 0.001 ARG M 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 270 time to evaluate : 2.017 Fit side-chains REVERT: A 113 ASP cc_start: 0.8285 (p0) cc_final: 0.7808 (p0) REVERT: A 190 MET cc_start: 0.8345 (tpp) cc_final: 0.7961 (ttm) REVERT: B 113 ASP cc_start: 0.8344 (p0) cc_final: 0.7801 (p0) REVERT: B 157 CYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8490 (p) REVERT: C 28 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7476 (ptm160) REVERT: C 64 ASP cc_start: 0.8049 (t0) cc_final: 0.7711 (t0) REVERT: C 113 ASP cc_start: 0.8204 (p0) cc_final: 0.7792 (p0) REVERT: C 157 CYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8391 (p) REVERT: C 190 MET cc_start: 0.8175 (tpp) cc_final: 0.7754 (ttm) REVERT: D 134 LYS cc_start: 0.8206 (tttt) cc_final: 0.7906 (ttpt) REVERT: D 157 CYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8453 (p) REVERT: E 113 ASP cc_start: 0.8341 (p0) cc_final: 0.7890 (p0) REVERT: E 190 MET cc_start: 0.8396 (tpp) cc_final: 0.8050 (ttm) REVERT: F 64 ASP cc_start: 0.7838 (t0) cc_final: 0.7585 (t0) REVERT: F 85 THR cc_start: 0.9331 (p) cc_final: 0.9128 (p) REVERT: F 113 ASP cc_start: 0.8296 (p0) cc_final: 0.7853 (p0) REVERT: F 157 CYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8581 (p) REVERT: F 190 MET cc_start: 0.8289 (tpp) cc_final: 0.8045 (ttm) REVERT: G 64 ASP cc_start: 0.7826 (t0) cc_final: 0.7499 (t0) REVERT: G 126 MET cc_start: 0.8952 (mmp) cc_final: 0.8658 (mmm) REVERT: I 50 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7642 (tt) REVERT: J 126 MET cc_start: 0.7491 (ptm) cc_final: 0.7169 (ptm) REVERT: K 126 MET cc_start: 0.7102 (ptm) cc_final: 0.6885 (ptm) REVERT: L 50 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7193 (tt) REVERT: L 83 MET cc_start: 0.7150 (mmt) cc_final: 0.6861 (mmm) REVERT: M 50 LEU cc_start: 0.7541 (tt) cc_final: 0.7268 (tt) REVERT: N 50 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7432 (tt) outliers start: 66 outliers final: 46 residues processed: 314 average time/residue: 0.3063 time to fit residues: 144.3036 Evaluate side-chains 304 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 250 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 157 CYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 107 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 6.9990 chunk 115 optimal weight: 0.0770 chunk 2 optimal weight: 0.5980 chunk 151 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 173 optimal weight: 0.2980 chunk 140 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS B 79 ASN B 116 HIS ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 HIS G 173 HIS ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN I 41 GLN ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN L 41 GLN L 101 GLN ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17738 Z= 0.382 Angle : 0.665 7.764 24010 Z= 0.340 Chirality : 0.049 0.167 2667 Planarity : 0.003 0.027 3066 Dihedral : 4.968 32.296 2352 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.31 % Allowed : 22.31 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.56 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.85 (0.16), residues: 994 loop : -1.14 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 93 HIS 0.004 0.001 HIS D 117 PHE 0.012 0.001 PHE K 56 TYR 0.019 0.002 TYR D 46 ARG 0.010 0.001 ARG L 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 279 time to evaluate : 2.101 Fit side-chains REVERT: A 64 ASP cc_start: 0.7956 (t0) cc_final: 0.7679 (t0) REVERT: A 83 MET cc_start: 0.8455 (mmm) cc_final: 0.8058 (mmm) REVERT: A 134 LYS cc_start: 0.8325 (tttt) cc_final: 0.7949 (ttpt) REVERT: B 64 ASP cc_start: 0.8029 (t0) cc_final: 0.7723 (t0) REVERT: C 64 ASP cc_start: 0.8200 (t0) cc_final: 0.7837 (t0) REVERT: D 64 ASP cc_start: 0.8205 (t0) cc_final: 0.7784 (t0) REVERT: D 134 LYS cc_start: 0.8372 (tttt) cc_final: 0.8009 (ttpt) REVERT: E 64 ASP cc_start: 0.8032 (t0) cc_final: 0.7754 (t0) REVERT: E 134 LYS cc_start: 0.8429 (tttt) cc_final: 0.8038 (ttpt) REVERT: E 174 TYR cc_start: 0.8550 (t80) cc_final: 0.8226 (t80) REVERT: F 28 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7390 (ptm160) REVERT: F 30 ASP cc_start: 0.6938 (p0) cc_final: 0.6438 (p0) REVERT: F 64 ASP cc_start: 0.8005 (t0) cc_final: 0.7740 (t0) REVERT: F 113 ASP cc_start: 0.8314 (p0) cc_final: 0.7829 (p0) REVERT: F 134 LYS cc_start: 0.8320 (tttt) cc_final: 0.7905 (ttpt) REVERT: G 64 ASP cc_start: 0.8012 (t0) cc_final: 0.7743 (t0) REVERT: G 134 LYS cc_start: 0.8451 (tttt) cc_final: 0.8050 (ttpt) REVERT: I 126 MET cc_start: 0.7339 (ptm) cc_final: 0.7135 (ptm) REVERT: J 126 MET cc_start: 0.7572 (ptm) cc_final: 0.7182 (ptm) REVERT: K 65 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8159 (mp) REVERT: K 126 MET cc_start: 0.7058 (ptm) cc_final: 0.6801 (ptm) REVERT: L 83 MET cc_start: 0.7433 (mmt) cc_final: 0.7201 (mmm) outliers start: 106 outliers final: 83 residues processed: 355 average time/residue: 0.2912 time to fit residues: 156.6976 Evaluate side-chains 352 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 267 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.9980 chunk 182 optimal weight: 0.0570 chunk 40 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 HIS ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17738 Z= 0.266 Angle : 0.623 9.000 24010 Z= 0.314 Chirality : 0.047 0.154 2667 Planarity : 0.003 0.028 3066 Dihedral : 4.788 29.653 2352 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.71 % Allowed : 22.96 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.67 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.91 (0.16), residues: 952 loop : -1.22 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 57 HIS 0.004 0.001 HIS N 79 PHE 0.011 0.001 PHE K 56 TYR 0.016 0.001 TYR D 46 ARG 0.005 0.001 ARG L 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 285 time to evaluate : 1.925 Fit side-chains REVERT: A 64 ASP cc_start: 0.7940 (t0) cc_final: 0.7673 (t0) REVERT: A 83 MET cc_start: 0.8431 (mmm) cc_final: 0.8040 (mmm) REVERT: A 134 LYS cc_start: 0.8260 (tttt) cc_final: 0.8022 (ttpt) REVERT: B 64 ASP cc_start: 0.8029 (t0) cc_final: 0.7726 (t0) REVERT: C 64 ASP cc_start: 0.8177 (t0) cc_final: 0.7805 (t0) REVERT: D 64 ASP cc_start: 0.8194 (t0) cc_final: 0.7765 (t0) REVERT: D 134 LYS cc_start: 0.8219 (tttt) cc_final: 0.7942 (ttpt) REVERT: E 64 ASP cc_start: 0.7947 (t0) cc_final: 0.7692 (t0) REVERT: E 113 ASP cc_start: 0.8311 (p0) cc_final: 0.7826 (p0) REVERT: E 134 LYS cc_start: 0.8352 (tttt) cc_final: 0.7884 (ttpt) REVERT: E 190 MET cc_start: 0.8429 (tpp) cc_final: 0.8015 (ttm) REVERT: F 64 ASP cc_start: 0.7976 (t0) cc_final: 0.7700 (t0) REVERT: F 113 ASP cc_start: 0.8301 (p0) cc_final: 0.7808 (p0) REVERT: F 134 LYS cc_start: 0.8199 (tttt) cc_final: 0.7782 (ttpt) REVERT: F 190 MET cc_start: 0.8468 (tpp) cc_final: 0.8118 (ttm) REVERT: G 64 ASP cc_start: 0.8010 (t0) cc_final: 0.7733 (t0) REVERT: G 114 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8229 (tppt) REVERT: G 134 LYS cc_start: 0.8375 (tttt) cc_final: 0.8001 (ttpt) REVERT: I 126 MET cc_start: 0.7317 (ptm) cc_final: 0.7109 (ptm) REVERT: J 126 MET cc_start: 0.7581 (ptm) cc_final: 0.7166 (ptm) REVERT: K 65 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8121 (mp) REVERT: K 126 MET cc_start: 0.7116 (ptm) cc_final: 0.6875 (ptm) REVERT: N 130 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6735 (tt) outliers start: 94 outliers final: 72 residues processed: 353 average time/residue: 0.3030 time to fit residues: 161.2044 Evaluate side-chains 349 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 274 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 130 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 171 optimal weight: 0.0020 chunk 113 optimal weight: 0.9990 chunk 202 optimal weight: 0.2980 chunk 126 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17738 Z= 0.193 Angle : 0.599 9.685 24010 Z= 0.299 Chirality : 0.046 0.150 2667 Planarity : 0.003 0.028 3066 Dihedral : 4.551 27.322 2352 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.06 % Allowed : 23.66 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.61 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.85 (0.16), residues: 952 loop : -1.19 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 57 HIS 0.003 0.001 HIS N 79 PHE 0.010 0.001 PHE H 56 TYR 0.012 0.001 TYR D 46 ARG 0.003 0.001 ARG K 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 293 time to evaluate : 2.114 Fit side-chains REVERT: A 28 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7236 (ptm160) REVERT: A 30 ASP cc_start: 0.6760 (p0) cc_final: 0.6320 (p0) REVERT: A 64 ASP cc_start: 0.7881 (t0) cc_final: 0.7616 (t0) REVERT: A 134 LYS cc_start: 0.8086 (tttt) cc_final: 0.7877 (ttpt) REVERT: A 190 MET cc_start: 0.8382 (tpp) cc_final: 0.7989 (ttm) REVERT: B 64 ASP cc_start: 0.7988 (t0) cc_final: 0.7687 (t0) REVERT: B 126 MET cc_start: 0.8599 (mmm) cc_final: 0.8328 (mmm) REVERT: C 28 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7364 (ptm160) REVERT: C 30 ASP cc_start: 0.7072 (p0) cc_final: 0.6673 (p0) REVERT: C 64 ASP cc_start: 0.8164 (t0) cc_final: 0.7769 (t0) REVERT: D 64 ASP cc_start: 0.8208 (t0) cc_final: 0.7777 (t0) REVERT: D 134 LYS cc_start: 0.8199 (tttt) cc_final: 0.7929 (ttpt) REVERT: E 64 ASP cc_start: 0.7912 (t0) cc_final: 0.7656 (t0) REVERT: E 134 LYS cc_start: 0.8304 (tttt) cc_final: 0.7861 (ttpt) REVERT: E 190 MET cc_start: 0.8404 (tpp) cc_final: 0.7994 (ttm) REVERT: F 28 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7013 (ptm160) REVERT: F 64 ASP cc_start: 0.7896 (t0) cc_final: 0.7600 (t0) REVERT: F 113 ASP cc_start: 0.8279 (p0) cc_final: 0.7785 (p0) REVERT: F 134 LYS cc_start: 0.8147 (tttt) cc_final: 0.7834 (ttpt) REVERT: G 64 ASP cc_start: 0.7941 (t0) cc_final: 0.7662 (t0) REVERT: G 126 MET cc_start: 0.8950 (mmp) cc_final: 0.8633 (mmm) REVERT: G 134 LYS cc_start: 0.8345 (tttt) cc_final: 0.8021 (ttpt) REVERT: J 126 MET cc_start: 0.7563 (ptm) cc_final: 0.7189 (ptm) REVERT: K 65 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8096 (mp) REVERT: K 126 MET cc_start: 0.7155 (ptm) cc_final: 0.6939 (ptm) outliers start: 81 outliers final: 65 residues processed: 349 average time/residue: 0.3151 time to fit residues: 163.3155 Evaluate side-chains 346 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 277 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 107 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 0.0020 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17738 Z= 0.194 Angle : 0.604 10.237 24010 Z= 0.298 Chirality : 0.046 0.160 2667 Planarity : 0.003 0.028 3066 Dihedral : 4.435 26.498 2352 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.86 % Allowed : 24.31 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.53 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.71 (0.17), residues: 882 loop : -1.22 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 57 HIS 0.006 0.001 HIS I 79 PHE 0.009 0.001 PHE J 56 TYR 0.012 0.001 TYR D 46 ARG 0.006 0.001 ARG L 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 281 time to evaluate : 2.052 Fit side-chains REVERT: A 30 ASP cc_start: 0.6696 (p0) cc_final: 0.6484 (p0) REVERT: A 64 ASP cc_start: 0.7926 (t0) cc_final: 0.7656 (t0) REVERT: A 134 LYS cc_start: 0.8111 (tttt) cc_final: 0.7864 (ttpt) REVERT: B 64 ASP cc_start: 0.7973 (t0) cc_final: 0.7659 (t0) REVERT: B 126 MET cc_start: 0.8562 (mmm) cc_final: 0.8297 (mmm) REVERT: C 28 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7446 (ptm160) REVERT: C 30 ASP cc_start: 0.7062 (p0) cc_final: 0.6735 (p0) REVERT: C 64 ASP cc_start: 0.8174 (t0) cc_final: 0.7777 (t0) REVERT: C 185 ASN cc_start: 0.8774 (t0) cc_final: 0.8361 (t0) REVERT: D 64 ASP cc_start: 0.8194 (t0) cc_final: 0.7763 (t0) REVERT: D 134 LYS cc_start: 0.8246 (tttt) cc_final: 0.7937 (ttpt) REVERT: E 134 LYS cc_start: 0.8272 (tttt) cc_final: 0.7817 (ttpt) REVERT: F 28 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.6901 (ptm160) REVERT: F 64 ASP cc_start: 0.7911 (t0) cc_final: 0.7601 (t0) REVERT: F 113 ASP cc_start: 0.8299 (p0) cc_final: 0.7755 (p0) REVERT: F 134 LYS cc_start: 0.8154 (tttt) cc_final: 0.7840 (ttpt) REVERT: G 64 ASP cc_start: 0.7941 (t0) cc_final: 0.7659 (t0) REVERT: G 126 MET cc_start: 0.8942 (mmp) cc_final: 0.8640 (mmm) REVERT: G 134 LYS cc_start: 0.8361 (tttt) cc_final: 0.8022 (ttpt) REVERT: I 126 MET cc_start: 0.7269 (ptm) cc_final: 0.6995 (ptm) REVERT: J 126 MET cc_start: 0.7590 (ptm) cc_final: 0.7213 (ptm) REVERT: K 65 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8085 (mp) REVERT: K 126 MET cc_start: 0.7143 (ptm) cc_final: 0.6940 (ptm) outliers start: 77 outliers final: 61 residues processed: 334 average time/residue: 0.3094 time to fit residues: 154.0072 Evaluate side-chains 334 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 270 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 107 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 7.9990 chunk 176 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 113 optimal weight: 0.0980 chunk 82 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 187 optimal weight: 0.0870 chunk 123 optimal weight: 0.2980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 HIS ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17738 Z= 0.166 Angle : 0.603 11.193 24010 Z= 0.295 Chirality : 0.045 0.162 2667 Planarity : 0.003 0.028 3066 Dihedral : 4.307 24.311 2352 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.21 % Allowed : 24.91 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.45 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.68 (0.16), residues: 952 loop : -1.15 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 57 HIS 0.007 0.001 HIS I 79 PHE 0.009 0.001 PHE L 56 TYR 0.010 0.001 TYR D 46 ARG 0.004 0.000 ARG L 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 280 time to evaluate : 2.124 Fit side-chains REVERT: A 64 ASP cc_start: 0.7852 (t0) cc_final: 0.7592 (t0) REVERT: A 134 LYS cc_start: 0.8078 (tttt) cc_final: 0.7802 (ttpt) REVERT: B 126 MET cc_start: 0.8545 (mmm) cc_final: 0.8298 (mmm) REVERT: C 28 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7532 (ptm160) REVERT: C 30 ASP cc_start: 0.7049 (p0) cc_final: 0.6841 (p0) REVERT: C 64 ASP cc_start: 0.8143 (t0) cc_final: 0.7740 (t0) REVERT: C 185 ASN cc_start: 0.8762 (t0) cc_final: 0.8384 (t0) REVERT: D 64 ASP cc_start: 0.8166 (t0) cc_final: 0.7737 (t0) REVERT: D 134 LYS cc_start: 0.8217 (tttt) cc_final: 0.7882 (ttpt) REVERT: E 64 ASP cc_start: 0.7857 (t0) cc_final: 0.7609 (t0) REVERT: E 134 LYS cc_start: 0.8239 (tttt) cc_final: 0.7790 (ttpt) REVERT: E 190 MET cc_start: 0.8433 (tpp) cc_final: 0.7990 (ttm) REVERT: F 64 ASP cc_start: 0.7939 (t0) cc_final: 0.7636 (t0) REVERT: F 113 ASP cc_start: 0.8319 (p0) cc_final: 0.7749 (p0) REVERT: F 126 MET cc_start: 0.8364 (mmp) cc_final: 0.8029 (mmm) REVERT: F 134 LYS cc_start: 0.8121 (tttt) cc_final: 0.7826 (ttpt) REVERT: G 64 ASP cc_start: 0.7906 (t0) cc_final: 0.7625 (t0) REVERT: G 126 MET cc_start: 0.8916 (mmp) cc_final: 0.8635 (mmm) REVERT: G 134 LYS cc_start: 0.8270 (tttt) cc_final: 0.7913 (ttpt) REVERT: I 126 MET cc_start: 0.7294 (ptm) cc_final: 0.7088 (ptm) REVERT: J 126 MET cc_start: 0.7622 (ptm) cc_final: 0.7256 (ptm) REVERT: K 65 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8078 (mp) REVERT: K 126 MET cc_start: 0.7129 (ptm) cc_final: 0.6886 (ptm) outliers start: 64 outliers final: 57 residues processed: 325 average time/residue: 0.3190 time to fit residues: 155.2642 Evaluate side-chains 334 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 209 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17738 Z= 0.206 Angle : 0.617 11.526 24010 Z= 0.301 Chirality : 0.046 0.148 2667 Planarity : 0.003 0.041 3066 Dihedral : 4.330 25.443 2352 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.21 % Allowed : 25.06 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.45 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.69 (0.16), residues: 952 loop : -1.15 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 57 HIS 0.005 0.001 HIS I 79 PHE 0.009 0.001 PHE L 56 TYR 0.013 0.001 TYR D 46 ARG 0.005 0.001 ARG H 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 275 time to evaluate : 2.046 Fit side-chains REVERT: A 64 ASP cc_start: 0.7911 (t0) cc_final: 0.7637 (t0) REVERT: A 134 LYS cc_start: 0.8110 (tttt) cc_final: 0.7810 (ttpt) REVERT: A 220 GLU cc_start: 0.6804 (mp0) cc_final: 0.6473 (mp0) REVERT: B 64 ASP cc_start: 0.7982 (t0) cc_final: 0.7676 (t0) REVERT: B 126 MET cc_start: 0.8593 (mmm) cc_final: 0.8319 (mmm) REVERT: C 28 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7371 (ptm160) REVERT: C 30 ASP cc_start: 0.7070 (p0) cc_final: 0.6715 (p0) REVERT: C 64 ASP cc_start: 0.8173 (t0) cc_final: 0.7766 (t0) REVERT: C 185 ASN cc_start: 0.8774 (t0) cc_final: 0.8370 (t0) REVERT: D 64 ASP cc_start: 0.8195 (t0) cc_final: 0.7763 (t0) REVERT: D 134 LYS cc_start: 0.8255 (tttt) cc_final: 0.7889 (ttpt) REVERT: E 64 ASP cc_start: 0.7880 (t0) cc_final: 0.7625 (t0) REVERT: E 134 LYS cc_start: 0.8299 (tttt) cc_final: 0.7824 (ttpt) REVERT: E 190 MET cc_start: 0.8435 (tpp) cc_final: 0.8075 (ttm) REVERT: F 28 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.6968 (ptm160) REVERT: F 64 ASP cc_start: 0.7973 (t0) cc_final: 0.7644 (t0) REVERT: F 113 ASP cc_start: 0.8315 (p0) cc_final: 0.7740 (p0) REVERT: F 134 LYS cc_start: 0.8172 (tttt) cc_final: 0.7833 (ttpt) REVERT: G 64 ASP cc_start: 0.7941 (t0) cc_final: 0.7658 (t0) REVERT: G 126 MET cc_start: 0.8959 (mmp) cc_final: 0.8652 (mmm) REVERT: G 134 LYS cc_start: 0.8272 (tttt) cc_final: 0.7888 (ttpt) REVERT: J 126 MET cc_start: 0.7615 (ptm) cc_final: 0.7253 (ptm) REVERT: K 65 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8071 (mp) REVERT: K 83 MET cc_start: 0.7530 (tpp) cc_final: 0.7243 (mmm) outliers start: 64 outliers final: 60 residues processed: 324 average time/residue: 0.3094 time to fit residues: 151.0956 Evaluate side-chains 339 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 276 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.0040 chunk 51 optimal weight: 0.7980 chunk 153 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 166 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 HIS ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.205389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.153616 restraints weight = 20626.575| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 3.02 r_work: 0.3425 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1015 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1006 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17738 Z= 0.180 Angle : 0.610 11.582 24010 Z= 0.297 Chirality : 0.046 0.182 2667 Planarity : 0.003 0.030 3066 Dihedral : 4.281 24.352 2352 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.26 % Allowed : 25.06 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.68 (0.16), residues: 952 loop : -1.13 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 57 HIS 0.004 0.001 HIS I 79 PHE 0.009 0.001 PHE L 56 TYR 0.012 0.001 TYR D 46 ARG 0.007 0.001 ARG H 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4228.72 seconds wall clock time: 78 minutes 35.13 seconds (4715.13 seconds total)