Starting phenix.real_space_refine on Thu Feb 22 03:01:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyt_28720/02_2024/8eyt_28720_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyt_28720/02_2024/8eyt_28720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyt_28720/02_2024/8eyt_28720.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyt_28720/02_2024/8eyt_28720.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyt_28720/02_2024/8eyt_28720_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eyt_28720/02_2024/8eyt_28720_updated.pdb" } resolution = 2.8 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 47363 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1415 5.49 5 S 79 5.16 5 C 26282 2.51 5 N 9442 2.21 5 O 13481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 169": "OE1" <-> "OE2" Residue "V GLU 16": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 50699 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 30367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1415, 30367 Classifications: {'RNA': 1415} Modifications used: {'rna2p_pur': 119, 'rna2p_pyr': 80, 'rna3p_pur': 689, 'rna3p_pyr': 527} Link IDs: {'rna2p': 198, 'rna3p': 1216} Chain breaks: 2 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1144 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "F" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 651 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "O" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "R" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "U" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "V" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 496 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "W" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1979 Classifications: {'peptide': 254} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 234} Time building chain proxies: 19.54, per 1000 atoms: 0.39 Number of scatterers: 50699 At special positions: 0 Unit cell: (210.33, 227.43, 162.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 1415 15.00 O 13481 8.00 N 9442 7.00 C 26282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 18.59 Conformation dependent library (CDL) restraints added in 2.9 seconds 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4802 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 97 helices and 23 sheets defined 36.9% alpha, 15.7% beta 406 base pairs and 775 stacking pairs defined. Time for finding SS restraints: 19.29 Creating SS restraints... Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 43 through 62 Proline residue: B 48 - end of helix removed outlier: 3.864A pdb=" N ALA B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 87 removed outlier: 4.642A pdb=" N SER B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 123 removed outlier: 3.587A pdb=" N ARG B 113 " --> pdb=" O GLN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'B' and resid 172 through 179 Processing helix chain 'B' and resid 207 through 226 Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 50 through 65 removed outlier: 3.729A pdb=" N GLN D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 96 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'E' and resid 109 through 118 Processing helix chain 'E' and resid 133 through 145 Processing helix chain 'E' and resid 150 through 157 Processing helix chain 'H' and resid 6 through 19 Processing helix chain 'H' and resid 31 through 42 Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 96 through 98 No H-bonds generated for 'chain 'H' and resid 96 through 98' Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 116 No H-bonds generated for 'chain 'L' and resid 114 through 116' Processing helix chain 'P' and resid 54 through 63 removed outlier: 3.635A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 81 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'T' and resid 5 through 41 removed outlier: 4.100A pdb=" N ILE T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE T 31 " --> pdb=" O MET T 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 63 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 69 through 85 removed outlier: 3.762A pdb=" N LYS T 85 " --> pdb=" O ALA T 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 30 through 46 Processing helix chain 'F' and resid 73 through 77 Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.973A pdb=" N LYS F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 111 No H-bonds generated for 'chain 'F' and resid 109 through 111' Processing helix chain 'F' and resid 113 through 124 Processing helix chain 'F' and resid 132 through 143 removed outlier: 3.539A pdb=" N ARG F 136 " --> pdb=" O ARG F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 159 No H-bonds generated for 'chain 'F' and resid 157 through 159' Processing helix chain 'G' and resid 23 through 30 Processing helix chain 'G' and resid 36 through 49 removed outlier: 3.959A pdb=" N ILE G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR G 44 " --> pdb=" O GLU G 40 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 67 Processing helix chain 'G' and resid 93 through 108 Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.659A pdb=" N ASN G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLU G 123 " --> pdb=" O ARG G 119 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 147 Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 44 through 54 removed outlier: 3.863A pdb=" N VAL I 48 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG I 49 " --> pdb=" O ARG I 45 " (cutoff:3.500A) Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 72 through 90 Processing helix chain 'I' and resid 95 through 99 Processing helix chain 'J' and resid 15 through 32 removed outlier: 3.835A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 89 Processing helix chain 'M' and resid 18 through 20 No H-bonds generated for 'chain 'M' and resid 18 through 20' Processing helix chain 'M' and resid 27 through 37 removed outlier: 3.597A pdb=" N LYS M 31 " --> pdb=" O LYS M 27 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA M 32 " --> pdb=" O THR M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 62 removed outlier: 3.567A pdb=" N LEU M 56 " --> pdb=" O GLN M 52 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP M 58 " --> pdb=" O ASP M 54 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA M 61 " --> pdb=" O ARG M 57 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 83 removed outlier: 3.524A pdb=" N ARG M 71 " --> pdb=" O GLY M 67 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU M 72 " --> pdb=" O ASP M 68 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET M 81 " --> pdb=" O ILE M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 93 removed outlier: 3.545A pdb=" N ARG M 90 " --> pdb=" O TYR M 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 19 removed outlier: 3.673A pdb=" N GLU N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL N 11 " --> pdb=" O LYS N 7 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP N 18 " --> pdb=" O VAL N 14 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 33 removed outlier: 3.661A pdb=" N ILE N 31 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER N 32 " --> pdb=" O LYS N 28 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP N 33 " --> pdb=" O ALA N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 49 removed outlier: 4.094A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 81 through 90 removed outlier: 3.584A pdb=" N ARG N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU N 86 " --> pdb=" O ILE N 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 23 removed outlier: 3.526A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU S 20 " --> pdb=" O LEU S 16 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA S 22 " --> pdb=" O LYS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 44 No H-bonds generated for 'chain 'S' and resid 42 through 44' Processing helix chain 'S' and resid 71 through 74 removed outlier: 3.657A pdb=" N PHE S 74 " --> pdb=" O LEU S 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 71 through 74' Processing helix chain 'O' and resid 18 through 32 removed outlier: 3.958A pdb=" N ALA O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 80 Processing helix chain 'O' and resid 101 through 105 Processing helix chain 'R' and resid 54 through 58 Processing helix chain 'R' and resid 60 through 72 Processing helix chain 'R' and resid 95 through 103 removed outlier: 3.579A pdb=" N ALA R 103 " --> pdb=" O ALA R 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 15 Processing helix chain 'U' and resid 25 through 45 removed outlier: 4.390A pdb=" N GLY U 41 " --> pdb=" O ASN U 37 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS U 42 " --> pdb=" O HIS U 38 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU U 45 " --> pdb=" O GLY U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 50 through 73 removed outlier: 4.512A pdb=" N GLY U 55 " --> pdb=" O HIS U 51 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG U 58 " --> pdb=" O ARG U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 85 Processing helix chain 'V' and resid 26 through 32 removed outlier: 4.180A pdb=" N ASN V 31 " --> pdb=" O ALA V 27 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR V 32 " --> pdb=" O THR V 28 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 45 No H-bonds generated for 'chain 'V' and resid 42 through 45' Processing helix chain 'V' and resid 49 through 64 Processing helix chain 'W' and resid 28 through 33 Processing helix chain 'W' and resid 69 through 75 Processing helix chain 'W' and resid 98 through 102 removed outlier: 3.940A pdb=" N GLU W 102 " --> pdb=" O GLU W 99 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 126 removed outlier: 4.638A pdb=" N MET W 123 " --> pdb=" O SER W 119 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE W 124 " --> pdb=" O THR W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'W' and resid 142 through 149 removed outlier: 3.590A pdb=" N ARG W 147 " --> pdb=" O GLU W 143 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 167 Processing helix chain 'W' and resid 207 through 220 removed outlier: 4.024A pdb=" N GLN W 220 " --> pdb=" O GLU W 216 " (cutoff:3.500A) Processing helix chain 'W' and resid 225 through 228 No H-bonds generated for 'chain 'W' and resid 225 through 228' Processing helix chain 'W' and resid 235 through 240 Processing helix chain 'W' and resid 249 through 251 No H-bonds generated for 'chain 'W' and resid 249 through 251' Processing helix chain 'W' and resid 254 through 266 removed outlier: 3.551A pdb=" N ALA W 261 " --> pdb=" O TYR W 257 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA W 265 " --> pdb=" O ALA W 261 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.651A pdb=" N PHE B 90 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA B 160 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL B 70 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE B 162 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE B 198 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL B 187 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 31 through 35 removed outlier: 7.068A pdb=" N ILE B 40 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 123 through 125 Processing sheet with id= D, first strand: chain 'E' and resid 46 through 53 removed outlier: 6.873A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= F, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.912A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.792A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.618A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'P' and resid 2 through 11 removed outlier: 3.588A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'Q' and resid 73 through 75 removed outlier: 7.825A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.678A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N VAL Q 78 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 99 through 105 removed outlier: 5.985A pdb=" N ILE F 64 " --> pdb=" O GLN F 100 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASN F 102 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL F 66 " --> pdb=" O ASN F 102 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA F 104 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE F 68 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG F 54 " --> pdb=" O HIS F 69 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 165 through 171 removed outlier: 3.508A pdb=" N GLY F 194 " --> pdb=" O THR F 191 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 73 through 75 removed outlier: 3.743A pdb=" N GLU G 74 " --> pdb=" O VAL G 89 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 6 through 12 Processing sheet with id= P, first strand: chain 'J' and resid 96 through 101 removed outlier: 3.721A pdb=" N ILE J 6 " --> pdb=" O ILE J 76 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE J 76 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= R, first strand: chain 'S' and resid 31 through 33 Processing sheet with id= S, first strand: chain 'O' and resid 43 through 45 removed outlier: 4.121A pdb=" N GLY O 43 " --> pdb=" O TYR O 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N HIS O 3 " --> pdb=" O THR O 92 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG O 86 " --> pdb=" O MET O 9 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 35 through 41 removed outlier: 6.566A pdb=" N ASN O 63 " --> pdb=" O HIS O 37 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU O 39 " --> pdb=" O LEU O 61 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU O 61 " --> pdb=" O LEU O 39 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'R' and resid 110 through 112 removed outlier: 6.495A pdb=" N VAL R 84 " --> pdb=" O THR R 111 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY R 43 " --> pdb=" O ILE R 34 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'W' and resid 62 through 65 Processing sheet with id= W, first strand: chain 'W' and resid 108 through 112 removed outlier: 8.264A pdb=" N VAL W 110 " --> pdb=" O ALA W 134 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N MET W 136 " --> pdb=" O VAL W 110 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N GLY W 112 " --> pdb=" O MET W 136 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE W 138 " --> pdb=" O GLY W 112 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA W 134 " --> pdb=" O PRO W 196 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE W 138 " --> pdb=" O VAL W 192 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ARG W 193 " --> pdb=" O PRO W 172 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL W 195 " --> pdb=" O VAL W 170 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL W 170 " --> pdb=" O VAL W 195 " (cutoff:3.500A) 751 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1011 hydrogen bonds 1592 hydrogen bond angles 0 basepair planarities 406 basepair parallelities 775 stacking parallelities Total time for adding SS restraints: 29.68 Time building geometry restraints manager: 20.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.66: 54483 1.66 - 2.19: 158 2.19 - 2.72: 0 2.72 - 3.25: 0 3.25 - 3.78: 2 Bond restraints: 54643 Sorted by residual: bond pdb=" N PRO M 10 " pdb=" CD PRO M 10 " ideal model delta sigma weight residual 1.473 3.781 -2.308 1.40e-02 5.10e+03 2.72e+04 bond pdb=" N PRO W 183 " pdb=" CD PRO W 183 " ideal model delta sigma weight residual 1.473 3.268 -1.795 1.40e-02 5.10e+03 1.64e+04 bond pdb=" O3' A A 949 " pdb=" P U A 950 " ideal model delta sigma weight residual 1.607 1.333 0.274 1.50e-02 4.44e+03 3.34e+02 bond pdb=" CA LEU S 5 " pdb=" C LEU S 5 " ideal model delta sigma weight residual 1.533 1.633 -0.099 5.60e-03 3.19e+04 3.16e+02 bond pdb=" N PRO B 29 " pdb=" CA PRO B 29 " ideal model delta sigma weight residual 1.472 1.693 -0.221 1.32e-02 5.74e+03 2.81e+02 ... (remaining 54638 not shown) Histogram of bond angle deviations from ideal: 10.68 - 39.64: 2 39.64 - 68.59: 0 68.59 - 97.54: 49 97.54 - 126.49: 76433 126.49 - 155.45: 4307 Bond angle restraints: 80791 Sorted by residual: angle pdb=" N PRO M 10 " pdb=" CD PRO M 10 " pdb=" CG PRO M 10 " ideal model delta sigma weight residual 103.20 10.68 92.52 1.50e+00 4.44e-01 3.80e+03 angle pdb=" N PRO W 183 " pdb=" CD PRO W 183 " pdb=" CG PRO W 183 " ideal model delta sigma weight residual 103.20 26.13 77.07 1.50e+00 4.44e-01 2.64e+03 angle pdb=" N LEU S 5 " pdb=" CA LEU S 5 " pdb=" C LEU S 5 " ideal model delta sigma weight residual 108.78 137.95 -29.17 8.20e-01 1.49e+00 1.27e+03 angle pdb=" C LYS L 44 " pdb=" N PRO L 45 " pdb=" CA PRO L 45 " ideal model delta sigma weight residual 119.84 155.45 -35.61 1.25e+00 6.40e-01 8.11e+02 angle pdb=" CA PRO M 10 " pdb=" N PRO M 10 " pdb=" CD PRO M 10 " ideal model delta sigma weight residual 112.00 72.12 39.88 1.40e+00 5.10e-01 8.11e+02 ... (remaining 80786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 31141 35.33 - 70.66: 3341 70.66 - 105.99: 395 105.99 - 141.32: 9 141.32 - 176.65: 16 Dihedral angle restraints: 34902 sinusoidal: 27474 harmonic: 7428 Sorted by residual: dihedral pdb=" O4' C A1533 " pdb=" C1' C A1533 " pdb=" N1 C A1533 " pdb=" C2 C A1533 " ideal model delta sinusoidal sigma weight residual 200.00 24.23 175.77 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U A1008 " pdb=" C1' U A1008 " pdb=" N1 U A1008 " pdb=" C2 U A1008 " ideal model delta sinusoidal sigma weight residual 200.00 27.00 173.00 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U A1017 " pdb=" C1' U A1017 " pdb=" N1 U A1017 " pdb=" C2 U A1017 " ideal model delta sinusoidal sigma weight residual -160.00 12.67 -172.67 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 34899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 9359 0.150 - 0.300: 714 0.300 - 0.451: 86 0.451 - 0.601: 24 0.601 - 0.751: 4 Chirality restraints: 10187 Sorted by residual: chirality pdb=" C3' G A1160 " pdb=" C4' G A1160 " pdb=" O3' G A1160 " pdb=" C2' G A1160 " both_signs ideal model delta sigma weight residual False -2.48 -1.73 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" C2' C A1141 " pdb=" C3' C A1141 " pdb=" O2' C A1141 " pdb=" C1' C A1141 " both_signs ideal model delta sigma weight residual False -2.52 -1.81 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" C1' G A 844 " pdb=" O4' G A 844 " pdb=" C2' G A 844 " pdb=" N9 G A 844 " both_signs ideal model delta sigma weight residual False 2.44 1.78 0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 10184 not shown) Planarity restraints: 5014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR W 182 " -0.180 5.00e-02 4.00e+02 2.19e-01 7.67e+01 pdb=" N PRO W 183 " 0.352 5.00e-02 4.00e+02 pdb=" CA PRO W 183 " -0.188 5.00e-02 4.00e+02 pdb=" CD PRO W 183 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A1018 " 0.118 2.00e-02 2.50e+03 5.04e-02 7.61e+01 pdb=" N9 G A1018 " -0.119 2.00e-02 2.50e+03 pdb=" C8 G A1018 " -0.016 2.00e-02 2.50e+03 pdb=" N7 G A1018 " 0.010 2.00e-02 2.50e+03 pdb=" C5 G A1018 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G A1018 " 0.012 2.00e-02 2.50e+03 pdb=" O6 G A1018 " 0.029 2.00e-02 2.50e+03 pdb=" N1 G A1018 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G A1018 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G A1018 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G A1018 " -0.022 2.00e-02 2.50e+03 pdb=" C4 G A1018 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 943 " 0.096 2.00e-02 2.50e+03 4.83e-02 5.24e+01 pdb=" N1 U A 943 " -0.050 2.00e-02 2.50e+03 pdb=" C2 U A 943 " -0.023 2.00e-02 2.50e+03 pdb=" O2 U A 943 " -0.014 2.00e-02 2.50e+03 pdb=" N3 U A 943 " -0.028 2.00e-02 2.50e+03 pdb=" C4 U A 943 " 0.061 2.00e-02 2.50e+03 pdb=" O4 U A 943 " 0.032 2.00e-02 2.50e+03 pdb=" C5 U A 943 " -0.024 2.00e-02 2.50e+03 pdb=" C6 U A 943 " -0.049 2.00e-02 2.50e+03 ... (remaining 5011 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 29 2.14 - 2.83: 15292 2.83 - 3.52: 62888 3.52 - 4.21: 147016 4.21 - 4.90: 209746 Nonbonded interactions: 434971 Sorted by model distance: nonbonded pdb=" C2 A A1004 " pdb=" C8 G A1026 " model vdw 1.450 3.560 nonbonded pdb=" N1 A A1004 " pdb=" C8 G A1026 " model vdw 1.524 3.340 nonbonded pdb=" O THR W 130 " pdb=" CD1 ILE W 133 " model vdw 1.610 3.460 nonbonded pdb=" N2 G A 79 " pdb=" C2 U A 91 " model vdw 1.671 3.340 nonbonded pdb=" OG1 THR B 72 " pdb=" CE1 HIS B 168 " model vdw 1.694 3.260 ... (remaining 434966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.440 Construct map_model_manager: 0.040 Extract box with map and model: 12.800 Check model and map are aligned: 0.550 Set scattering table: 0.390 Process input model: 123.370 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 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 : 0.018 2.308 54643 Z= 0.918 Angle : 1.451 92.515 80791 Z= 0.912 Chirality : 0.086 0.751 10187 Planarity : 0.010 0.219 5014 Dihedral : 22.869 176.645 30100 Min Nonbonded Distance : 1.450 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.94 % Allowed : 5.15 % Favored : 93.91 % Rotamer: Outliers : 1.31 % Allowed : 28.48 % Favored : 70.21 % Cbeta Deviations : 0.75 % 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: -0.61 (0.16), residues: 2545 helix: 0.54 (0.17), residues: 976 sheet: 0.14 (0.25), residues: 411 loop : -1.43 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP F 18 HIS 0.028 0.003 HIS W 78 PHE 0.039 0.003 PHE N 73 TYR 0.043 0.003 TYR I 7 ARG 0.014 0.001 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 344 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 138 SER cc_start: 0.9033 (m) cc_final: 0.8717 (p) REVERT: D 141 ASP cc_start: 0.8471 (m-30) cc_final: 0.8194 (m-30) REVERT: E 130 SER cc_start: 0.8898 (p) cc_final: 0.8661 (p) REVERT: H 67 GLN cc_start: 0.7858 (pt0) cc_final: 0.7629 (pp30) REVERT: H 114 ARG cc_start: 0.8583 (ttm-80) cc_final: 0.8378 (ttp80) REVERT: L 75 GLN cc_start: 0.8579 (mt0) cc_final: 0.8351 (pm20) REVERT: L 77 HIS cc_start: 0.8252 (m-70) cc_final: 0.7938 (m90) REVERT: P 76 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8526 (tttm) REVERT: S 6 LYS cc_start: 0.4650 (OUTLIER) cc_final: 0.3268 (ptpt) REVERT: S 44 MET cc_start: -0.3331 (mtt) cc_final: -0.4291 (ttt) REVERT: O 65 GLU cc_start: 0.7904 (tt0) cc_final: 0.7665 (tm-30) REVERT: R 40 ASN cc_start: 0.8746 (m110) cc_final: 0.8504 (m110) REVERT: U 37 ASN cc_start: 0.8388 (m-40) cc_final: 0.8059 (m-40) REVERT: W 61 GLN cc_start: 0.7073 (pt0) cc_final: 0.6813 (tm130) REVERT: W 167 TYR cc_start: 0.8441 (m-80) cc_final: 0.8014 (m-10) outliers start: 28 outliers final: 11 residues processed: 371 average time/residue: 1.5171 time to fit residues: 685.4584 Evaluate side-chains 286 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 274 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain L residue 45 PRO Chi-restraints excluded: chain Q residue 4 LYS Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain W residue 133 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 330 optimal weight: 9.9990 chunk 296 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 chunk 158 optimal weight: 40.0000 chunk 306 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 355 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN L 46 ASN F 8 ASN I 126 GLN N 66 GLN ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 HIS R 64 GLN U 20 ASN U 40 GLN W 18 ASN ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 GLN ** W 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 267 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 54643 Z= 0.299 Angle : 0.683 25.273 80791 Z= 0.350 Chirality : 0.041 0.317 10187 Planarity : 0.007 0.206 5014 Dihedral : 22.582 174.733 25009 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.77 % Favored : 96.03 % Rotamer: Outliers : 5.08 % Allowed : 26.81 % Favored : 68.11 % 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: -0.34 (0.16), residues: 2545 helix: 0.68 (0.17), residues: 994 sheet: 0.13 (0.24), residues: 440 loop : -1.17 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 42 HIS 0.011 0.001 HIS W 78 PHE 0.024 0.002 PHE W 138 TYR 0.021 0.002 TYR E 50 ARG 0.023 0.001 ARG I 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 296 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 GLU cc_start: -0.2903 (OUTLIER) cc_final: -0.3458 (tt0) REVERT: D 138 SER cc_start: 0.9043 (m) cc_final: 0.8697 (p) REVERT: D 141 ASP cc_start: 0.8455 (m-30) cc_final: 0.8227 (m-30) REVERT: H 67 GLN cc_start: 0.7801 (pt0) cc_final: 0.7523 (pp30) REVERT: H 91 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8116 (mp0) REVERT: L 47 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7903 (t) REVERT: L 77 HIS cc_start: 0.8251 (m-70) cc_final: 0.7946 (m90) REVERT: L 86 ARG cc_start: 0.8332 (ptm160) cc_final: 0.8040 (ptm160) REVERT: P 76 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8578 (tttm) REVERT: F 127 ARG cc_start: 0.3299 (OUTLIER) cc_final: 0.3077 (mtt180) REVERT: I 88 MET cc_start: 0.5654 (mmm) cc_final: 0.5358 (mpm) REVERT: S 6 LYS cc_start: 0.4273 (OUTLIER) cc_final: 0.3005 (ptpt) REVERT: S 66 MET cc_start: 0.0269 (tmt) cc_final: -0.0122 (tmm) REVERT: O 9 MET cc_start: 0.7087 (ptt) cc_final: 0.6705 (ptp) REVERT: O 59 TYR cc_start: 0.8436 (m-80) cc_final: 0.7818 (m-80) REVERT: O 65 GLU cc_start: 0.7971 (tt0) cc_final: 0.7650 (tm-30) REVERT: R 86 VAL cc_start: 0.7437 (OUTLIER) cc_final: 0.7232 (m) REVERT: W 18 ASN cc_start: 0.4650 (OUTLIER) cc_final: 0.4166 (m110) REVERT: W 41 MET cc_start: 0.3256 (mpt) cc_final: 0.0479 (tpp) REVERT: W 100 LEU cc_start: 0.5838 (OUTLIER) cc_final: 0.5577 (tt) REVERT: W 109 ARG cc_start: 0.5915 (mmm160) cc_final: 0.4398 (ttt180) REVERT: W 167 TYR cc_start: 0.8261 (m-80) cc_final: 0.7976 (m-10) REVERT: W 183 PRO cc_start: 0.8383 (OUTLIER) cc_final: 0.8085 (Cg_exo) outliers start: 109 outliers final: 40 residues processed: 378 average time/residue: 1.3947 time to fit residues: 651.1802 Evaluate side-chains 319 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 271 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 4 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain F residue 127 ARG Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 61 PHE Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain W residue 18 ASN Chi-restraints excluded: chain W residue 28 SER Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 100 LEU Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 183 PRO Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 295 optimal weight: 8.9990 chunk 241 optimal weight: 0.0050 chunk 97 optimal weight: 40.0000 chunk 355 optimal weight: 10.0000 chunk 384 optimal weight: 4.9990 chunk 316 optimal weight: 50.0000 chunk 352 optimal weight: 8.9990 chunk 121 optimal weight: 50.0000 chunk 285 optimal weight: 6.9990 overall best weight: 5.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN E 82 GLN H 76 GLN P 79 ASN F 8 ASN F 123 GLN I 5 GLN N 49 GLN N 66 GLN R 24 HIS U 20 ASN ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 54643 Z= 0.363 Angle : 0.660 21.860 80791 Z= 0.339 Chirality : 0.041 0.312 10187 Planarity : 0.007 0.198 5014 Dihedral : 22.484 178.416 24997 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.09 % Favored : 95.72 % Rotamer: Outliers : 5.64 % Allowed : 25.59 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -0.27 (0.16), residues: 2545 helix: 0.78 (0.17), residues: 977 sheet: 0.10 (0.24), residues: 451 loop : -1.14 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 42 HIS 0.006 0.001 HIS W 78 PHE 0.036 0.002 PHE W 19 TYR 0.021 0.002 TYR E 50 ARG 0.013 0.001 ARG I 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 295 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.2146 (mmp) cc_final: 0.1926 (mmp) REVERT: D 138 SER cc_start: 0.9031 (m) cc_final: 0.8677 (p) REVERT: D 141 ASP cc_start: 0.8507 (m-30) cc_final: 0.8279 (m-30) REVERT: E 10 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7064 (pp20) REVERT: H 36 ILE cc_start: 0.9218 (mt) cc_final: 0.9000 (mm) REVERT: H 91 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8128 (mp0) REVERT: L 47 SER cc_start: 0.8170 (OUTLIER) cc_final: 0.7875 (t) REVERT: L 77 HIS cc_start: 0.8279 (m-70) cc_final: 0.7982 (m90) REVERT: L 86 ARG cc_start: 0.8361 (ptm160) cc_final: 0.8149 (ptm160) REVERT: P 76 LYS cc_start: 0.9039 (ttmm) cc_final: 0.8559 (tttm) REVERT: S 6 LYS cc_start: 0.4518 (OUTLIER) cc_final: 0.3067 (ptpt) REVERT: S 38 SER cc_start: 0.4191 (m) cc_final: 0.3855 (t) REVERT: S 66 MET cc_start: 0.1207 (tmt) cc_final: 0.0272 (tmm) REVERT: O 9 MET cc_start: 0.7093 (ptt) cc_final: 0.6800 (ptt) REVERT: O 65 GLU cc_start: 0.8099 (tt0) cc_final: 0.7659 (tm-30) REVERT: R 86 VAL cc_start: 0.7311 (OUTLIER) cc_final: 0.7084 (m) REVERT: W 28 SER cc_start: 0.8489 (OUTLIER) cc_final: 0.8228 (p) REVERT: W 41 MET cc_start: 0.3166 (mpt) cc_final: 0.0572 (mmt) REVERT: W 59 LEU cc_start: 0.4867 (mp) cc_final: 0.4313 (mp) REVERT: W 100 LEU cc_start: 0.5917 (OUTLIER) cc_final: 0.5633 (tt) REVERT: W 123 MET cc_start: 0.3643 (OUTLIER) cc_final: 0.2970 (ttm) REVERT: W 167 TYR cc_start: 0.8352 (m-80) cc_final: 0.8093 (m-10) REVERT: W 259 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8255 (tm-30) outliers start: 121 outliers final: 58 residues processed: 388 average time/residue: 1.3538 time to fit residues: 655.2856 Evaluate side-chains 346 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 280 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain W residue 18 ASN Chi-restraints excluded: chain W residue 28 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 77 THR Chi-restraints excluded: chain W residue 86 THR Chi-restraints excluded: chain W residue 100 LEU Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 123 MET Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 259 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 351 optimal weight: 0.9980 chunk 267 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 238 optimal weight: 0.8980 chunk 356 optimal weight: 7.9990 chunk 377 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 338 optimal weight: 7.9990 chunk 101 optimal weight: 40.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 196 ASN H 76 GLN L 112 GLN F 123 GLN N 66 GLN S 14 HIS U 20 ASN W 18 ASN W 89 GLN W 106 GLN ** W 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 141 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 54643 Z= 0.135 Angle : 0.526 11.547 80791 Z= 0.274 Chirality : 0.034 0.283 10187 Planarity : 0.005 0.147 5014 Dihedral : 22.346 179.605 24993 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.34 % Favored : 96.42 % Rotamer: Outliers : 4.29 % Allowed : 27.13 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: 0.08 (0.17), residues: 2545 helix: 1.10 (0.17), residues: 978 sheet: 0.37 (0.25), residues: 443 loop : -1.00 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 201 HIS 0.006 0.001 HIS F 6 PHE 0.019 0.001 PHE I 127 TYR 0.013 0.001 TYR W 166 ARG 0.016 0.000 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 291 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 GLU cc_start: -0.2795 (OUTLIER) cc_final: -0.3355 (tt0) REVERT: D 138 SER cc_start: 0.9060 (m) cc_final: 0.8708 (p) REVERT: D 141 ASP cc_start: 0.8409 (m-30) cc_final: 0.8168 (m-30) REVERT: D 177 LYS cc_start: 0.7947 (tptp) cc_final: 0.7711 (tptp) REVERT: E 10 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.6990 (pp20) REVERT: E 96 MET cc_start: 0.8953 (mtm) cc_final: 0.8673 (mtm) REVERT: H 36 ILE cc_start: 0.9149 (mt) cc_final: 0.8946 (mm) REVERT: H 91 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8047 (mp0) REVERT: L 77 HIS cc_start: 0.8235 (m-70) cc_final: 0.7975 (m90) REVERT: P 76 LYS cc_start: 0.9005 (ttmm) cc_final: 0.8553 (tttm) REVERT: Q 43 LYS cc_start: 0.8903 (mtmt) cc_final: 0.8690 (mtpm) REVERT: I 84 THR cc_start: 0.6031 (m) cc_final: 0.5617 (m) REVERT: S 6 LYS cc_start: 0.4508 (OUTLIER) cc_final: 0.3089 (ptpt) REVERT: S 38 SER cc_start: 0.4275 (m) cc_final: 0.3950 (t) REVERT: S 66 MET cc_start: 0.1043 (tmt) cc_final: 0.0086 (tmm) REVERT: O 9 MET cc_start: 0.7008 (ptt) cc_final: 0.6698 (ptt) REVERT: O 39 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7455 (mt) REVERT: O 65 GLU cc_start: 0.8060 (tt0) cc_final: 0.7492 (tm-30) REVERT: W 41 MET cc_start: 0.3036 (mpt) cc_final: -0.0222 (tpp) REVERT: W 106 GLN cc_start: 0.3887 (OUTLIER) cc_final: 0.3263 (pp30) REVERT: W 109 ARG cc_start: 0.5794 (mmm160) cc_final: 0.4326 (ttt-90) outliers start: 92 outliers final: 35 residues processed: 361 average time/residue: 1.4069 time to fit residues: 635.1700 Evaluate side-chains 316 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 276 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 86 THR Chi-restraints excluded: chain W residue 106 GLN Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 128 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 314 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 281 optimal weight: 8.9990 chunk 155 optimal weight: 50.0000 chunk 322 optimal weight: 0.8980 chunk 261 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 339 optimal weight: 7.9990 chunk 95 optimal weight: 50.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 GLN F 123 GLN N 66 GLN U 20 ASN W 78 HIS ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 141 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 54643 Z= 0.360 Angle : 0.635 9.054 80791 Z= 0.326 Chirality : 0.040 0.268 10187 Planarity : 0.006 0.144 5014 Dihedral : 22.389 179.611 24993 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.05 % Favored : 95.72 % Rotamer: Outliers : 4.76 % Allowed : 27.32 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: -0.09 (0.16), residues: 2545 helix: 0.95 (0.17), residues: 983 sheet: 0.18 (0.24), residues: 453 loop : -1.06 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 42 HIS 0.011 0.001 HIS W 78 PHE 0.014 0.001 PHE W 181 TYR 0.022 0.002 TYR W 167 ARG 0.014 0.001 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 276 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 138 SER cc_start: 0.9054 (m) cc_final: 0.8764 (t) REVERT: D 177 LYS cc_start: 0.7952 (tptp) cc_final: 0.7594 (tptp) REVERT: E 10 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.6993 (pp20) REVERT: H 91 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8113 (mp0) REVERT: L 77 HIS cc_start: 0.8278 (m-70) cc_final: 0.8005 (m90) REVERT: P 76 LYS cc_start: 0.9034 (ttmm) cc_final: 0.8573 (tttm) REVERT: Q 16 LYS cc_start: 0.9102 (mttm) cc_final: 0.8846 (mttp) REVERT: S 38 SER cc_start: 0.4396 (m) cc_final: 0.4042 (t) REVERT: O 9 MET cc_start: 0.7053 (ptt) cc_final: 0.6810 (ptt) REVERT: O 38 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7338 (ttp-110) REVERT: O 65 GLU cc_start: 0.8012 (tt0) cc_final: 0.7453 (tm-30) REVERT: W 41 MET cc_start: 0.3228 (mpt) cc_final: 0.0444 (mmt) REVERT: W 59 LEU cc_start: 0.4934 (mp) cc_final: 0.4338 (mp) REVERT: W 109 ARG cc_start: 0.5712 (mmm160) cc_final: 0.4437 (ttt-90) REVERT: W 250 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8158 (pt0) REVERT: W 259 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8273 (tm-30) outliers start: 102 outliers final: 54 residues processed: 348 average time/residue: 1.3751 time to fit residues: 594.7291 Evaluate side-chains 324 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 266 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 86 THR Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 227 ASN Chi-restraints excluded: chain W residue 250 GLU Chi-restraints excluded: chain W residue 259 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 127 optimal weight: 40.0000 chunk 340 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 221 optimal weight: 0.8980 chunk 93 optimal weight: 50.0000 chunk 378 optimal weight: 9.9990 chunk 314 optimal weight: 8.9990 chunk 175 optimal weight: 0.0470 chunk 31 optimal weight: 4.9990 chunk 125 optimal weight: 30.0000 chunk 198 optimal weight: 0.0970 overall best weight: 2.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN F 123 GLN N 35 ASN ** O 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 ASN ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 54643 Z= 0.208 Angle : 0.555 17.385 80791 Z= 0.286 Chirality : 0.036 0.265 10187 Planarity : 0.005 0.169 5014 Dihedral : 22.335 179.119 24989 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.42 % Favored : 96.35 % Rotamer: Outliers : 4.52 % Allowed : 27.74 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: 0.07 (0.17), residues: 2545 helix: 1.11 (0.17), residues: 975 sheet: 0.24 (0.24), residues: 447 loop : -0.97 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 201 HIS 0.007 0.001 HIS F 6 PHE 0.028 0.001 PHE I 127 TYR 0.019 0.001 TYR W 166 ARG 0.010 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 283 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 138 SER cc_start: 0.9006 (m) cc_final: 0.8685 (p) REVERT: D 141 ASP cc_start: 0.8481 (m-30) cc_final: 0.8212 (m-30) REVERT: D 177 LYS cc_start: 0.8034 (tptp) cc_final: 0.7652 (tptp) REVERT: E 10 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.6976 (pp20) REVERT: H 91 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8073 (mp0) REVERT: L 77 HIS cc_start: 0.8275 (m-70) cc_final: 0.8020 (m90) REVERT: P 76 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8577 (tttm) REVERT: Q 16 LYS cc_start: 0.9078 (mttm) cc_final: 0.8821 (mttp) REVERT: G 116 MET cc_start: 0.0584 (pmm) cc_final: -0.1575 (ptt) REVERT: I 35 LEU cc_start: 0.5055 (OUTLIER) cc_final: 0.4667 (tp) REVERT: M 81 MET cc_start: 0.4555 (mmt) cc_final: 0.4113 (mmm) REVERT: S 38 SER cc_start: 0.4322 (m) cc_final: 0.3997 (t) REVERT: O 9 MET cc_start: 0.6928 (ptt) cc_final: 0.6589 (ptt) REVERT: O 38 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7326 (ttp-110) REVERT: O 65 GLU cc_start: 0.7841 (tt0) cc_final: 0.7341 (tm-30) REVERT: W 41 MET cc_start: 0.2861 (mpt) cc_final: -0.0034 (mmt) REVERT: W 59 LEU cc_start: 0.4902 (mp) cc_final: 0.4553 (mp) REVERT: W 109 ARG cc_start: 0.5705 (mmm160) cc_final: 0.4578 (ttt180) REVERT: W 241 MET cc_start: 0.7440 (mtp) cc_final: 0.7236 (mtm) REVERT: W 259 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8225 (tm-30) outliers start: 97 outliers final: 54 residues processed: 350 average time/residue: 1.4191 time to fit residues: 614.0856 Evaluate side-chains 332 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 274 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain O residue 21 MET Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain W residue 18 ASN Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 86 THR Chi-restraints excluded: chain W residue 106 GLN Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 227 ASN Chi-restraints excluded: chain W residue 259 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 364 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 276 optimal weight: 8.9990 chunk 214 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 376 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN F 123 GLN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 ASN ** W 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 267 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 54643 Z= 0.234 Angle : 0.565 15.154 80791 Z= 0.290 Chirality : 0.036 0.263 10187 Planarity : 0.005 0.146 5014 Dihedral : 22.318 177.949 24989 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.69 % Favored : 96.07 % Rotamer: Outliers : 3.87 % Allowed : 28.39 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.99 % 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: 0.13 (0.17), residues: 2545 helix: 1.18 (0.17), residues: 975 sheet: 0.32 (0.24), residues: 442 loop : -0.97 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 201 HIS 0.007 0.001 HIS F 6 PHE 0.021 0.001 PHE W 127 TYR 0.021 0.002 TYR W 166 ARG 0.011 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 273 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 GLU cc_start: -0.2934 (OUTLIER) cc_final: -0.3414 (tt0) REVERT: D 138 SER cc_start: 0.9010 (m) cc_final: 0.8662 (p) REVERT: D 156 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8418 (mmmm) REVERT: D 177 LYS cc_start: 0.8101 (tptp) cc_final: 0.7849 (tptp) REVERT: E 10 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.6946 (pp20) REVERT: L 77 HIS cc_start: 0.8253 (m-70) cc_final: 0.8009 (m90) REVERT: P 76 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8581 (tttm) REVERT: Q 16 LYS cc_start: 0.9086 (mttm) cc_final: 0.8838 (mttp) REVERT: F 134 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.6064 (mmt) REVERT: G 116 MET cc_start: 0.0037 (pmm) cc_final: -0.1636 (mtm) REVERT: G 118 LEU cc_start: -0.0722 (OUTLIER) cc_final: -0.0951 (pp) REVERT: I 35 LEU cc_start: 0.4919 (OUTLIER) cc_final: 0.4603 (tp) REVERT: S 38 SER cc_start: 0.4146 (m) cc_final: 0.3908 (t) REVERT: O 38 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7283 (ttp-110) REVERT: O 65 GLU cc_start: 0.7824 (tt0) cc_final: 0.7300 (tm-30) REVERT: W 41 MET cc_start: 0.2702 (mpt) cc_final: -0.0375 (mmt) REVERT: W 109 ARG cc_start: 0.5759 (mmm160) cc_final: 0.4365 (ttt180) REVERT: W 122 LEU cc_start: 0.7066 (mm) cc_final: 0.6791 (pp) REVERT: W 259 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8341 (tm-30) outliers start: 83 outliers final: 51 residues processed: 337 average time/residue: 1.3962 time to fit residues: 583.6440 Evaluate side-chains 326 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 267 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 86 THR Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 227 ASN Chi-restraints excluded: chain W residue 259 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 233 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 225 optimal weight: 2.9990 chunk 113 optimal weight: 40.0000 chunk 74 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 239 optimal weight: 2.9990 chunk 256 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 296 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN F 123 GLN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN ** O 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 HIS U 20 ASN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 54643 Z= 0.356 Angle : 0.641 14.266 80791 Z= 0.327 Chirality : 0.040 0.262 10187 Planarity : 0.005 0.138 5014 Dihedral : 22.419 175.409 24989 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.81 % Favored : 95.99 % Rotamer: Outliers : 4.20 % Allowed : 28.39 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.98 % 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: -0.04 (0.17), residues: 2545 helix: 1.04 (0.17), residues: 968 sheet: 0.13 (0.24), residues: 451 loop : -1.01 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 42 HIS 0.010 0.001 HIS F 6 PHE 0.031 0.002 PHE I 127 TYR 0.023 0.002 TYR D 76 ARG 0.015 0.001 ARG U 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 287 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 138 SER cc_start: 0.8982 (m) cc_final: 0.8645 (p) REVERT: D 156 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8419 (mmmm) REVERT: D 177 LYS cc_start: 0.8157 (tptp) cc_final: 0.7893 (tptp) REVERT: D 196 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8231 (p0) REVERT: E 10 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.6940 (pp20) REVERT: L 77 HIS cc_start: 0.8267 (m-70) cc_final: 0.8013 (m90) REVERT: P 76 LYS cc_start: 0.9037 (ttmm) cc_final: 0.8595 (tttm) REVERT: Q 16 LYS cc_start: 0.9090 (mttm) cc_final: 0.8636 (mtpp) REVERT: G 116 MET cc_start: 0.0230 (pmm) cc_final: -0.1417 (mtm) REVERT: S 38 SER cc_start: 0.4328 (m) cc_final: 0.4031 (t) REVERT: O 9 MET cc_start: 0.6973 (ptt) cc_final: 0.6665 (ptt) REVERT: O 38 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7293 (ttp-110) REVERT: O 65 GLU cc_start: 0.7811 (tt0) cc_final: 0.7320 (tm-30) REVERT: W 41 MET cc_start: 0.2551 (mpt) cc_final: 0.0046 (mmt) REVERT: W 59 LEU cc_start: 0.5194 (mp) cc_final: 0.4513 (mp) REVERT: W 109 ARG cc_start: 0.5751 (mmm160) cc_final: 0.4348 (ttt180) REVERT: W 122 LEU cc_start: 0.7359 (mm) cc_final: 0.7087 (pp) REVERT: W 206 ASP cc_start: 0.6980 (t70) cc_final: 0.6530 (t0) REVERT: W 250 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8129 (pt0) outliers start: 90 outliers final: 54 residues processed: 354 average time/residue: 1.4168 time to fit residues: 623.1485 Evaluate side-chains 339 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 280 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain O residue 21 MET Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 86 THR Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 168 CYS Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 227 ASN Chi-restraints excluded: chain W residue 250 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 342 optimal weight: 0.9990 chunk 361 optimal weight: 50.0000 chunk 329 optimal weight: 20.0000 chunk 351 optimal weight: 20.0000 chunk 360 optimal weight: 40.0000 chunk 211 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 275 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 317 optimal weight: 2.9990 chunk 332 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN F 123 GLN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 HIS R 40 ASN U 20 ASN W 18 ASN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 54643 Z= 0.308 Angle : 0.610 14.443 80791 Z= 0.312 Chirality : 0.038 0.253 10187 Planarity : 0.005 0.137 5014 Dihedral : 22.415 174.620 24989 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.87 % Rotamer: Outliers : 3.26 % Allowed : 29.93 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.98 % 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: -0.06 (0.17), residues: 2545 helix: 1.04 (0.17), residues: 968 sheet: 0.07 (0.24), residues: 456 loop : -1.02 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 201 HIS 0.009 0.001 HIS F 6 PHE 0.019 0.001 PHE W 127 TYR 0.021 0.002 TYR D 76 ARG 0.017 0.001 ARG S 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 278 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 138 SER cc_start: 0.8933 (m) cc_final: 0.8637 (p) REVERT: D 141 ASP cc_start: 0.8468 (m-30) cc_final: 0.8218 (m-30) REVERT: D 177 LYS cc_start: 0.8197 (tptp) cc_final: 0.7893 (tptp) REVERT: D 196 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8241 (p0) REVERT: E 10 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.6876 (pp20) REVERT: L 76 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7567 (mm-30) REVERT: L 77 HIS cc_start: 0.8277 (m-70) cc_final: 0.7997 (m90) REVERT: P 76 LYS cc_start: 0.9037 (ttmm) cc_final: 0.8597 (tttm) REVERT: Q 16 LYS cc_start: 0.9106 (mttm) cc_final: 0.8665 (mtpp) REVERT: Q 80 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7488 (tm-30) REVERT: T 49 LYS cc_start: 0.8452 (tppt) cc_final: 0.8167 (tppt) REVERT: G 116 MET cc_start: 0.0310 (pmm) cc_final: -0.1217 (mtm) REVERT: S 38 SER cc_start: 0.4087 (m) cc_final: 0.3865 (t) REVERT: O 65 GLU cc_start: 0.7843 (tt0) cc_final: 0.7367 (tm-30) REVERT: R 65 VAL cc_start: 0.8149 (t) cc_final: 0.7811 (m) REVERT: W 41 MET cc_start: 0.2574 (mpt) cc_final: 0.0073 (mmt) REVERT: W 59 LEU cc_start: 0.5171 (mp) cc_final: 0.4530 (mp) REVERT: W 109 ARG cc_start: 0.5655 (mmm160) cc_final: 0.4234 (ttt180) outliers start: 70 outliers final: 54 residues processed: 332 average time/residue: 1.4286 time to fit residues: 585.5200 Evaluate side-chains 325 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 269 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain O residue 21 MET Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 85 LEU Chi-restraints excluded: chain W residue 86 THR Chi-restraints excluded: chain W residue 91 ASP Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 227 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 349 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 226 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 258 optimal weight: 20.0000 chunk 389 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 chunk 310 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN F 8 ASN F 123 GLN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 HIS R 40 ASN U 20 ASN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 54643 Z= 0.263 Angle : 0.596 15.343 80791 Z= 0.304 Chirality : 0.037 0.252 10187 Planarity : 0.005 0.136 5014 Dihedral : 22.394 174.239 24989 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.93 % Favored : 95.87 % Rotamer: Outliers : 2.98 % Allowed : 30.30 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.98 % 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: 0.03 (0.17), residues: 2545 helix: 1.12 (0.17), residues: 962 sheet: 0.15 (0.24), residues: 452 loop : -0.97 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 201 HIS 0.005 0.001 HIS O 37 PHE 0.034 0.001 PHE I 127 TYR 0.025 0.001 TYR D 76 ARG 0.018 0.001 ARG U 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 273 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 138 SER cc_start: 0.8940 (m) cc_final: 0.8614 (p) REVERT: D 177 LYS cc_start: 0.8193 (tptp) cc_final: 0.7896 (tptp) REVERT: D 196 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8217 (p0) REVERT: E 10 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.6937 (pp20) REVERT: L 76 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7632 (mm-30) REVERT: L 77 HIS cc_start: 0.8219 (m-70) cc_final: 0.7917 (m90) REVERT: P 76 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8587 (tttm) REVERT: Q 16 LYS cc_start: 0.9116 (mttm) cc_final: 0.8879 (mttp) REVERT: Q 80 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7562 (tm-30) REVERT: G 116 MET cc_start: 0.0454 (pmm) cc_final: -0.0976 (mtm) REVERT: I 57 MET cc_start: 0.3668 (tpp) cc_final: 0.2837 (pmm) REVERT: S 38 SER cc_start: 0.4214 (m) cc_final: 0.4000 (t) REVERT: O 65 GLU cc_start: 0.7847 (tt0) cc_final: 0.7319 (tm-30) REVERT: R 65 VAL cc_start: 0.8169 (t) cc_final: 0.7821 (m) REVERT: W 41 MET cc_start: 0.2342 (mpt) cc_final: -0.0150 (mmt) REVERT: W 59 LEU cc_start: 0.5134 (mp) cc_final: 0.4484 (mp) REVERT: W 74 ARG cc_start: 0.7495 (tpm170) cc_final: 0.7080 (tmm160) REVERT: W 109 ARG cc_start: 0.5643 (mmm160) cc_final: 0.4205 (ttt180) REVERT: W 247 MET cc_start: 0.8062 (ppp) cc_final: 0.7636 (ppp) outliers start: 64 outliers final: 55 residues processed: 321 average time/residue: 1.4634 time to fit residues: 579.4258 Evaluate side-chains 328 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 271 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain H residue 9 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 57 ASP Chi-restraints excluded: chain Q residue 60 GLU Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 84 THR Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 50 SER Chi-restraints excluded: chain R residue 53 ARG Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 85 LEU Chi-restraints excluded: chain W residue 86 THR Chi-restraints excluded: chain W residue 110 VAL Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 168 CYS Chi-restraints excluded: chain W residue 170 VAL Chi-restraints excluded: chain W residue 227 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 190 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 330 optimal weight: 20.0000 chunk 95 optimal weight: 40.0000 chunk 286 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 310 optimal weight: 30.0000 chunk 130 optimal weight: 50.0000 chunk 319 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN F 8 ASN F 19 ASN F 123 GLN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 HIS U 20 ASN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 125 HIS ** W 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.145784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.083363 restraints weight = 104722.675| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.98 r_work: 0.2814 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 54643 Z= 0.349 Angle : 0.644 13.853 80791 Z= 0.329 Chirality : 0.040 0.261 10187 Planarity : 0.006 0.137 5014 Dihedral : 22.470 175.086 24989 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.01 % Favored : 95.80 % Rotamer: Outliers : 3.08 % Allowed : 30.63 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.98 % 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: -0.10 (0.17), residues: 2545 helix: 0.99 (0.17), residues: 961 sheet: 0.05 (0.24), residues: 449 loop : -1.00 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 201 HIS 0.006 0.001 HIS O 37 PHE 0.017 0.001 PHE W 127 TYR 0.026 0.002 TYR D 76 ARG 0.013 0.001 ARG S 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13135.40 seconds wall clock time: 230 minutes 32.21 seconds (13832.21 seconds total)