Starting phenix.real_space_refine on Tue Sep 24 06:19:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wid_37564/09_2024/8wid_37564.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wid_37564/09_2024/8wid_37564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wid_37564/09_2024/8wid_37564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wid_37564/09_2024/8wid_37564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wid_37564/09_2024/8wid_37564.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wid_37564/09_2024/8wid_37564.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1533 5.49 5 S 33 5.16 5 C 26132 2.51 5 N 9640 2.21 5 O 13970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 51308 Number of models: 1 Model: "" Number of chains: 23 Chain: "a" Number of atoms: 32521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1515, 32521 Classifications: {'RNA': 1515} Modifications used: {'rna2p_pur': 111, 'rna2p_pyr': 85, 'rna3p_pur': 739, 'rna3p_pyr': 580} Link IDs: {'rna2p': 196, 'rna3p': 1318} Chain: "b" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 382 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 15} Chain: "v" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 271 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "d" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1660 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain: "e" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1641 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "f" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1208 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 8, 'TRANS': 157} Chain: "g" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "h" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1207 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "i" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "j" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "k" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 784 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "l" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 855 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "m" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "n" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "o" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 819 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "p" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "q" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "r" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 748 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "s" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 513 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "t" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 662 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "u" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 660 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "x" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "w" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 22.18, per 1000 atoms: 0.43 Number of scatterers: 51308 At special positions: 0 Unit cell: (219.35, 206.51, 185.11, 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 33 16.00 P 1533 15.00 O 13970 8.00 N 9640 7.00 C 26132 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.56 Conformation dependent library (CDL) restraints added in 2.2 seconds 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4292 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 22 sheets defined 44.8% alpha, 20.7% beta 523 base pairs and 809 stacking pairs defined. Time for finding SS restraints: 19.94 Creating SS restraints... Processing helix chain 'v' and resid 4 through 24 Processing helix chain 'v' and resid 24 through 32 Processing helix chain 'd' and resid 6 through 11 Processing helix chain 'd' and resid 27 through 46 Processing helix chain 'd' and resid 71 through 76 removed outlier: 3.736A pdb=" N VAL d 75 " --> pdb=" O ARG d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 80 through 92 Processing helix chain 'd' and resid 107 through 110 Processing helix chain 'd' and resid 111 through 126 removed outlier: 3.690A pdb=" N ASN d 125 " --> pdb=" O GLU d 121 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG d 126 " --> pdb=" O GLN d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 128 through 142 Processing helix chain 'd' and resid 156 through 160 Processing helix chain 'e' and resid 8 through 16 removed outlier: 3.547A pdb=" N SER e 12 " --> pdb=" O ALA e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 29 removed outlier: 3.796A pdb=" N GLU e 27 " --> pdb=" O ASP e 23 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 60 removed outlier: 3.622A pdb=" N TYR e 60 " --> pdb=" O ALA e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 77 Processing helix chain 'e' and resid 80 through 91 Processing helix chain 'e' and resid 92 through 100 Processing helix chain 'e' and resid 105 through 115 Processing helix chain 'e' and resid 142 through 145 Processing helix chain 'e' and resid 147 through 155 Processing helix chain 'e' and resid 182 through 187 removed outlier: 4.510A pdb=" N ASP e 187 " --> pdb=" O ARG e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 200 removed outlier: 3.969A pdb=" N ILE e 195 " --> pdb=" O THR e 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 80 through 95 Processing helix chain 'f' and resid 133 through 144 Processing helix chain 'f' and resid 157 through 171 Processing helix chain 'f' and resid 174 through 183 Processing helix chain 'f' and resid 185 through 190 Processing helix chain 'f' and resid 191 through 200 Processing helix chain 'g' and resid 15 through 17 No H-bonds generated for 'chain 'g' and resid 15 through 17' Processing helix chain 'g' and resid 18 through 35 removed outlier: 4.731A pdb=" N VAL g 29 " --> pdb=" O THR g 25 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE g 30 " --> pdb=" O PHE g 26 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY g 34 " --> pdb=" O ILE g 30 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY g 35 " --> pdb=" O ARG g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 82 Processing helix chain 'h' and resid 20 through 31 removed outlier: 3.947A pdb=" N THR h 24 " --> pdb=" O SER h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 55 Processing helix chain 'h' and resid 57 through 70 removed outlier: 3.829A pdb=" N THR h 61 " --> pdb=" O ASP h 57 " (cutoff:3.500A) Processing helix chain 'h' and resid 92 through 110 Processing helix chain 'h' and resid 115 through 129 Processing helix chain 'h' and resid 132 through 148 Processing helix chain 'h' and resid 149 through 154 removed outlier: 4.423A pdb=" N HIS h 153 " --> pdb=" O ALA h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 20 Processing helix chain 'i' and resid 30 through 43 Processing helix chain 'i' and resid 97 through 101 Processing helix chain 'i' and resid 115 through 122 Processing helix chain 'j' and resid 61 through 76 Proline residue: j 71 - end of helix Processing helix chain 'j' and resid 91 through 111 Processing helix chain 'j' and resid 114 through 121 removed outlier: 3.555A pdb=" N ALA j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 14 through 32 Processing helix chain 'k' and resid 80 through 88 Processing helix chain 'l' and resid 57 through 60 removed outlier: 3.764A pdb=" N GLY l 60 " --> pdb=" O GLY l 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 57 through 60' Processing helix chain 'l' and resid 62 through 67 Processing helix chain 'l' and resid 68 through 85 Processing helix chain 'l' and resid 101 through 112 Processing helix chain 'm' and resid 3 through 11 Processing helix chain 'm' and resid 113 through 117 Processing helix chain 'n' and resid 14 through 21 removed outlier: 3.809A pdb=" N TYR n 21 " --> pdb=" O ILE n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 27 through 38 Processing helix chain 'n' and resid 44 through 48 removed outlier: 3.973A pdb=" N LEU n 48 " --> pdb=" O THR n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 64 Processing helix chain 'n' and resid 67 through 84 Processing helix chain 'n' and resid 86 through 94 Processing helix chain 'n' and resid 107 through 112 Processing helix chain 'o' and resid 3 through 21 removed outlier: 3.516A pdb=" N GLU o 11 " --> pdb=" O ILE o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 33 removed outlier: 3.787A pdb=" N LYS o 28 " --> pdb=" O ARG o 24 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG o 29 " --> pdb=" O ALA o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 38 through 43 removed outlier: 3.735A pdb=" N ALA o 42 " --> pdb=" O PRO o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 43 through 51 removed outlier: 3.606A pdb=" N LEU o 51 " --> pdb=" O ALA o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 60 Proline residue: o 57 - end of helix Processing helix chain 'o' and resid 81 through 90 Processing helix chain 'p' and resid 4 through 16 Processing helix chain 'p' and resid 24 through 44 Processing helix chain 'p' and resid 49 through 74 Processing helix chain 'p' and resid 74 through 86 Processing helix chain 'q' and resid 52 through 63 Processing helix chain 'q' and resid 67 through 78 Processing helix chain 'q' and resid 78 through 85 Processing helix chain 'q' and resid 101 through 114 Processing helix chain 's' and resid 35 through 40 Processing helix chain 's' and resid 50 through 55 Processing helix chain 's' and resid 57 through 74 Processing helix chain 't' and resid 12 through 24 Processing helix chain 't' and resid 41 through 45 removed outlier: 3.991A pdb=" N ILE t 45 " --> pdb=" O PRO t 42 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 75 Processing helix chain 'u' and resid 4 through 42 Processing helix chain 'u' and resid 43 through 64 removed outlier: 3.893A pdb=" N ALA u 47 " --> pdb=" O ASP u 43 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 86 Processing helix chain 'x' and resid 57 through 65 Processing helix chain 'w' and resid 13 through 24 removed outlier: 3.797A pdb=" N ARG w 24 " --> pdb=" O GLU w 20 " (cutoff:3.500A) Processing helix chain 'w' and resid 73 through 93 Processing helix chain 'w' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'd' and resid 20 through 21 removed outlier: 3.521A pdb=" N ARG d 58 " --> pdb=" O ARG d 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP d 53 " --> pdb=" O HIS d 68 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL d 63 " --> pdb=" O GLN d 99 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ASN d 101 " --> pdb=" O VAL d 63 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL d 65 " --> pdb=" O ASN d 101 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU d 103 " --> pdb=" O VAL d 65 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE d 67 " --> pdb=" O LEU d 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 164 through 171 removed outlier: 3.581A pdb=" N GLU d 166 " --> pdb=" O CYS d 153 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS d 204 " --> pdb=" O ASP d 181 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASP d 181 " --> pdb=" O LYS d 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'f' and resid 37 through 49 removed outlier: 5.493A pdb=" N GLU f 38 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLY f 65 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL f 40 " --> pdb=" O ILE f 63 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE f 63 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER f 42 " --> pdb=" O LEU f 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 101 through 102 Processing sheet with id=AA6, first strand: chain 'f' and resid 110 through 114 removed outlier: 6.153A pdb=" N ILE f 131 " --> pdb=" O ALA f 150 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER f 152 " --> pdb=" O ILE f 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'g' and resid 37 through 47 removed outlier: 3.924A pdb=" N VAL g 37 " --> pdb=" O LYS g 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP g 64 " --> pdb=" O LYS g 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR g 60 " --> pdb=" O TRP g 43 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY g 58 " --> pdb=" O ARG g 45 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 73 through 79 Processing sheet with id=AA9, first strand: chain 'i' and resid 24 through 28 removed outlier: 3.738A pdb=" N ASP i 48 " --> pdb=" O GLN i 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'i' and resid 76 through 79 Processing sheet with id=AB2, first strand: chain 'i' and resid 76 through 79 removed outlier: 6.032A pdb=" N VAL i 127 " --> pdb=" O SER i 107 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER i 107 " --> pdb=" O VAL i 127 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA i 129 " --> pdb=" O ILE i 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'j' and resid 27 through 32 removed outlier: 3.556A pdb=" N THR j 28 " --> pdb=" O VAL j 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.092A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS k 11 " --> pdb=" O ASP k 97 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.092A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'l' and resid 49 through 55 removed outlier: 7.026A pdb=" N ILE l 43 " --> pdb=" O ILE l 51 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TRP l 53 " --> pdb=" O VAL l 41 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL l 41 " --> pdb=" O TRP l 53 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER l 55 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR l 39 " --> pdb=" O SER l 55 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL l 91 " --> pdb=" O GLY l 117 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE l 119 " --> pdb=" O VAL l 91 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL l 93 " --> pdb=" O ILE l 119 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP l 121 " --> pdb=" O VAL l 93 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL l 95 " --> pdb=" O ASP l 121 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'm' and resid 29 through 40 removed outlier: 6.527A pdb=" N ARG m 54 " --> pdb=" O THR m 35 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL m 37 " --> pdb=" O VAL m 52 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL m 52 " --> pdb=" O VAL m 37 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR m 39 " --> pdb=" O ARG m 50 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG m 50 " --> pdb=" O THR m 39 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N TYR m 95 " --> pdb=" O GLU m 62 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR m 64 " --> pdb=" O TYR m 95 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ILE m 97 " --> pdb=" O THR m 64 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR m 66 " --> pdb=" O ILE m 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'n' and resid 3 through 4 Processing sheet with id=AB9, first strand: chain 'o' and resid 73 through 74 removed outlier: 3.580A pdb=" N LEU o 79 " --> pdb=" O LEU o 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'q' and resid 49 through 51 removed outlier: 5.956A pdb=" N VAL q 36 " --> pdb=" O VAL q 22 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL q 22 " --> pdb=" O VAL q 36 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY q 38 " --> pdb=" O ILE q 20 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL q 3 " --> pdb=" O GLN q 65 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'r' and resid 22 through 32 removed outlier: 16.057A pdb=" N THR r 22 " --> pdb=" O ARG r 43 " (cutoff:3.500A) removed outlier: 12.316A pdb=" N ARG r 43 " --> pdb=" O THR r 22 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE r 24 " --> pdb=" O GLU r 41 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU r 41 " --> pdb=" O ILE r 24 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL r 37 " --> pdb=" O VAL r 28 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASP r 30 " --> pdb=" O THR r 35 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR r 35 " --> pdb=" O ASP r 30 " (cutoff:3.500A) removed outlier: 16.370A pdb=" N LYS r 86 " --> pdb=" O THR r 56 " (cutoff:3.500A) removed outlier: 13.567A pdb=" N LYS r 58 " --> pdb=" O LYS r 86 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N TRP r 88 " --> pdb=" O LYS r 58 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS r 60 " --> pdb=" O TRP r 88 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU r 90 " --> pdb=" O LYS r 60 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS r 62 " --> pdb=" O LEU r 90 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N GLU r 92 " --> pdb=" O HIS r 62 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ARG r 87 " --> pdb=" O THR r 79 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER r 75 " --> pdb=" O VAL r 91 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE r 93 " --> pdb=" O ARG r 73 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG r 73 " --> pdb=" O ILE r 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 't' and resid 31 through 32 removed outlier: 6.869A pdb=" N ILE t 31 " --> pdb=" O ALA t 50 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N HIS t 52 " --> pdb=" O ILE t 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'w' and resid 4 through 6 removed outlier: 3.545A pdb=" N LEU w 40 " --> pdb=" O SER w 6 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP w 59 " --> pdb=" O LEU w 34 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA w 36 " --> pdb=" O ASN w 57 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN w 57 " --> pdb=" O ALA w 36 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL w 38 " --> pdb=" O GLN w 55 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN w 55 " --> pdb=" O VAL w 38 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU w 40 " --> pdb=" O ILE w 53 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE w 53 " --> pdb=" O LEU w 40 " (cutoff:3.500A) 930 hydrogen bonds defined for protein. 2643 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1334 hydrogen bonds 2066 hydrogen bond angles 0 basepair planarities 523 basepair parallelities 809 stacking parallelities Total time for adding SS restraints: 41.94 Time building geometry restraints manager: 10.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8844 1.33 - 1.45: 22069 1.45 - 1.58: 21473 1.58 - 1.70: 3065 1.70 - 1.82: 57 Bond restraints: 55508 Sorted by residual: bond pdb=" C ASP o 33 " pdb=" N PRO o 34 " ideal model delta sigma weight residual 1.335 1.351 -0.016 8.70e-03 1.32e+04 3.48e+00 bond pdb=" CG1 ILE n 17 " pdb=" CD1 ILE n 17 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.23e+00 bond pdb=" CA ASP e 126 " pdb=" CB ASP e 126 " ideal model delta sigma weight residual 1.531 1.582 -0.052 3.12e-02 1.03e+03 2.73e+00 bond pdb=" CB ASP s 34 " pdb=" CG ASP s 34 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.71e+00 bond pdb=" CB ASP g 15 " pdb=" CG ASP g 15 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.50e+00 ... (remaining 55503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 82007 2.85 - 5.70: 514 5.70 - 8.55: 42 8.55 - 11.40: 3 11.40 - 14.25: 1 Bond angle restraints: 82567 Sorted by residual: angle pdb=" CB MET k 88 " pdb=" CG MET k 88 " pdb=" SD MET k 88 " ideal model delta sigma weight residual 112.70 126.95 -14.25 3.00e+00 1.11e-01 2.26e+01 angle pdb=" C SER u 48 " pdb=" N GLU u 49 " pdb=" CA GLU u 49 " ideal model delta sigma weight residual 121.14 114.11 7.03 1.75e+00 3.27e-01 1.61e+01 angle pdb=" C3' C a1149 " pdb=" O3' C a1149 " pdb=" P A a1150 " ideal model delta sigma weight residual 120.20 126.08 -5.88 1.50e+00 4.44e-01 1.54e+01 angle pdb=" CB MET d 162 " pdb=" CG MET d 162 " pdb=" SD MET d 162 " ideal model delta sigma weight residual 112.70 123.67 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA ILE j 26 " pdb=" CB ILE j 26 " pdb=" CG1 ILE j 26 " ideal model delta sigma weight residual 110.40 116.60 -6.20 1.70e+00 3.46e-01 1.33e+01 ... (remaining 82562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 31462 35.87 - 71.74: 3959 71.74 - 107.60: 432 107.60 - 143.47: 17 143.47 - 179.34: 21 Dihedral angle restraints: 35891 sinusoidal: 29232 harmonic: 6659 Sorted by residual: dihedral pdb=" O4' U a1303 " pdb=" C1' U a1303 " pdb=" N1 U a1303 " pdb=" C2 U a1303 " ideal model delta sinusoidal sigma weight residual 200.00 38.10 161.90 1 1.50e+01 4.44e-03 8.32e+01 dihedral pdb=" O4' U a 200 " pdb=" C1' U a 200 " pdb=" N1 U a 200 " pdb=" C2 U a 200 " ideal model delta sinusoidal sigma weight residual 200.00 39.54 160.46 1 1.50e+01 4.44e-03 8.29e+01 dihedral pdb=" O4' C a 415 " pdb=" C1' C a 415 " pdb=" N1 C a 415 " pdb=" C2 C a 415 " ideal model delta sinusoidal sigma weight residual -160.00 -2.12 -157.88 1 1.50e+01 4.44e-03 8.22e+01 ... (remaining 35888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 9311 0.052 - 0.105: 933 0.105 - 0.157: 171 0.157 - 0.209: 31 0.209 - 0.262: 9 Chirality restraints: 10455 Sorted by residual: chirality pdb=" C3' U a1482 " pdb=" C4' U a1482 " pdb=" O3' U a1482 " pdb=" C2' U a1482 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CG LEU i 27 " pdb=" CB LEU i 27 " pdb=" CD1 LEU i 27 " pdb=" CD2 LEU i 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1' C a1109 " pdb=" O4' C a1109 " pdb=" C2' C a1109 " pdb=" N1 C a1109 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 10452 not shown) Planarity restraints: 4800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP t 34 " 0.025 2.00e-02 2.50e+03 3.14e-02 2.46e+01 pdb=" CG TRP t 34 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP t 34 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP t 34 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP t 34 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP t 34 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP t 34 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP t 34 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP t 34 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP t 34 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG j 115 " -0.068 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO j 116 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO j 116 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO j 116 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A a 940 " 0.034 2.00e-02 2.50e+03 1.60e-02 7.07e+00 pdb=" N9 A a 940 " -0.039 2.00e-02 2.50e+03 pdb=" C8 A a 940 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A a 940 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A a 940 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A a 940 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A a 940 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A a 940 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A a 940 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A a 940 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A a 940 " -0.005 2.00e-02 2.50e+03 ... (remaining 4797 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 2570 2.67 - 3.23: 44889 3.23 - 3.78: 102475 3.78 - 4.34: 134180 4.34 - 4.90: 183441 Nonbonded interactions: 467555 Sorted by model distance: nonbonded pdb=" O2' A a 728 " pdb=" N7 A a 729 " model vdw 2.111 3.120 nonbonded pdb=" O2' U a 438 " pdb=" O2 U a 439 " model vdw 2.112 3.040 nonbonded pdb=" OP2 U a1265 " pdb=" O2' U a1266 " model vdw 2.171 3.040 nonbonded pdb=" O2' A a 92 " pdb=" O5' C a 93 " model vdw 2.186 3.040 nonbonded pdb=" OP2 U a 943 " pdb=" O2' C a1204 " model vdw 2.197 3.040 ... (remaining 467550 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.480 Check model and map are aligned: 0.290 Set scattering table: 0.360 Process input model: 118.840 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.180 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: 0.030 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 55508 Z= 0.221 Angle : 0.591 14.246 82567 Z= 0.309 Chirality : 0.035 0.262 10455 Planarity : 0.005 0.100 4800 Dihedral : 23.776 179.339 31599 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 0.78 % Allowed : 33.04 % Favored : 66.18 % 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: 0.66 (0.18), residues: 2284 helix: 1.60 (0.17), residues: 920 sheet: 0.26 (0.26), residues: 423 loop : -0.60 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP t 34 HIS 0.013 0.001 HIS k 15 PHE 0.028 0.002 PHE w 124 TYR 0.014 0.001 TYR d 168 ARG 0.026 0.001 ARG k 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 249 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 12 MET cc_start: 0.8998 (tpt) cc_final: 0.8752 (tpt) REVERT: d 92 LYS cc_start: 0.9345 (mmmm) cc_final: 0.8976 (tptp) REVERT: j 82 ASP cc_start: 0.7791 (m-30) cc_final: 0.7426 (t0) REVERT: k 24 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8194 (ttpt) REVERT: k 88 MET cc_start: 0.8555 (mpp) cc_final: 0.8202 (mpp) REVERT: o 10 ASN cc_start: 0.8786 (t0) cc_final: 0.8585 (t0) REVERT: o 11 GLU cc_start: 0.9074 (mp0) cc_final: 0.8807 (mm-30) REVERT: o 15 GLU cc_start: 0.8714 (pp20) cc_final: 0.8423 (pp20) REVERT: p 14 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7787 (pp30) REVERT: q 52 ASP cc_start: 0.8326 (t0) cc_final: 0.7526 (t0) REVERT: t 13 ASP cc_start: 0.7631 (p0) cc_final: 0.7318 (p0) REVERT: t 25 LYS cc_start: 0.8217 (pmtt) cc_final: 0.7722 (pmtt) outliers start: 15 outliers final: 5 residues processed: 254 average time/residue: 0.5107 time to fit residues: 222.3447 Evaluate side-chains 225 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 219 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain j residue 88 ASP Chi-restraints excluded: chain j residue 108 ILE Chi-restraints excluded: chain k residue 24 LYS Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain t residue 56 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 8.9990 chunk 284 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 341 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 51 GLN ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 GLN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 47 GLN l 84 GLN l 128 ASN ** m 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 49 GLN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 55508 Z= 0.289 Angle : 0.588 8.209 82567 Z= 0.306 Chirality : 0.036 0.273 10455 Planarity : 0.005 0.064 4800 Dihedral : 23.798 179.719 26897 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 3.88 % Allowed : 27.25 % Favored : 68.87 % 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: 0.77 (0.18), residues: 2284 helix: 1.73 (0.17), residues: 942 sheet: 0.28 (0.26), residues: 423 loop : -0.62 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP t 34 HIS 0.006 0.001 HIS w 30 PHE 0.012 0.002 PHE e 150 TYR 0.021 0.001 TYR x 65 ARG 0.009 0.001 ARG s 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 231 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 12 MET cc_start: 0.8993 (tpt) cc_final: 0.8772 (tpt) REVERT: d 99 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7464 (pp30) REVERT: f 91 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8370 (tm-30) REVERT: h 12 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8047 (pp) REVERT: j 58 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7661 (t80) REVERT: j 66 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8626 (tm-30) REVERT: j 82 ASP cc_start: 0.8017 (m-30) cc_final: 0.7369 (t0) REVERT: j 150 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7349 (ptm160) REVERT: k 88 MET cc_start: 0.8508 (mpp) cc_final: 0.8267 (mmm) REVERT: l 45 ASP cc_start: 0.8643 (t0) cc_final: 0.8125 (p0) REVERT: n 43 MET cc_start: 0.8447 (tmm) cc_final: 0.8205 (ppp) REVERT: o 60 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8550 (mm) REVERT: p 14 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8143 (tm-30) REVERT: p 19 ASP cc_start: 0.8120 (p0) cc_final: 0.7791 (p0) REVERT: r 14 GLU cc_start: 0.8545 (tp30) cc_final: 0.8150 (tm-30) REVERT: s 18 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7527 (pmm-80) REVERT: t 25 LYS cc_start: 0.8367 (pmtt) cc_final: 0.7980 (pttt) REVERT: t 27 THR cc_start: 0.7125 (t) cc_final: 0.6800 (t) REVERT: t 32 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8425 (tmtp) REVERT: t 45 ILE cc_start: 0.9091 (mm) cc_final: 0.8871 (mm) REVERT: x 65 TYR cc_start: 0.8609 (m-80) cc_final: 0.8323 (m-80) outliers start: 75 outliers final: 24 residues processed: 293 average time/residue: 0.5216 time to fit residues: 256.7696 Evaluate side-chains 243 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 212 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 99 GLN Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 134 ARG Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain f residue 152 SER Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 150 ARG Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain l residue 73 GLN Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 60 LEU Chi-restraints excluded: chain s residue 18 ARG Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 30 VAL Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 63 SER Chi-restraints excluded: chain u residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 342 optimal weight: 10.0000 chunk 369 optimal weight: 10.0000 chunk 304 optimal weight: 9.9990 chunk 339 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 274 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 63 GLN l 24 ASN l 128 ASN o 49 GLN p 18 HIS u 7 GLN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 55508 Z= 0.412 Angle : 0.651 8.017 82567 Z= 0.337 Chirality : 0.040 0.304 10455 Planarity : 0.005 0.060 4800 Dihedral : 23.767 179.292 26882 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 4.81 % Allowed : 26.68 % Favored : 68.51 % 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: 0.58 (0.18), residues: 2284 helix: 1.58 (0.17), residues: 949 sheet: 0.17 (0.26), residues: 421 loop : -0.74 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP t 34 HIS 0.006 0.001 HIS w 30 PHE 0.017 0.002 PHE e 150 TYR 0.023 0.002 TYR d 168 ARG 0.006 0.001 ARG k 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 220 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 15 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9099 (tttm) REVERT: d 99 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7187 (pp30) REVERT: f 63 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8469 (mm) REVERT: f 91 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8434 (tm-30) REVERT: f 141 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8552 (mt-10) REVERT: h 144 MET cc_start: 0.7909 (tpp) cc_final: 0.7621 (tpp) REVERT: j 58 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.7646 (t80) REVERT: j 66 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8600 (tm-30) REVERT: j 82 ASP cc_start: 0.8034 (m-30) cc_final: 0.7422 (t0) REVERT: k 72 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7412 (mmt90) REVERT: m 35 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8496 (p) REVERT: n 15 MET cc_start: 0.8667 (mmm) cc_final: 0.8356 (tpp) REVERT: n 39 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8873 (mt) REVERT: n 43 MET cc_start: 0.8472 (tmm) cc_final: 0.7987 (tmm) REVERT: n 65 LYS cc_start: 0.8792 (ptmm) cc_final: 0.8574 (ptpp) REVERT: n 102 ARG cc_start: 0.9432 (OUTLIER) cc_final: 0.8124 (ttm-80) REVERT: o 15 GLU cc_start: 0.8447 (pp20) cc_final: 0.8235 (pp20) REVERT: o 16 LEU cc_start: 0.8744 (tp) cc_final: 0.8530 (tp) REVERT: p 19 ASP cc_start: 0.8257 (p0) cc_final: 0.7909 (p0) REVERT: q 52 ASP cc_start: 0.8221 (t0) cc_final: 0.7945 (t0) REVERT: q 98 PRO cc_start: 0.8327 (Cg_exo) cc_final: 0.8126 (Cg_endo) REVERT: s 18 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7804 (pmm-80) REVERT: t 24 GLU cc_start: 0.8659 (pp20) cc_final: 0.8446 (pp20) REVERT: u 45 ASP cc_start: 0.8169 (p0) cc_final: 0.7813 (p0) REVERT: w 123 TYR cc_start: 0.3882 (OUTLIER) cc_final: 0.3100 (t80) outliers start: 93 outliers final: 46 residues processed: 291 average time/residue: 0.5281 time to fit residues: 259.7683 Evaluate side-chains 261 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 205 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 15 LYS Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 99 GLN Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 172 ARG Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 30 SER Chi-restraints excluded: chain i residue 48 ASP Chi-restraints excluded: chain i residue 51 THR Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain j residue 26 ILE Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 150 ARG Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 28 THR Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 67 MET Chi-restraints excluded: chain k residue 72 ARG Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 73 GLN Chi-restraints excluded: chain m residue 35 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 39 ILE Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 23 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 18 ARG Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 43 ASP Chi-restraints excluded: chain u residue 63 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 123 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 343 optimal weight: 3.9990 chunk 363 optimal weight: 9.9990 chunk 179 optimal weight: 0.4980 chunk 325 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 185 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 24 ASN l 128 ASN o 49 GLN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 55508 Z= 0.260 Angle : 0.575 8.063 82567 Z= 0.299 Chirality : 0.036 0.267 10455 Planarity : 0.004 0.062 4800 Dihedral : 23.762 178.820 26882 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.14 % Allowed : 26.53 % Favored : 69.34 % 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: 0.78 (0.18), residues: 2284 helix: 1.79 (0.17), residues: 949 sheet: 0.18 (0.26), residues: 425 loop : -0.65 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP t 34 HIS 0.005 0.001 HIS w 30 PHE 0.012 0.001 PHE e 150 TYR 0.016 0.001 TYR d 168 ARG 0.005 0.000 ARG g 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 222 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 12 MET cc_start: 0.9035 (tpt) cc_final: 0.8781 (tpt) REVERT: d 99 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.6769 (pp30) REVERT: d 101 ASN cc_start: 0.7763 (m-40) cc_final: 0.7459 (m-40) REVERT: f 63 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8450 (mm) REVERT: f 91 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8161 (tm-30) REVERT: h 144 MET cc_start: 0.8023 (tpp) cc_final: 0.7729 (tpp) REVERT: j 58 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7703 (t80) REVERT: j 66 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8565 (tm-30) REVERT: j 82 ASP cc_start: 0.8024 (m-30) cc_final: 0.7356 (t0) REVERT: n 15 MET cc_start: 0.8727 (mmm) cc_final: 0.8422 (tpp) REVERT: n 39 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8852 (mt) REVERT: n 43 MET cc_start: 0.8543 (tmm) cc_final: 0.7980 (tmm) REVERT: n 65 LYS cc_start: 0.8748 (ptmm) cc_final: 0.8473 (ptpp) REVERT: n 102 ARG cc_start: 0.9333 (OUTLIER) cc_final: 0.8401 (ttm-80) REVERT: o 15 GLU cc_start: 0.8475 (pp20) cc_final: 0.8237 (pp20) REVERT: p 19 ASP cc_start: 0.8283 (p0) cc_final: 0.7937 (p0) REVERT: p 20 THR cc_start: 0.9176 (m) cc_final: 0.8975 (p) REVERT: s 18 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7820 (pmm-80) REVERT: t 32 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8722 (tmtp) REVERT: w 123 TYR cc_start: 0.4024 (OUTLIER) cc_final: 0.3217 (t80) outliers start: 80 outliers final: 35 residues processed: 288 average time/residue: 0.5123 time to fit residues: 250.3164 Evaluate side-chains 249 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 206 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 99 GLN Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain e residue 172 ARG Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 162 VAL Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 30 SER Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 93 ASN Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 66 GLU Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 73 GLN Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 39 ILE Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 18 ARG Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 63 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 123 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 270 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 chunk 251 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 326 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 167 GLN ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 128 ASN o 49 GLN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 55508 Z= 0.256 Angle : 0.566 7.978 82567 Z= 0.294 Chirality : 0.035 0.269 10455 Planarity : 0.004 0.061 4800 Dihedral : 23.724 178.570 26882 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.57 % Allowed : 26.58 % Favored : 69.86 % 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: 0.81 (0.18), residues: 2284 helix: 1.85 (0.17), residues: 949 sheet: 0.15 (0.26), residues: 428 loop : -0.64 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP t 34 HIS 0.005 0.001 HIS w 30 PHE 0.027 0.001 PHE x 61 TYR 0.017 0.001 TYR d 168 ARG 0.004 0.000 ARG l 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 212 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 99 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6765 (pp30) REVERT: d 101 ASN cc_start: 0.7827 (m-40) cc_final: 0.7555 (m-40) REVERT: f 63 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8445 (mm) REVERT: f 91 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8412 (tm-30) REVERT: g 68 GLU cc_start: 0.7934 (mp0) cc_final: 0.7555 (mp0) REVERT: h 144 MET cc_start: 0.8048 (tpp) cc_final: 0.7773 (tpp) REVERT: j 58 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7552 (t80) REVERT: j 66 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8488 (tm-30) REVERT: j 82 ASP cc_start: 0.8008 (m-30) cc_final: 0.7395 (t0) REVERT: n 15 MET cc_start: 0.8703 (mmm) cc_final: 0.8403 (tpp) REVERT: n 43 MET cc_start: 0.8646 (tmm) cc_final: 0.8066 (tmm) REVERT: n 102 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.8316 (ttm-80) REVERT: o 15 GLU cc_start: 0.8599 (pp20) cc_final: 0.8285 (pp20) REVERT: p 19 ASP cc_start: 0.8331 (p0) cc_final: 0.7997 (p0) REVERT: p 20 THR cc_start: 0.9190 (m) cc_final: 0.8958 (p) REVERT: p 83 GLU cc_start: 0.7769 (mp0) cc_final: 0.7551 (mp0) REVERT: s 18 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7827 (pmm-80) REVERT: t 32 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8468 (tmtp) REVERT: u 45 ASP cc_start: 0.8238 (p0) cc_final: 0.7955 (p0) REVERT: w 123 TYR cc_start: 0.4040 (OUTLIER) cc_final: 0.3327 (t80) outliers start: 69 outliers final: 38 residues processed: 268 average time/residue: 0.5202 time to fit residues: 238.9442 Evaluate side-chains 250 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 205 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 99 GLN Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 162 VAL Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 30 SER Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 93 ASN Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 24 LYS Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 73 GLN Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 79 MET Chi-restraints excluded: chain m residue 105 GLN Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 18 ARG Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 57 LYS Chi-restraints excluded: chain u residue 63 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 123 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 10.0000 chunk 327 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 213 optimal weight: 0.0970 chunk 89 optimal weight: 10.0000 chunk 363 optimal weight: 10.0000 chunk 301 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 24 ASN l 128 ASN o 49 GLN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 55508 Z= 0.207 Angle : 0.552 9.861 82567 Z= 0.286 Chirality : 0.034 0.257 10455 Planarity : 0.004 0.061 4800 Dihedral : 23.725 178.610 26882 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.72 % Allowed : 26.99 % Favored : 69.29 % 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: 0.87 (0.18), residues: 2284 helix: 1.92 (0.17), residues: 949 sheet: 0.15 (0.26), residues: 428 loop : -0.63 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP t 34 HIS 0.005 0.001 HIS w 30 PHE 0.020 0.001 PHE x 61 TYR 0.015 0.001 TYR d 168 ARG 0.005 0.000 ARG o 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 215 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 99 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6708 (pp30) REVERT: d 101 ASN cc_start: 0.7937 (m-40) cc_final: 0.7711 (m-40) REVERT: f 63 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8418 (mm) REVERT: f 91 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8395 (tm-30) REVERT: h 144 MET cc_start: 0.8008 (tpp) cc_final: 0.7748 (tpp) REVERT: j 33 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8072 (ptmt) REVERT: j 58 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7498 (t80) REVERT: j 66 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8513 (tm-30) REVERT: j 82 ASP cc_start: 0.8003 (m-30) cc_final: 0.7361 (t0) REVERT: n 15 MET cc_start: 0.8706 (mmm) cc_final: 0.8438 (tpp) REVERT: n 43 MET cc_start: 0.8617 (tmm) cc_final: 0.8160 (tmm) REVERT: n 102 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8372 (ttm-80) REVERT: o 15 GLU cc_start: 0.8615 (pp20) cc_final: 0.8337 (pp20) REVERT: p 19 ASP cc_start: 0.8368 (p0) cc_final: 0.8031 (p0) REVERT: p 20 THR cc_start: 0.9173 (m) cc_final: 0.8941 (p) REVERT: p 83 GLU cc_start: 0.7736 (mp0) cc_final: 0.7506 (mp0) REVERT: r 39 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7896 (tp30) REVERT: s 18 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7872 (pmm-80) REVERT: t 6 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8233 (pttt) REVERT: t 28 LYS cc_start: 0.8609 (mttp) cc_final: 0.8316 (mttt) REVERT: t 32 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8570 (tmtp) REVERT: u 45 ASP cc_start: 0.8120 (p0) cc_final: 0.7853 (p0) REVERT: w 123 TYR cc_start: 0.4112 (OUTLIER) cc_final: 0.3428 (t80) outliers start: 72 outliers final: 37 residues processed: 276 average time/residue: 0.4997 time to fit residues: 234.6355 Evaluate side-chains 250 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 203 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 99 GLN Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain e residue 172 ARG Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 113 GLU Chi-restraints excluded: chain f residue 162 VAL Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 30 SER Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 24 LYS Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 79 MET Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 39 GLU Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 18 ARG Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 57 LYS Chi-restraints excluded: chain u residue 63 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 123 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 265 optimal weight: 7.9990 chunk 205 optimal weight: 20.0000 chunk 306 optimal weight: 0.0770 chunk 203 optimal weight: 5.9990 chunk 362 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 128 ASN o 49 GLN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 55508 Z= 0.295 Angle : 0.584 10.951 82567 Z= 0.302 Chirality : 0.036 0.279 10455 Planarity : 0.004 0.059 4800 Dihedral : 23.687 178.519 26882 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.72 % Allowed : 27.20 % Favored : 69.08 % 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: 0.81 (0.18), residues: 2284 helix: 1.90 (0.17), residues: 948 sheet: 0.08 (0.26), residues: 428 loop : -0.67 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP t 34 HIS 0.005 0.001 HIS w 30 PHE 0.019 0.001 PHE x 61 TYR 0.017 0.001 TYR d 168 ARG 0.006 0.000 ARG l 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 210 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 99 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6481 (pp30) REVERT: d 101 ASN cc_start: 0.7906 (m-40) cc_final: 0.7677 (m-40) REVERT: f 63 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8423 (mm) REVERT: f 91 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: h 144 MET cc_start: 0.8035 (tpp) cc_final: 0.7774 (tpp) REVERT: j 33 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8133 (ptmt) REVERT: j 58 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.7614 (t80) REVERT: j 66 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8493 (tm-30) REVERT: j 82 ASP cc_start: 0.7978 (m-30) cc_final: 0.7361 (t0) REVERT: l 45 ASP cc_start: 0.8592 (t0) cc_final: 0.8035 (p0) REVERT: n 15 MET cc_start: 0.8743 (mmm) cc_final: 0.8409 (tpp) REVERT: n 43 MET cc_start: 0.8646 (tmm) cc_final: 0.8058 (tmm) REVERT: n 102 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.8323 (ttm-80) REVERT: o 15 GLU cc_start: 0.8641 (pp20) cc_final: 0.8350 (pp20) REVERT: p 19 ASP cc_start: 0.8382 (p0) cc_final: 0.8074 (p0) REVERT: p 20 THR cc_start: 0.9199 (m) cc_final: 0.8990 (p) REVERT: p 83 GLU cc_start: 0.7788 (mp0) cc_final: 0.7566 (mp0) REVERT: r 39 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7939 (tp30) REVERT: s 18 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7834 (pmm-80) REVERT: t 6 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8239 (pttt) REVERT: t 32 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8591 (tmtp) REVERT: t 73 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: u 45 ASP cc_start: 0.8131 (p0) cc_final: 0.7901 (p0) REVERT: w 123 TYR cc_start: 0.3771 (OUTLIER) cc_final: 0.3409 (t80) outliers start: 72 outliers final: 48 residues processed: 271 average time/residue: 0.4967 time to fit residues: 230.4183 Evaluate side-chains 263 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 203 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 99 GLN Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 172 ARG Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 91 GLU Chi-restraints excluded: chain f residue 97 PHE Chi-restraints excluded: chain f residue 113 GLU Chi-restraints excluded: chain f residue 162 VAL Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 57 ASP Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 30 SER Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 93 ASN Chi-restraints excluded: chain j residue 33 LYS Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 24 LYS Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 73 GLN Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 79 MET Chi-restraints excluded: chain m residue 107 VAL Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 39 GLU Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 18 ARG Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 63 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 123 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 284 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 61 ASN l 24 ASN l 128 ASN o 49 GLN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 84 ASN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 55508 Z= 0.406 Angle : 0.648 10.650 82567 Z= 0.334 Chirality : 0.039 0.302 10455 Planarity : 0.005 0.057 4800 Dihedral : 23.704 179.041 26882 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.72 % Allowed : 27.61 % Favored : 68.67 % 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: 0.64 (0.18), residues: 2284 helix: 1.76 (0.17), residues: 948 sheet: -0.07 (0.26), residues: 430 loop : -0.72 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP t 34 HIS 0.005 0.001 HIS w 30 PHE 0.019 0.002 PHE x 61 TYR 0.019 0.002 TYR d 168 ARG 0.011 0.000 ARG n 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 207 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 99 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6470 (pp30) REVERT: d 101 ASN cc_start: 0.7768 (m-40) cc_final: 0.7325 (m-40) REVERT: f 63 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8467 (mm) REVERT: h 144 MET cc_start: 0.8079 (tpp) cc_final: 0.7776 (tpt) REVERT: j 58 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7583 (t80) REVERT: j 66 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8483 (tm-30) REVERT: j 82 ASP cc_start: 0.8024 (m-30) cc_final: 0.7436 (t0) REVERT: n 15 MET cc_start: 0.8764 (mmm) cc_final: 0.8366 (tpp) REVERT: n 43 MET cc_start: 0.8699 (tmm) cc_final: 0.7952 (tmm) REVERT: n 102 ARG cc_start: 0.9444 (OUTLIER) cc_final: 0.8278 (ttm-80) REVERT: o 15 GLU cc_start: 0.8683 (pp20) cc_final: 0.8384 (pp20) REVERT: p 19 ASP cc_start: 0.8360 (p0) cc_final: 0.8080 (p0) REVERT: p 20 THR cc_start: 0.9253 (m) cc_final: 0.9043 (p) REVERT: r 39 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7963 (tp30) REVERT: s 18 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7848 (pmm-80) REVERT: t 6 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8287 (pttt) REVERT: t 28 LYS cc_start: 0.8543 (mttp) cc_final: 0.8277 (mttt) REVERT: t 32 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8845 (tmtp) REVERT: t 73 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: u 45 ASP cc_start: 0.8165 (p0) cc_final: 0.7819 (p0) REVERT: w 43 HIS cc_start: 0.9102 (OUTLIER) cc_final: 0.8865 (m-70) outliers start: 72 outliers final: 49 residues processed: 267 average time/residue: 0.4919 time to fit residues: 226.9290 Evaluate side-chains 256 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 197 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 99 GLN Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 172 ARG Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 97 PHE Chi-restraints excluded: chain f residue 113 GLU Chi-restraints excluded: chain f residue 162 VAL Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 30 SER Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 93 ASN Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 24 LYS Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain l residue 73 GLN Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 107 VAL Chi-restraints excluded: chain n residue 4 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 73 VAL Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 39 GLU Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 18 ARG Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 63 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 41 THR Chi-restraints excluded: chain w residue 43 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 9.9990 chunk 347 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 337 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 305 optimal weight: 0.0670 chunk 319 optimal weight: 0.9980 chunk 336 optimal weight: 5.9990 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 24 ASN l 128 ASN o 49 GLN t 22 GLN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 55508 Z= 0.212 Angle : 0.571 11.146 82567 Z= 0.295 Chirality : 0.035 0.257 10455 Planarity : 0.004 0.061 4800 Dihedral : 23.722 178.628 26882 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.10 % Allowed : 28.02 % Favored : 68.87 % 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: 0.85 (0.18), residues: 2284 helix: 1.95 (0.17), residues: 940 sheet: 0.04 (0.26), residues: 433 loop : -0.62 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP t 34 HIS 0.005 0.001 HIS w 30 PHE 0.018 0.001 PHE x 61 TYR 0.014 0.001 TYR d 168 ARG 0.012 0.000 ARG l 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 215 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 101 ASN cc_start: 0.7853 (m-40) cc_final: 0.7560 (m-40) REVERT: f 63 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8364 (mm) REVERT: f 91 GLU cc_start: 0.8808 (tt0) cc_final: 0.8245 (tm-30) REVERT: g 68 GLU cc_start: 0.8007 (mp0) cc_final: 0.7674 (mp0) REVERT: h 144 MET cc_start: 0.8082 (tpp) cc_final: 0.7771 (tpt) REVERT: j 58 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.7628 (t80) REVERT: j 66 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8538 (tm-30) REVERT: j 82 ASP cc_start: 0.7952 (m-30) cc_final: 0.7316 (t0) REVERT: n 15 MET cc_start: 0.8661 (mmm) cc_final: 0.8364 (tpp) REVERT: n 43 MET cc_start: 0.8629 (tmm) cc_final: 0.7985 (tmm) REVERT: n 102 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.8444 (ttm-80) REVERT: o 15 GLU cc_start: 0.8646 (pp20) cc_final: 0.8372 (pp20) REVERT: p 19 ASP cc_start: 0.8347 (p0) cc_final: 0.8057 (p0) REVERT: p 20 THR cc_start: 0.9205 (m) cc_final: 0.8987 (p) REVERT: r 39 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7944 (tp30) REVERT: s 18 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7812 (pmm-80) REVERT: t 6 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8259 (pttt) REVERT: t 28 LYS cc_start: 0.8722 (mttp) cc_final: 0.8356 (mmtt) REVERT: t 32 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.8520 (tmtp) REVERT: t 73 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8258 (mt-10) REVERT: u 45 ASP cc_start: 0.8178 (p0) cc_final: 0.7974 (p0) outliers start: 60 outliers final: 45 residues processed: 265 average time/residue: 0.4911 time to fit residues: 225.8303 Evaluate side-chains 266 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 213 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 99 GLN Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 97 PHE Chi-restraints excluded: chain f residue 113 GLU Chi-restraints excluded: chain f residue 162 VAL Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 30 SER Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 93 ASN Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 24 LYS Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 39 GLU Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 18 ARG Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 57 LYS Chi-restraints excluded: chain u residue 63 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 7.9990 chunk 357 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 374 optimal weight: 10.0000 chunk 344 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 24 ASN l 128 ASN ** m 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 49 GLN t 22 GLN ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 55508 Z= 0.285 Angle : 0.591 10.983 82567 Z= 0.305 Chirality : 0.036 0.275 10455 Planarity : 0.004 0.058 4800 Dihedral : 23.689 178.513 26882 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.90 % Allowed : 28.34 % Favored : 68.77 % 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: 0.81 (0.18), residues: 2284 helix: 1.91 (0.17), residues: 942 sheet: -0.02 (0.26), residues: 434 loop : -0.62 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP t 34 HIS 0.005 0.001 HIS w 30 PHE 0.017 0.001 PHE x 61 TYR 0.015 0.001 TYR d 168 ARG 0.012 0.000 ARG l 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4568 Ramachandran restraints generated. 2284 Oldfield, 0 Emsley, 2284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 210 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 101 ASN cc_start: 0.7843 (m-40) cc_final: 0.7574 (m-40) REVERT: f 63 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8363 (mm) REVERT: h 144 MET cc_start: 0.8103 (tpp) cc_final: 0.7790 (tpt) REVERT: i 24 GLU cc_start: 0.7417 (tp30) cc_final: 0.7197 (tp30) REVERT: j 58 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7646 (t80) REVERT: j 66 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8447 (tm-30) REVERT: j 82 ASP cc_start: 0.7994 (m-30) cc_final: 0.7404 (t0) REVERT: n 15 MET cc_start: 0.8719 (mmm) cc_final: 0.8392 (tpp) REVERT: n 43 MET cc_start: 0.8648 (tmm) cc_final: 0.7984 (tmm) REVERT: n 61 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8143 (mm-30) REVERT: n 102 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8296 (ttm-80) REVERT: o 15 GLU cc_start: 0.8657 (pp20) cc_final: 0.8377 (pp20) REVERT: p 19 ASP cc_start: 0.8360 (p0) cc_final: 0.8084 (p0) REVERT: p 20 THR cc_start: 0.9210 (m) cc_final: 0.8989 (p) REVERT: r 39 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7953 (tp30) REVERT: s 18 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7817 (pmm-80) REVERT: t 6 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8286 (pttt) REVERT: t 28 LYS cc_start: 0.8643 (mttp) cc_final: 0.8251 (mttt) REVERT: t 32 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8553 (tmtp) REVERT: t 73 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: u 45 ASP cc_start: 0.8174 (p0) cc_final: 0.7902 (p0) outliers start: 56 outliers final: 45 residues processed: 256 average time/residue: 0.4914 time to fit residues: 218.2350 Evaluate side-chains 262 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 209 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 99 GLN Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 97 PHE Chi-restraints excluded: chain f residue 113 GLU Chi-restraints excluded: chain f residue 162 VAL Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 20 SER Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 94 ASP Chi-restraints excluded: chain i residue 9 ASP Chi-restraints excluded: chain i residue 25 VAL Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 30 SER Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 93 ASN Chi-restraints excluded: chain j residue 58 TYR Chi-restraints excluded: chain j residue 147 TYR Chi-restraints excluded: chain k residue 15 HIS Chi-restraints excluded: chain k residue 24 LYS Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 102 ARG Chi-restraints excluded: chain o residue 48 LEU Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 66 VAL Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain q residue 48 LEU Chi-restraints excluded: chain q residue 86 LEU Chi-restraints excluded: chain r residue 39 GLU Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 18 ARG Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain t residue 32 LYS Chi-restraints excluded: chain t residue 34 TRP Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 57 LYS Chi-restraints excluded: chain u residue 63 SER Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain w residue 40 LEU Chi-restraints excluded: chain w residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 10.0000 chunk 317 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 275 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 overall best weight: 6.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 GLN ** i 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 128 ASN ** m 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.031223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.024290 restraints weight = 430356.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.024873 restraints weight = 173537.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.025229 restraints weight = 113607.792| |-----------------------------------------------------------------------------| r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 55508 Z= 0.374 Angle : 0.633 10.733 82567 Z= 0.325 Chirality : 0.038 0.293 10455 Planarity : 0.005 0.057 4800 Dihedral : 23.684 178.737 26882 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.15 % Allowed : 28.18 % Favored : 68.67 % 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: 0.71 (0.18), residues: 2284 helix: 1.85 (0.17), residues: 943 sheet: -0.11 (0.26), residues: 430 loop : -0.67 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP t 34 HIS 0.005 0.001 HIS w 30 PHE 0.018 0.002 PHE x 61 TYR 0.020 0.001 TYR d 168 ARG 0.013 0.000 ARG l 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6168.80 seconds wall clock time: 110 minutes 53.04 seconds (6653.04 seconds total)