Starting phenix.real_space_refine on Tue Nov 19 08:08:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh7_16049/11_2024/8bh7_16049.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh7_16049/11_2024/8bh7_16049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh7_16049/11_2024/8bh7_16049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh7_16049/11_2024/8bh7_16049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh7_16049/11_2024/8bh7_16049.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh7_16049/11_2024/8bh7_16049.cif" } resolution = 4.23 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= 0.020 sd= 1.022 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 1541 5.49 5 S 54 5.16 5 C 27043 2.51 5 N 9674 2.21 5 O 14303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 52615 Number of models: 1 Model: "" Number of chains: 21 Chain: "a" Number of atoms: 33006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1541, 33006 Classifications: {'RNA': 1541} Modifications used: {'rna2p_pur': 120, 'rna2p_pyr': 96, 'rna3p_pur': 747, 'rna3p_pyr': 578} Link IDs: {'rna2p': 215, 'rna3p': 1325} Chain: "A" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1242 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 147} Chain: "b" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1725 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 6, 'TRANS': 209} Chain breaks: 1 Chain: "d" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1570 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 183} Chain breaks: 1 Chain: "c" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1638 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "e" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1178 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain: "f" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 798 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "g" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1189 Classifications: {'peptide': 147} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 139} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "h" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 125} Chain: "k" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 869 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 108} Chain: "l" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1062 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 126} Chain: "i" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 118} Chain: "j" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 813 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 95} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 945 Classifications: {'peptide': 119} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 113} Chain: "n" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 502 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "s" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "o" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 738 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 712 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 83} Chain: "q" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 707 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "r" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 589 Classifications: {'peptide': 71} Link IDs: {'CIS': 4, 'PTRANS': 2, 'TRANS': 64} Chain: "t" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 606 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Time building chain proxies: 26.90, per 1000 atoms: 0.51 Number of scatterers: 52615 At special positions: 0 Unit cell: (144, 190.8, 247.2, 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 54 16.00 P 1541 15.00 O 14303 8.00 N 9674 7.00 C 27043 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: 12.40 Conformation dependent library (CDL) restraints added in 3.0 seconds 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4590 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 25 sheets defined 39.6% alpha, 14.4% beta 443 base pairs and 779 stacking pairs defined. Time for finding SS restraints: 25.68 Creating SS restraints... Processing helix chain 'A' and resid 1 through 20 removed outlier: 3.764A pdb=" N LYS A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Proline residue: A 15 - end of helix Processing helix chain 'A' and resid 50 through 66 removed outlier: 4.010A pdb=" N ALA A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 96 removed outlier: 3.577A pdb=" N ALA A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 43 through 63 removed outlier: 3.655A pdb=" N LYS b 48 " --> pdb=" O GLN b 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 87 Processing helix chain 'b' and resid 103 through 120 removed outlier: 4.858A pdb=" N LYS b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 123 No H-bonds generated for 'chain 'b' and resid 121 through 123' Processing helix chain 'b' and resid 130 through 148 removed outlier: 5.353A pdb=" N GLU b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS b 139 " --> pdb=" O VAL b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 177 Processing helix chain 'b' and resid 206 through 227 Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 45 through 62 removed outlier: 4.397A pdb=" N LEU d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 74 removed outlier: 5.090A pdb=" N ASN d 70 " --> pdb=" O ARG d 66 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR d 71 " --> pdb=" O GLN d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 75 through 78 removed outlier: 3.908A pdb=" N LYS d 78 " --> pdb=" O ALA d 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 75 through 78' Processing helix chain 'd' and resid 82 through 93 Processing helix chain 'd' and resid 93 through 101 removed outlier: 4.152A pdb=" N VAL d 97 " --> pdb=" O ARG d 93 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL d 98 " --> pdb=" O LEU d 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 117 removed outlier: 3.684A pdb=" N ALA d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN d 112 " --> pdb=" O ARG d 108 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU d 113 " --> pdb=" O GLN d 109 " (cutoff:3.500A) Processing helix chain 'd' and resid 142 through 146 Processing helix chain 'd' and resid 148 through 157 Processing helix chain 'd' and resid 190 through 200 removed outlier: 3.650A pdb=" N ARG d 200 " --> pdb=" O GLU d 196 " (cutoff:3.500A) Processing helix chain 'c' and resid 7 through 12 removed outlier: 3.516A pdb=" N VAL c 12 " --> pdb=" O ILE c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 50 removed outlier: 4.400A pdb=" N ASN c 44 " --> pdb=" O LYS c 40 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU c 45 " --> pdb=" O PHE c 41 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU c 48 " --> pdb=" O ASN c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 76 removed outlier: 4.375A pdb=" N VAL c 75 " --> pdb=" O LYS c 71 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE c 76 " --> pdb=" O PRO c 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 71 through 76' Processing helix chain 'c' and resid 81 through 94 Processing helix chain 'c' and resid 111 through 125 removed outlier: 3.519A pdb=" N VAL c 115 " --> pdb=" O ASP c 111 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.813A pdb=" N VAL c 132 " --> pdb=" O SER c 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 70 removed outlier: 3.752A pdb=" N LYS e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 117 Processing helix chain 'e' and resid 132 through 146 Processing helix chain 'e' and resid 149 through 157 Processing helix chain 'f' and resid 15 through 32 Processing helix chain 'f' and resid 72 through 80 removed outlier: 4.141A pdb=" N ARG f 78 " --> pdb=" O ASP f 74 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 31 removed outlier: 4.238A pdb=" N ASN g 28 " --> pdb=" O THR g 24 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS g 29 " --> pdb=" O LYS g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 53 Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.640A pdb=" N ARG g 96 " --> pdb=" O ARG g 92 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 128 Processing helix chain 'g' and resid 132 through 145 Processing helix chain 'g' and resid 148 through 153 removed outlier: 3.899A pdb=" N ALA g 152 " --> pdb=" O ASN g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.632A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 114 through 122 Processing helix chain 'k' and resid 53 through 57 Processing helix chain 'k' and resid 59 through 79 removed outlier: 3.969A pdb=" N LEU k 79 " --> pdb=" O MET k 75 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 102 Processing helix chain 'l' and resid 3 through 9 Processing helix chain 'l' and resid 124 through 128 removed outlier: 4.149A pdb=" N SER l 128 " --> pdb=" O GLN l 125 " (cutoff:3.500A) Processing helix chain 'i' and resid 36 through 40 Processing helix chain 'i' and resid 46 through 57 removed outlier: 4.170A pdb=" N LEU i 50 " --> pdb=" O LEU i 46 " (cutoff:3.500A) Proline residue: i 53 - end of helix Processing helix chain 'i' and resid 73 through 93 removed outlier: 3.738A pdb=" N ALA i 80 " --> pdb=" O GLY i 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 96 through 104 Processing helix chain 'j' and resid 14 through 32 Processing helix chain 'j' and resid 80 through 88 removed outlier: 3.747A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.231A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 38 removed outlier: 3.860A pdb=" N GLU m 36 " --> pdb=" O LYS m 32 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 61 removed outlier: 3.543A pdb=" N LEU m 53 " --> pdb=" O THR m 49 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG m 55 " --> pdb=" O ASP m 51 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 83 removed outlier: 3.831A pdb=" N ARG m 71 " --> pdb=" O GLY m 67 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 91 Processing helix chain 'm' and resid 92 through 94 No H-bonds generated for 'chain 'm' and resid 92 through 94' Processing helix chain 'n' and resid 3 through 12 removed outlier: 3.787A pdb=" N GLN n 10 " --> pdb=" O MET n 6 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS n 12 " --> pdb=" O ALA n 8 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 Processing helix chain 's' and resid 14 through 25 Processing helix chain 's' and resid 41 through 45 Processing helix chain 'o' and resid 4 through 13 Processing helix chain 'o' and resid 24 through 46 removed outlier: 4.401A pdb=" N GLN o 28 " --> pdb=" O SER o 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 50 through 73 Processing helix chain 'o' and resid 75 through 85 removed outlier: 4.311A pdb=" N ARG o 79 " --> pdb=" O ILE o 75 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 63 Processing helix chain 'p' and resid 68 through 79 Processing helix chain 'p' and resid 79 through 90 removed outlier: 3.553A pdb=" N ALA p 90 " --> pdb=" O GLU p 86 " (cutoff:3.500A) Processing helix chain 'r' and resid 16 through 21 removed outlier: 4.362A pdb=" N ALA r 20 " --> pdb=" O TYR r 17 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 38 removed outlier: 3.506A pdb=" N LEU r 34 " --> pdb=" O ASP r 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG r 36 " --> pdb=" O GLU r 32 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE r 38 " --> pdb=" O LEU r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 50 removed outlier: 3.546A pdb=" N THR r 50 " --> pdb=" O ARG r 47 " (cutoff:3.500A) Processing helix chain 'r' and resid 53 through 70 Processing helix chain 't' and resid 7 through 41 removed outlier: 4.439A pdb=" N GLU t 18 " --> pdb=" O THR t 14 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER t 23 " --> pdb=" O ALA t 19 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 63 removed outlier: 3.913A pdb=" N GLU t 48 " --> pdb=" O ASP t 44 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 80 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 30 removed outlier: 4.112A pdb=" N ASP A 26 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 80 " --> pdb=" O VAL l 50 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL l 50 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N CYS l 47 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG l 69 " --> pdb=" O CYS l 47 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS l 64 " --> pdb=" O ILE l 80 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE l 76 " --> pdb=" O VAL l 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 30 removed outlier: 4.112A pdb=" N ASP A 26 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 80 " --> pdb=" O VAL l 50 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL l 50 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 118 removed outlier: 5.326A pdb=" N LYS A 113 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR A 106 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE A 147 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.880A pdb=" N ASN A 123 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 131 through 133 removed outlier: 3.656A pdb=" N LYS A 138 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 31 through 35 removed outlier: 6.363A pdb=" N ILE b 40 " --> pdb=" O PHE b 32 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU b 34 " --> pdb=" O ILE b 38 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE b 38 " --> pdb=" O GLU b 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 91 through 92 removed outlier: 7.639A pdb=" N ILE b 92 " --> pdb=" O VAL b 67 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE b 69 " --> pdb=" O ILE b 92 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU b 68 " --> pdb=" O PHE b 162 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU b 161 " --> pdb=" O VAL b 184 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE b 186 " --> pdb=" O LEU b 161 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL b 163 " --> pdb=" O ILE b 186 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY b 185 " --> pdb=" O TYR b 198 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE b 200 " --> pdb=" O GLY b 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'd' and resid 120 through 121 Processing sheet with id=AA9, first strand: chain 'c' and resid 53 through 57 removed outlier: 3.549A pdb=" N HIS c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN c 101 " --> pdb=" O ILE c 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.681A pdb=" N GLY c 196 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL c 199 " --> pdb=" O ALA c 184 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA c 184 " --> pdb=" O VAL c 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'e' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'e' and resid 38 through 40 Processing sheet with id=AB4, first strand: chain 'e' and resid 86 through 87 Processing sheet with id=AB5, first strand: chain 'f' and resid 37 through 42 removed outlier: 6.425A pdb=" N ARG f 64 " --> pdb=" O LEU f 38 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA f 40 " --> pdb=" O ILE f 62 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE f 62 " --> pdb=" O ALA f 40 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP f 42 " --> pdb=" O TYR f 60 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR f 60 " --> pdb=" O ASP f 42 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE f 9 " --> pdb=" O ARG f 88 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG f 88 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'g' and resid 74 through 78 removed outlier: 3.603A pdb=" N GLU g 74 " --> pdb=" O VAL g 89 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG g 78 " --> pdb=" O TYR g 85 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR g 85 " --> pdb=" O ARG g 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 24 through 28 Processing sheet with id=AB8, first strand: chain 'h' and resid 76 through 79 Processing sheet with id=AB9, first strand: chain 'h' and resid 88 through 89 Processing sheet with id=AC1, first strand: chain 'k' and resid 41 through 45 removed outlier: 3.877A pdb=" N SER k 43 " --> pdb=" O ILE k 34 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER k 45 " --> pdb=" O VAL k 32 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY k 19 " --> pdb=" O THR k 81 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG k 111 " --> pdb=" O VAL k 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'l' and resid 95 through 97 Processing sheet with id=AC3, first strand: chain 'i' and resid 8 through 13 removed outlier: 6.088A pdb=" N ASN i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL i 67 " --> pdb=" O ASN i 29 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N THR i 31 " --> pdb=" O VAL i 67 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL i 69 " --> pdb=" O THR i 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'j' and resid 40 through 45 removed outlier: 4.494A pdb=" N LEU j 73 " --> pdb=" O PRO j 41 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 's' and resid 50 through 52 removed outlier: 4.050A pdb=" N VAL s 51 " --> pdb=" O VAL s 58 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'p' and resid 4 through 7 removed outlier: 3.851A pdb=" N ILE p 20 " --> pdb=" O GLY p 38 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY p 38 " --> pdb=" O ILE p 20 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL p 22 " --> pdb=" O GLN p 36 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLN p 36 " --> pdb=" O VAL p 22 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN p 41 " --> pdb=" O GLU p 49 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU p 49 " --> pdb=" O ASN p 41 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'q' and resid 12 through 19 removed outlier: 3.547A pdb=" N LYS q 13 " --> pdb=" O LEU q 26 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR q 24 " --> pdb=" O VAL q 15 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP q 17 " --> pdb=" O THR q 22 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N THR q 22 " --> pdb=" O ASP q 17 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL q 27 " --> pdb=" O LYS q 44 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ARG q 74 " --> pdb=" O LYS q 45 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N LYS q 47 " --> pdb=" O ARG q 74 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG q 76 " --> pdb=" O LYS q 47 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N HIS q 49 " --> pdb=" O ARG q 76 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL q 78 " --> pdb=" O HIS q 49 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS q 73 " --> pdb=" O LEU q 69 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE q 75 " --> pdb=" O ARG q 67 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG q 67 " --> pdb=" O PHE q 75 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N LEU q 77 " --> pdb=" O GLU q 65 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLU q 65 " --> pdb=" O LEU q 77 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLU q 79 " --> pdb=" O ILE q 63 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ILE q 63 " --> pdb=" O GLU q 79 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL q 81 " --> pdb=" O VAL q 61 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL q 61 " --> pdb=" O VAL q 81 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP q 59 " --> pdb=" O VAL q 14 " (cutoff:3.500A) 807 hydrogen bonds defined for protein. 2301 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1087 hydrogen bonds 1800 hydrogen bond angles 0 basepair planarities 443 basepair parallelities 779 stacking parallelities Total time for adding SS restraints: 50.02 Time building geometry restraints manager: 14.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5703 1.32 - 1.44: 23891 1.44 - 1.57: 24070 1.57 - 1.69: 3081 1.69 - 1.82: 99 Bond restraints: 56844 Sorted by residual: bond pdb=" C1' C a1414 " pdb=" N1 C a1414 " ideal model delta sigma weight residual 1.480 1.549 -0.069 1.50e-02 4.44e+03 2.15e+01 bond pdb=" CA LEU j 42 " pdb=" C LEU j 42 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.18e-02 7.18e+03 9.41e+00 bond pdb=" CA HIS k 118 " pdb=" C HIS k 118 " ideal model delta sigma weight residual 1.526 1.497 0.029 1.11e-02 8.12e+03 6.83e+00 bond pdb=" CA THR b 189 " pdb=" C THR b 189 " ideal model delta sigma weight residual 1.522 1.565 -0.043 1.72e-02 3.38e+03 6.37e+00 bond pdb=" CA ARG d 93 " pdb=" C ARG d 93 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.34e-02 5.57e+03 4.34e+00 ... (remaining 56839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 81583 2.23 - 4.47: 2596 4.47 - 6.70: 144 6.70 - 8.94: 14 8.94 - 11.17: 6 Bond angle restraints: 84343 Sorted by residual: angle pdb=" N LYS n 58 " pdb=" CA LYS n 58 " pdb=" C LYS n 58 " ideal model delta sigma weight residual 108.42 119.13 -10.71 1.54e+00 4.22e-01 4.84e+01 angle pdb=" N SER m 28 " pdb=" CA SER m 28 " pdb=" C SER m 28 " ideal model delta sigma weight residual 113.50 105.34 8.16 1.23e+00 6.61e-01 4.40e+01 angle pdb=" C ILE r 26 " pdb=" N ASP r 27 " pdb=" CA ASP r 27 " ideal model delta sigma weight residual 121.70 132.87 -11.17 1.80e+00 3.09e-01 3.85e+01 angle pdb=" C PHE k 38 " pdb=" N GLY k 39 " pdb=" CA GLY k 39 " ideal model delta sigma weight residual 121.70 132.10 -10.40 1.80e+00 3.09e-01 3.34e+01 angle pdb=" C ASN h 99 " pdb=" CA ASN h 99 " pdb=" CB ASN h 99 " ideal model delta sigma weight residual 116.54 109.94 6.60 1.15e+00 7.56e-01 3.29e+01 ... (remaining 84338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 30989 35.54 - 71.09: 4688 71.09 - 106.63: 564 106.63 - 142.18: 30 142.18 - 177.72: 13 Dihedral angle restraints: 36284 sinusoidal: 29178 harmonic: 7106 Sorted by residual: dihedral pdb=" C4' U a 746 " pdb=" C3' U a 746 " pdb=" C2' U a 746 " pdb=" C1' U a 746 " ideal model delta sinusoidal sigma weight residual -35.00 31.52 -66.52 1 8.00e+00 1.56e-02 9.02e+01 dihedral pdb=" O4' C a1088 " pdb=" C1' C a1088 " pdb=" N1 C a1088 " pdb=" C2 C a1088 " ideal model delta sinusoidal sigma weight residual 200.00 22.28 177.72 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U a 477 " pdb=" C1' U a 477 " pdb=" N1 U a 477 " pdb=" C2 U a 477 " ideal model delta sinusoidal sigma weight residual 200.00 24.20 175.80 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 36281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 8810 0.081 - 0.163: 1590 0.163 - 0.244: 295 0.244 - 0.326: 0 0.326 - 0.407: 1 Chirality restraints: 10696 Sorted by residual: chirality pdb=" CB VAL s 11 " pdb=" CA VAL s 11 " pdb=" CG1 VAL s 11 " pdb=" CG2 VAL s 11 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" C3' G a1060 " pdb=" C4' G a1060 " pdb=" O3' G a1060 " pdb=" C2' G a1060 " both_signs ideal model delta sigma weight residual False -2.48 -2.72 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1' A a1122 " pdb=" O4' A a1122 " pdb=" C2' A a1122 " pdb=" N9 A a1122 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 10693 not shown) Planarity restraints: 4990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR b 104 " -0.021 2.00e-02 2.50e+03 2.19e-02 9.58e+00 pdb=" CG TYR b 104 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR b 104 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR b 104 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR b 104 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR b 104 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR b 104 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR b 104 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A a 389 " -0.036 2.00e-02 2.50e+03 1.84e-02 9.35e+00 pdb=" N9 A a 389 " 0.048 2.00e-02 2.50e+03 pdb=" C8 A a 389 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A a 389 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A a 389 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A a 389 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A a 389 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A a 389 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A a 389 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A a 389 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A a 389 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS k 72 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C LYS k 72 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS k 72 " -0.020 2.00e-02 2.50e+03 pdb=" N SER k 73 " -0.018 2.00e-02 2.50e+03 ... (remaining 4987 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 5171 2.69 - 3.24: 64978 3.24 - 3.79: 131412 3.79 - 4.35: 155756 4.35 - 4.90: 201160 Nonbonded interactions: 558477 Sorted by model distance: nonbonded pdb=" O2' A a 270 " pdb=" O4' A a 271 " model vdw 2.136 3.040 nonbonded pdb=" O ILE m 83 " pdb=" OG SER m 84 " model vdw 2.143 3.040 nonbonded pdb=" O2' G a1517 " pdb=" O4' U a1518 " model vdw 2.143 3.040 nonbonded pdb=" O2' A a1525 " pdb=" O5' U a1526 " model vdw 2.168 3.040 nonbonded pdb=" O2' A a 390 " pdb=" O4' A a 391 " model vdw 2.169 3.040 ... (remaining 558472 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.820 Check model and map are aligned: 0.370 Set scattering table: 0.440 Process input model: 148.360 Find NCS groups from input model: 0.580 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: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.005 0.069 56844 Z= 0.291 Angle : 0.829 11.171 84343 Z= 0.504 Chirality : 0.066 0.407 10696 Planarity : 0.005 0.074 4990 Dihedral : 25.729 177.723 31694 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 63.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.43 % Allowed : 1.61 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.15), residues: 2418 helix: -1.14 (0.16), residues: 821 sheet: -2.89 (0.27), residues: 301 loop : -2.92 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP s 34 HIS 0.011 0.002 HIS k 22 PHE 0.025 0.002 PHE b 56 TYR 0.054 0.002 TYR b 104 ARG 0.015 0.001 ARG g 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 3.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 141 TYR cc_start: 0.8908 (t80) cc_final: 0.8658 (t80) REVERT: b 154 MET cc_start: 0.7593 (pmm) cc_final: 0.6726 (pmm) REVERT: e 136 MET cc_start: 0.6625 (ptt) cc_final: 0.6357 (ptt) REVERT: g 70 MET cc_start: 0.6527 (mmp) cc_final: 0.6257 (mmp) REVERT: k 61 PHE cc_start: 0.9639 (t80) cc_final: 0.9332 (t80) REVERT: k 65 MET cc_start: 0.9465 (ptt) cc_final: 0.9231 (ptt) REVERT: l 39 ASN cc_start: 0.9492 (m-40) cc_final: 0.9106 (t0) REVERT: n 58 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8066 (ttpt) REVERT: p 81 MET cc_start: 0.8904 (mmp) cc_final: 0.8703 (mmm) REVERT: r 25 HIS cc_start: 0.6648 (p-80) cc_final: 0.6354 (p-80) REVERT: r 40 GLU cc_start: 0.9462 (pm20) cc_final: 0.9242 (pm20) REVERT: r 59 MET cc_start: 0.7175 (ptp) cc_final: 0.6283 (mmt) REVERT: r 77 LYS cc_start: 0.9646 (tmtt) cc_final: 0.9420 (tptt) REVERT: r 78 GLU cc_start: 0.9788 (pm20) cc_final: 0.9341 (pm20) outliers start: 9 outliers final: 1 residues processed: 153 average time/residue: 0.7670 time to fit residues: 186.9240 Evaluate side-chains 104 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 330 optimal weight: 8.9990 chunk 296 optimal weight: 0.5980 chunk 164 optimal weight: 10.0000 chunk 101 optimal weight: 30.0000 chunk 199 optimal weight: 7.9990 chunk 158 optimal weight: 0.0770 chunk 306 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 355 optimal weight: 6.9990 overall best weight: 4.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 55 ASN ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 53 HIS ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN e 166 ASN g 28 ASN h 18 ASN k 119 ASN l 6 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 16 ASN i 33 ASN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 56844 Z= 0.243 Angle : 0.804 11.531 84343 Z= 0.401 Chirality : 0.042 0.343 10696 Planarity : 0.006 0.058 4990 Dihedral : 26.689 179.972 26638 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 40.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 0.24 % Allowed : 8.06 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.55 % 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: -2.97 (0.16), residues: 2418 helix: -0.75 (0.16), residues: 862 sheet: -2.88 (0.25), residues: 322 loop : -2.67 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP g 156 HIS 0.009 0.002 HIS o 42 PHE 0.025 0.002 PHE g 62 TYR 0.019 0.002 TYR m 86 ARG 0.011 0.001 ARG g 119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRP g 156 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8260 (ppp) cc_final: 0.7905 (ppp) REVERT: b 154 MET cc_start: 0.6649 (pmm) cc_final: 0.6440 (pmm) REVERT: h 19 MET cc_start: 0.8478 (ppp) cc_final: 0.8105 (ppp) REVERT: k 61 PHE cc_start: 0.9681 (t80) cc_final: 0.9290 (t80) REVERT: k 65 MET cc_start: 0.9380 (ptt) cc_final: 0.8992 (ptt) REVERT: l 39 ASN cc_start: 0.9563 (m-40) cc_final: 0.9226 (t0) REVERT: p 85 ASP cc_start: 0.6026 (OUTLIER) cc_final: 0.5403 (p0) REVERT: r 25 HIS cc_start: 0.6687 (p-80) cc_final: 0.6420 (p-80) REVERT: r 59 MET cc_start: 0.7011 (ptp) cc_final: 0.6288 (mmt) REVERT: r 65 LYS cc_start: 0.9596 (ttmt) cc_final: 0.9289 (tppt) outliers start: 5 outliers final: 4 residues processed: 145 average time/residue: 0.7388 time to fit residues: 173.8441 Evaluate side-chains 106 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 2.9990 chunk 110 optimal weight: 30.0000 chunk 295 optimal weight: 20.0000 chunk 241 optimal weight: 2.9990 chunk 97 optimal weight: 50.0000 chunk 355 optimal weight: 10.0000 chunk 384 optimal weight: 9.9990 chunk 316 optimal weight: 40.0000 chunk 352 optimal weight: 9.9990 chunk 121 optimal weight: 30.0000 chunk 285 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 133 GLN ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN k 119 ASN l 6 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 HIS ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 24 GLN t 62 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 56844 Z= 0.296 Angle : 0.815 14.317 84343 Z= 0.405 Chirality : 0.042 0.350 10696 Planarity : 0.006 0.054 4990 Dihedral : 26.756 178.015 26638 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 48.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 0.05 % Allowed : 6.26 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.55 % 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: -2.87 (0.16), residues: 2418 helix: -0.70 (0.17), residues: 862 sheet: -2.84 (0.26), residues: 317 loop : -2.57 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP c 200 HIS 0.012 0.002 HIS o 42 PHE 0.022 0.002 PHE A 37 TYR 0.031 0.002 TYR b 104 ARG 0.016 0.001 ARG g 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 3.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRP g 156 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8606 (ppp) cc_final: 0.8276 (ppp) REVERT: b 119 LYS cc_start: 0.8849 (pptt) cc_final: 0.8646 (pptt) REVERT: d 86 PHE cc_start: 0.9409 (t80) cc_final: 0.9080 (t80) REVERT: e 136 MET cc_start: 0.6741 (ptt) cc_final: 0.6373 (ptt) REVERT: h 19 MET cc_start: 0.8566 (ppp) cc_final: 0.8080 (ppp) REVERT: k 61 PHE cc_start: 0.9678 (t80) cc_final: 0.9258 (t80) REVERT: k 65 MET cc_start: 0.9374 (ptt) cc_final: 0.8918 (ptt) REVERT: l 39 ASN cc_start: 0.9689 (m-40) cc_final: 0.9422 (t0) REVERT: s 66 MET cc_start: 0.5768 (mtm) cc_final: 0.5269 (mtt) REVERT: p 81 MET cc_start: 0.8906 (mmp) cc_final: 0.8678 (mmm) REVERT: r 25 HIS cc_start: 0.6451 (p-80) cc_final: 0.6205 (p-80) REVERT: r 40 GLU cc_start: 0.9453 (pm20) cc_final: 0.9221 (pm20) REVERT: r 65 LYS cc_start: 0.9656 (ttmt) cc_final: 0.9413 (tppt) REVERT: r 70 MET cc_start: 0.8892 (tpt) cc_final: 0.8667 (tpt) outliers start: 1 outliers final: 1 residues processed: 132 average time/residue: 0.7612 time to fit residues: 163.3742 Evaluate side-chains 99 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 351 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 169 optimal weight: 50.0000 chunk 238 optimal weight: 8.9990 chunk 356 optimal weight: 1.9990 chunk 377 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 338 optimal weight: 20.0000 chunk 101 optimal weight: 30.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 ASN ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN f 53 ASN ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN l 6 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 56844 Z= 0.262 Angle : 0.778 15.935 84343 Z= 0.389 Chirality : 0.042 0.412 10696 Planarity : 0.006 0.079 4990 Dihedral : 26.699 178.950 26638 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 44.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 0.05 % Allowed : 5.92 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.55 % 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: -2.73 (0.16), residues: 2418 helix: -0.53 (0.17), residues: 873 sheet: -2.81 (0.26), residues: 317 loop : -2.54 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP p 60 HIS 0.012 0.002 HIS s 14 PHE 0.018 0.002 PHE A 37 TYR 0.029 0.002 TYR f 4 ARG 0.019 0.001 ARG r 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRP g 156 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 90 PHE cc_start: 0.5803 (p90) cc_final: 0.5473 (p90) REVERT: e 136 MET cc_start: 0.6842 (ptt) cc_final: 0.6479 (ptt) REVERT: f 7 MET cc_start: 0.8374 (tpp) cc_final: 0.8116 (tpp) REVERT: h 19 MET cc_start: 0.8699 (ppp) cc_final: 0.8315 (ppp) REVERT: k 61 PHE cc_start: 0.9691 (t80) cc_final: 0.9265 (t80) REVERT: k 65 MET cc_start: 0.9394 (ptt) cc_final: 0.8955 (ptt) REVERT: l 39 ASN cc_start: 0.9678 (m-40) cc_final: 0.9402 (t0) REVERT: j 57 MET cc_start: 0.4429 (pmm) cc_final: 0.4198 (pmm) REVERT: p 81 MET cc_start: 0.8982 (mmp) cc_final: 0.8665 (mmm) REVERT: r 65 LYS cc_start: 0.9655 (ttmt) cc_final: 0.9436 (tppt) REVERT: r 70 MET cc_start: 0.8722 (tpt) cc_final: 0.8456 (tpt) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.7374 time to fit residues: 156.8632 Evaluate side-chains 94 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 314 optimal weight: 20.0000 chunk 214 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 281 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 322 optimal weight: 50.0000 chunk 261 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 339 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 40 GLN ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 76 ASN ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 56844 Z= 0.364 Angle : 0.884 16.865 84343 Z= 0.438 Chirality : 0.045 0.379 10696 Planarity : 0.006 0.054 4990 Dihedral : 26.957 178.278 26638 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 58.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.89 (0.16), residues: 2418 helix: -0.70 (0.17), residues: 871 sheet: -2.86 (0.26), residues: 326 loop : -2.59 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP g 103 HIS 0.011 0.002 HIS g 18 PHE 0.022 0.002 PHE q 75 TYR 0.031 0.003 TYR f 4 ARG 0.015 0.001 ARG r 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRP g 156 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 90 PHE cc_start: 0.5796 (p90) cc_final: 0.5427 (p90) REVERT: e 136 MET cc_start: 0.7009 (ptt) cc_final: 0.6558 (ptt) REVERT: h 19 MET cc_start: 0.8499 (ppp) cc_final: 0.8237 (ppp) REVERT: k 61 PHE cc_start: 0.9670 (t80) cc_final: 0.9086 (t80) REVERT: k 65 MET cc_start: 0.9410 (ptt) cc_final: 0.8864 (ptt) REVERT: l 39 ASN cc_start: 0.9697 (m-40) cc_final: 0.9417 (t0) REVERT: j 57 MET cc_start: 0.4632 (pmm) cc_final: 0.4400 (pmm) REVERT: p 81 MET cc_start: 0.9034 (mmp) cc_final: 0.8734 (mmm) REVERT: r 25 HIS cc_start: 0.6571 (p-80) cc_final: 0.6337 (p-80) REVERT: r 40 GLU cc_start: 0.8951 (pp20) cc_final: 0.8608 (pp20) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.7652 time to fit residues: 160.4114 Evaluate side-chains 96 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 127 optimal weight: 30.0000 chunk 340 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 378 optimal weight: 4.9990 chunk 314 optimal weight: 30.0000 chunk 175 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 198 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 56844 Z= 0.271 Angle : 0.798 17.351 84343 Z= 0.400 Chirality : 0.043 0.399 10696 Planarity : 0.006 0.066 4990 Dihedral : 26.803 178.836 26638 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 47.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.55 % 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: -2.77 (0.16), residues: 2418 helix: -0.60 (0.17), residues: 869 sheet: -2.76 (0.26), residues: 326 loop : -2.53 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP f 43 HIS 0.008 0.002 HIS s 14 PHE 0.020 0.002 PHE A 37 TYR 0.050 0.002 TYR b 104 ARG 0.011 0.001 ARG g 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRP g 156 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 90 PHE cc_start: 0.5852 (p90) cc_final: 0.5441 (p90) REVERT: b 119 LYS cc_start: 0.8716 (pptt) cc_final: 0.8486 (pptt) REVERT: e 136 MET cc_start: 0.6989 (ptt) cc_final: 0.6625 (ptt) REVERT: f 7 MET cc_start: 0.8026 (tpp) cc_final: 0.7727 (tpp) REVERT: g 31 MET cc_start: 0.6854 (tmm) cc_final: 0.6326 (tmm) REVERT: h 19 MET cc_start: 0.8618 (ppp) cc_final: 0.8275 (ppp) REVERT: k 61 PHE cc_start: 0.9673 (t80) cc_final: 0.9207 (t80) REVERT: k 65 MET cc_start: 0.9410 (ptt) cc_final: 0.8947 (ptt) REVERT: l 39 ASN cc_start: 0.9695 (m-40) cc_final: 0.9389 (t0) REVERT: j 57 MET cc_start: 0.4616 (pmm) cc_final: 0.4411 (pmm) REVERT: p 81 MET cc_start: 0.8875 (mmp) cc_final: 0.8590 (mmm) REVERT: r 25 HIS cc_start: 0.6505 (p-80) cc_final: 0.6302 (p-80) REVERT: r 40 GLU cc_start: 0.9077 (pp20) cc_final: 0.8810 (pp20) REVERT: r 70 MET cc_start: 0.9025 (tpt) cc_final: 0.8748 (tpp) outliers start: 1 outliers final: 1 residues processed: 126 average time/residue: 0.6995 time to fit residues: 147.5320 Evaluate side-chains 94 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 364 optimal weight: 0.5980 chunk 42 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 276 optimal weight: 3.9990 chunk 214 optimal weight: 40.0000 chunk 318 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 376 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 229 optimal weight: 20.0000 chunk 173 optimal weight: 8.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN A 123 ASN ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** f 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 74 ASN ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN ** t 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 56844 Z= 0.232 Angle : 0.757 16.090 84343 Z= 0.380 Chirality : 0.041 0.349 10696 Planarity : 0.006 0.095 4990 Dihedral : 26.608 178.823 26638 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 41.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.55 % 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: -2.60 (0.16), residues: 2418 helix: -0.50 (0.17), residues: 868 sheet: -2.53 (0.26), residues: 345 loop : -2.43 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP s 34 HIS 0.009 0.002 HIS s 14 PHE 0.021 0.002 PHE A 37 TYR 0.027 0.002 TYR f 4 ARG 0.020 0.001 ARG r 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRP g 156 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 90 PHE cc_start: 0.5917 (p90) cc_final: 0.5438 (p90) REVERT: e 136 MET cc_start: 0.6995 (ptt) cc_final: 0.6616 (ptt) REVERT: f 7 MET cc_start: 0.8051 (tpp) cc_final: 0.7636 (tpp) REVERT: h 19 MET cc_start: 0.8602 (ppp) cc_final: 0.8214 (ppp) REVERT: k 61 PHE cc_start: 0.9699 (t80) cc_final: 0.9288 (t80) REVERT: k 65 MET cc_start: 0.9353 (ptt) cc_final: 0.8884 (ptt) REVERT: l 39 ASN cc_start: 0.9705 (m-40) cc_final: 0.9376 (t0) REVERT: j 57 MET cc_start: 0.4971 (pmm) cc_final: 0.4764 (pmm) REVERT: p 81 MET cc_start: 0.8938 (mmp) cc_final: 0.8647 (mmm) REVERT: r 40 GLU cc_start: 0.9258 (pp20) cc_final: 0.8984 (pp20) REVERT: r 70 MET cc_start: 0.8768 (tpt) cc_final: 0.8524 (tpt) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.7501 time to fit residues: 158.5469 Evaluate side-chains 96 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 233 optimal weight: 10.0000 chunk 150 optimal weight: 30.0000 chunk 225 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 239 optimal weight: 7.9990 chunk 256 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 296 optimal weight: 7.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** f 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 129 ASN ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS ** t 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 67 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 56844 Z= 0.322 Angle : 0.842 15.965 84343 Z= 0.419 Chirality : 0.044 0.353 10696 Planarity : 0.006 0.088 4990 Dihedral : 26.837 178.844 26638 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 54.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % Rotamer: Outliers : 0.05 % Allowed : 1.28 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.72 (0.16), residues: 2418 helix: -0.62 (0.17), residues: 865 sheet: -2.79 (0.25), residues: 347 loop : -2.41 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP s 34 HIS 0.014 0.002 HIS t 67 PHE 0.028 0.002 PHE b 56 TYR 0.031 0.002 TYR f 4 ARG 0.024 0.001 ARG r 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 3.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRP g 156 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 90 PHE cc_start: 0.5955 (p90) cc_final: 0.5439 (p90) REVERT: b 154 MET cc_start: 0.7169 (pmm) cc_final: 0.6800 (pmm) REVERT: d 86 PHE cc_start: 0.9437 (t80) cc_final: 0.9183 (t80) REVERT: e 136 MET cc_start: 0.7145 (ptt) cc_final: 0.6764 (ptt) REVERT: f 7 MET cc_start: 0.8162 (tpp) cc_final: 0.7889 (tpp) REVERT: h 19 MET cc_start: 0.8545 (ppp) cc_final: 0.8043 (ppp) REVERT: k 61 PHE cc_start: 0.9661 (t80) cc_final: 0.9158 (t80) REVERT: k 65 MET cc_start: 0.9344 (ptt) cc_final: 0.8778 (ptt) REVERT: l 39 ASN cc_start: 0.9709 (m-40) cc_final: 0.9418 (t0) REVERT: s 43 ASN cc_start: 0.9727 (m-40) cc_final: 0.9496 (t0) REVERT: p 81 MET cc_start: 0.8919 (mmp) cc_final: 0.8663 (mmm) REVERT: r 40 GLU cc_start: 0.9244 (pp20) cc_final: 0.8976 (pp20) REVERT: r 70 MET cc_start: 0.8970 (tpt) cc_final: 0.8569 (tpt) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.7052 time to fit residues: 146.9172 Evaluate side-chains 93 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 342 optimal weight: 7.9990 chunk 361 optimal weight: 0.5980 chunk 329 optimal weight: 4.9990 chunk 351 optimal weight: 4.9990 chunk 360 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 275 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 317 optimal weight: 7.9990 chunk 332 optimal weight: 4.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 36 HIS A 67 ASN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** f 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 41 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 56844 Z= 0.223 Angle : 0.750 15.801 84343 Z= 0.377 Chirality : 0.040 0.337 10696 Planarity : 0.006 0.076 4990 Dihedral : 26.556 179.870 26638 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 39.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 0.05 % Allowed : 1.28 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.55 % 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: -2.57 (0.17), residues: 2418 helix: -0.50 (0.17), residues: 881 sheet: -2.54 (0.25), residues: 347 loop : -2.40 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP f 43 HIS 0.007 0.002 HIS o 50 PHE 0.023 0.002 PHE A 37 TYR 0.027 0.002 TYR f 4 ARG 0.017 0.001 ARG r 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRP g 156 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ARG cc_start: 0.9176 (mtm110) cc_final: 0.8698 (ptt-90) REVERT: b 90 PHE cc_start: 0.5606 (p90) cc_final: 0.5235 (p90) REVERT: b 154 MET cc_start: 0.6982 (pmm) cc_final: 0.6496 (pmm) REVERT: d 86 PHE cc_start: 0.9376 (t80) cc_final: 0.9165 (t80) REVERT: e 136 MET cc_start: 0.6999 (ptt) cc_final: 0.6660 (ptt) REVERT: f 1 MET cc_start: 0.8602 (tpt) cc_final: 0.8325 (pmm) REVERT: f 7 MET cc_start: 0.8146 (tpp) cc_final: 0.7820 (tpp) REVERT: g 70 MET cc_start: 0.6461 (mmp) cc_final: 0.6256 (mmp) REVERT: h 19 MET cc_start: 0.8579 (ppp) cc_final: 0.8126 (ppp) REVERT: k 61 PHE cc_start: 0.9695 (t80) cc_final: 0.9289 (t80) REVERT: k 65 MET cc_start: 0.9408 (ptt) cc_final: 0.8937 (ptt) REVERT: l 39 ASN cc_start: 0.9692 (m-40) cc_final: 0.9382 (t0) REVERT: p 81 MET cc_start: 0.8916 (mmp) cc_final: 0.8625 (mmm) REVERT: r 25 HIS cc_start: 0.6551 (p-80) cc_final: 0.6162 (p-80) REVERT: r 40 GLU cc_start: 0.9248 (pp20) cc_final: 0.8964 (pp20) REVERT: r 70 MET cc_start: 0.8682 (tpt) cc_final: 0.8356 (tpt) outliers start: 1 outliers final: 1 residues processed: 127 average time/residue: 0.7091 time to fit residues: 150.1312 Evaluate side-chains 100 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 349 optimal weight: 7.9990 chunk 230 optimal weight: 6.9990 chunk 371 optimal weight: 9.9990 chunk 226 optimal weight: 0.9980 chunk 176 optimal weight: 20.0000 chunk 258 optimal weight: 6.9990 chunk 389 optimal weight: 6.9990 chunk 358 optimal weight: 8.9990 chunk 310 optimal weight: 50.0000 chunk 32 optimal weight: 20.0000 chunk 239 optimal weight: 7.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** f 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 56844 Z= 0.257 Angle : 0.771 16.436 84343 Z= 0.386 Chirality : 0.041 0.350 10696 Planarity : 0.006 0.076 4990 Dihedral : 26.588 178.282 26638 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 44.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 0.05 % Allowed : 0.62 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.55 % 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: -2.56 (0.17), residues: 2418 helix: -0.50 (0.17), residues: 880 sheet: -2.62 (0.25), residues: 333 loop : -2.36 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP s 34 HIS 0.010 0.002 HIS r 69 PHE 0.028 0.002 PHE b 56 TYR 0.027 0.002 TYR f 4 ARG 0.017 0.001 ARG r 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 3.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TRP g 156 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ARG cc_start: 0.9260 (mtm110) cc_final: 0.8821 (ptt-90) REVERT: b 90 PHE cc_start: 0.5806 (p90) cc_final: 0.5320 (p90) REVERT: b 154 MET cc_start: 0.7073 (pmm) cc_final: 0.6443 (pmm) REVERT: d 63 MET cc_start: 0.8235 (ppp) cc_final: 0.7005 (ppp) REVERT: d 86 PHE cc_start: 0.9393 (t80) cc_final: 0.9171 (t80) REVERT: e 136 MET cc_start: 0.7060 (ptt) cc_final: 0.6716 (ptt) REVERT: f 7 MET cc_start: 0.8129 (tpp) cc_final: 0.7844 (tpp) REVERT: h 19 MET cc_start: 0.8540 (ppp) cc_final: 0.8012 (ppp) REVERT: k 61 PHE cc_start: 0.9680 (t80) cc_final: 0.9264 (t80) REVERT: k 65 MET cc_start: 0.9332 (ptt) cc_final: 0.8823 (ptt) REVERT: l 39 ASN cc_start: 0.9703 (m-40) cc_final: 0.9406 (t0) REVERT: p 81 MET cc_start: 0.8934 (mmp) cc_final: 0.8651 (mmm) REVERT: r 17 TYR cc_start: 0.7719 (p90) cc_final: 0.7373 (p90) REVERT: r 40 GLU cc_start: 0.9260 (pp20) cc_final: 0.9026 (pp20) REVERT: r 70 MET cc_start: 0.8675 (tpt) cc_final: 0.8291 (tpt) outliers start: 1 outliers final: 1 residues processed: 122 average time/residue: 0.7126 time to fit residues: 144.7898 Evaluate side-chains 95 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 190 optimal weight: 20.0000 chunk 246 optimal weight: 1.9990 chunk 330 optimal weight: 30.0000 chunk 95 optimal weight: 30.0000 chunk 286 optimal weight: 4.9990 chunk 45 optimal weight: 30.0000 chunk 86 optimal weight: 20.0000 chunk 310 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 319 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN e 19 ASN ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 70 HIS ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.032530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.024369 restraints weight = 1187151.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.024826 restraints weight = 742001.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.025111 restraints weight = 520049.847| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 56844 Z= 0.455 Angle : 1.008 17.208 84343 Z= 0.497 Chirality : 0.049 0.348 10696 Planarity : 0.008 0.084 4990 Dihedral : 27.198 178.960 26638 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 72.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.52 % Favored : 86.48 % Rotamer: Outliers : 0.05 % Allowed : 0.71 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.16), residues: 2418 helix: -0.99 (0.16), residues: 893 sheet: -3.13 (0.24), residues: 337 loop : -2.48 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP s 34 HIS 0.012 0.003 HIS o 42 PHE 0.035 0.003 PHE b 69 TYR 0.037 0.003 TYR f 4 ARG 0.023 0.001 ARG r 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7182.19 seconds wall clock time: 136 minutes 32.10 seconds (8192.10 seconds total)