Starting phenix.real_space_refine on Tue Mar 26 00:36:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh7_16049/03_2024/8bh7_16049.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh7_16049/03_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_16049/03_2024/8bh7_16049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh7_16049/03_2024/8bh7_16049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh7_16049/03_2024/8bh7_16049.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bh7_16049/03_2024/8bh7_16049.pdb" } 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 Residue "A ASP 49": "OD1" <-> "OD2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 27.30, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.41 Conformation dependent library (CDL) restraints added in 3.8 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: 25.09 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: 50.56 Time building geometry restraints manager: 41.65 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: 97.96 - 105.21: 7171 105.21 - 112.45: 32855 112.45 - 119.69: 19533 119.69 - 126.93: 20791 126.93 - 134.17: 3993 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 2.440 nonbonded pdb=" O ILE m 83 " pdb=" OG SER m 84 " model vdw 2.143 2.440 nonbonded pdb=" O2' G a1517 " pdb=" O4' U a1518 " model vdw 2.143 2.440 nonbonded pdb=" O2' A a1525 " pdb=" O5' U a1526 " model vdw 2.168 2.440 nonbonded pdb=" O2' A a 390 " pdb=" O4' A a 391 " model vdw 2.169 2.440 ... (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 ========== 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: 2.980 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: 0.060 Extract box with map and model: 14.600 Check model and map are aligned: 0.720 Set scattering table: 0.470 Process input model: 196.900 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 220.060 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 3.334 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: 0.7755 time to fit residues: 188.8884 Evaluate side-chains 104 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 3.099 ------------------------------------------------------------------------------- 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: 2.9990 chunk 296 optimal weight: 0.1980 chunk 164 optimal weight: 0.7980 chunk 101 optimal weight: 30.0000 chunk 199 optimal weight: 0.6980 chunk 158 optimal weight: 7.9990 chunk 306 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 228 optimal weight: 20.0000 chunk 355 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 53 HIS c 151 GLN c 166 GLN e 166 ASN g 28 ASN k 119 ASN l 6 GLN ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 33 ASN ** m 105 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 37 ASN ** 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 ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 56844 Z= 0.190 Angle : 0.736 11.849 84343 Z= 0.368 Chirality : 0.039 0.366 10696 Planarity : 0.005 0.054 4990 Dihedral : 26.482 176.189 26638 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 41.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.73 % Favored : 91.23 % Rotamer: Outliers : 0.14 % Allowed : 7.01 % Favored : 92.84 % 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: -0.66 (0.17), residues: 868 sheet: -2.81 (0.26), residues: 322 loop : -2.63 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP c 200 HIS 0.008 0.002 HIS o 42 PHE 0.024 0.002 PHE g 62 TYR 0.021 0.002 TYR m 86 ARG 0.006 0.001 ARG n 57 *********************** 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 143 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 3.194 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8303 (ppp) cc_final: 0.8002 (ppp) REVERT: e 31 PHE cc_start: 0.9659 (p90) cc_final: 0.9433 (p90) REVERT: h 19 MET cc_start: 0.8386 (ppp) cc_final: 0.8029 (ppp) REVERT: k 61 PHE cc_start: 0.9655 (t80) cc_final: 0.9254 (t80) REVERT: k 65 MET cc_start: 0.9486 (ptt) cc_final: 0.9111 (ptt) REVERT: l 39 ASN cc_start: 0.9561 (m-40) cc_final: 0.9207 (t0) REVERT: p 81 MET cc_start: 0.8819 (mmp) cc_final: 0.8527 (mmm) REVERT: r 25 HIS cc_start: 0.6642 (p-80) cc_final: 0.6391 (p-80) REVERT: r 59 MET cc_start: 0.6920 (ptp) cc_final: 0.6143 (mmt) REVERT: r 65 LYS cc_start: 0.9550 (ttmt) cc_final: 0.9216 (tppt) REVERT: r 77 LYS cc_start: 0.9672 (tmtt) cc_final: 0.9380 (tptt) REVERT: r 78 GLU cc_start: 0.9732 (pm20) cc_final: 0.9159 (pm20) outliers start: 3 outliers final: 3 residues processed: 143 average time/residue: 0.7461 time to fit residues: 173.1145 Evaluate side-chains 106 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 3.297 ------------------------------------------------------------------------------- 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: 20.0000 chunk 110 optimal weight: 30.0000 chunk 295 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 97 optimal weight: 50.0000 chunk 355 optimal weight: 20.0000 chunk 384 optimal weight: 8.9990 chunk 316 optimal weight: 10.0000 chunk 352 optimal weight: 8.9990 chunk 121 optimal weight: 30.0000 chunk 285 optimal weight: 8.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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 123 ASN b 55 ASN b 89 GLN ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN h 18 ASN ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 HIS ** i 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 GLN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 62 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2003 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= 0.327 Angle : 0.829 15.632 84343 Z= 0.409 Chirality : 0.043 0.354 10696 Planarity : 0.006 0.084 4990 Dihedral : 26.767 176.407 26638 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 64.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 0.19 % Allowed : 6.73 % Favored : 93.08 % 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: -2.89 (0.16), residues: 2418 helix: -0.71 (0.17), residues: 869 sheet: -2.79 (0.25), residues: 319 loop : -2.61 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP c 200 HIS 0.015 0.002 HIS o 42 PHE 0.015 0.002 PHE g 62 TYR 0.024 0.002 TYR f 4 ARG 0.014 0.001 ARG r 48 *********************** 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 138 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 3.539 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: A 64 MET cc_start: 0.8561 (ppp) cc_final: 0.8193 (ppp) REVERT: d 63 MET cc_start: 0.7880 (ppp) cc_final: 0.6721 (ppp) REVERT: d 86 PHE cc_start: 0.9438 (t80) cc_final: 0.9186 (t80) REVERT: e 136 MET cc_start: 0.6809 (ptt) cc_final: 0.6484 (ptt) REVERT: h 19 MET cc_start: 0.8547 (ppp) cc_final: 0.8148 (ppp) REVERT: k 61 PHE cc_start: 0.9640 (t80) cc_final: 0.9228 (t80) REVERT: k 65 MET cc_start: 0.9381 (ptt) cc_final: 0.8982 (ptt) REVERT: l 39 ASN cc_start: 0.9718 (m-40) cc_final: 0.9427 (t0) REVERT: p 81 MET cc_start: 0.8932 (mmp) cc_final: 0.8707 (mmm) REVERT: r 25 HIS cc_start: 0.6320 (p-80) cc_final: 0.6104 (p-80) REVERT: r 40 GLU cc_start: 0.9478 (pm20) cc_final: 0.9261 (pm20) REVERT: r 59 MET cc_start: 0.7184 (ptp) cc_final: 0.6372 (mmt) REVERT: r 65 LYS cc_start: 0.9614 (ttmt) cc_final: 0.9378 (tppt) REVERT: r 70 MET cc_start: 0.8964 (tpt) cc_final: 0.8590 (tpt) REVERT: t 79 MET cc_start: 0.7619 (ptm) cc_final: 0.7246 (ptm) outliers start: 4 outliers final: 3 residues processed: 138 average time/residue: 0.7650 time to fit residues: 170.1749 Evaluate side-chains 100 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 3.410 ------------------------------------------------------------------------------- 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: 5.9990 chunk 267 optimal weight: 20.0000 chunk 184 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 chunk 238 optimal weight: 20.0000 chunk 356 optimal weight: 30.0000 chunk 377 optimal weight: 5.9990 chunk 186 optimal weight: 20.0000 chunk 338 optimal weight: 7.9990 chunk 101 optimal weight: 30.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- 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 123 ASN ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 74 ASN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 5 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** ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 56844 Z= 0.344 Angle : 0.871 17.948 84343 Z= 0.433 Chirality : 0.045 0.358 10696 Planarity : 0.006 0.060 4990 Dihedral : 27.032 178.848 26638 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 70.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.45 % Favored : 87.55 % Rotamer: Outliers : 0.19 % Allowed : 6.78 % Favored : 93.03 % 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: -3.02 (0.16), residues: 2418 helix: -0.82 (0.16), residues: 872 sheet: -2.92 (0.26), residues: 302 loop : -2.70 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP f 43 HIS 0.014 0.002 HIS s 14 PHE 0.019 0.002 PHE h 63 TYR 0.029 0.003 TYR f 4 ARG 0.011 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 130 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 3.056 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: b 90 PHE cc_start: 0.5800 (p90) cc_final: 0.5525 (p90) REVERT: d 86 PHE cc_start: 0.9437 (t80) cc_final: 0.9001 (t80) REVERT: e 136 MET cc_start: 0.6923 (ptt) cc_final: 0.6494 (ptt) REVERT: h 19 MET cc_start: 0.8659 (ppp) cc_final: 0.8448 (ppp) REVERT: k 61 PHE cc_start: 0.9629 (t80) cc_final: 0.9398 (t80) REVERT: l 39 ASN cc_start: 0.9737 (m-40) cc_final: 0.9432 (t0) REVERT: p 81 MET cc_start: 0.9065 (mmp) cc_final: 0.8788 (mmm) REVERT: r 25 HIS cc_start: 0.6349 (p-80) cc_final: 0.6019 (p-80) REVERT: r 40 GLU cc_start: 0.9420 (pm20) cc_final: 0.9067 (pm20) REVERT: r 41 ARG cc_start: 0.8828 (mmp-170) cc_final: 0.7812 (mmm160) outliers start: 4 outliers final: 3 residues processed: 130 average time/residue: 0.7374 time to fit residues: 155.9104 Evaluate side-chains 98 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 3.044 ------------------------------------------------------------------------------- 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: 0.9980 chunk 214 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 281 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 322 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 192 optimal weight: 0.8980 chunk 339 optimal weight: 0.0970 chunk 95 optimal weight: 20.0000 overall best weight: 2.1982 ------------------------------------------------------------------------------- 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 ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN b 18 HIS d 149 ASN ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN f 53 ASN ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN l 6 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 68 ASN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 29 GLN ** 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 64 GLN t 62 GLN t 67 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 56844 Z= 0.191 Angle : 0.721 16.715 84343 Z= 0.363 Chirality : 0.039 0.351 10696 Planarity : 0.006 0.130 4990 Dihedral : 26.411 176.145 26638 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 42.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.82 % 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: -2.66 (0.16), residues: 2418 helix: -0.47 (0.17), residues: 876 sheet: -2.55 (0.26), residues: 314 loop : -2.57 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 200 HIS 0.018 0.002 HIS t 67 PHE 0.020 0.002 PHE A 37 TYR 0.032 0.002 TYR b 104 ARG 0.017 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 137 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 3.655 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: b 90 PHE cc_start: 0.5675 (p90) cc_final: 0.5316 (p90) REVERT: d 63 MET cc_start: 0.7612 (ppp) cc_final: 0.6073 (ppp) REVERT: e 136 MET cc_start: 0.6735 (ptt) cc_final: 0.6321 (ptt) REVERT: g 31 MET cc_start: 0.7060 (tmm) cc_final: 0.6402 (tmm) REVERT: h 19 MET cc_start: 0.8252 (ppp) cc_final: 0.7985 (ppp) REVERT: k 61 PHE cc_start: 0.9686 (t80) cc_final: 0.9283 (t80) REVERT: k 65 MET cc_start: 0.9399 (ptt) cc_final: 0.8987 (ptt) REVERT: l 39 ASN cc_start: 0.9676 (m-40) cc_final: 0.9302 (t0) REVERT: j 57 MET cc_start: 0.4472 (pmm) cc_final: 0.4234 (pmm) REVERT: p 81 MET cc_start: 0.8896 (mmp) cc_final: 0.8578 (mmm) REVERT: r 25 HIS cc_start: 0.6221 (p-80) cc_final: 0.5984 (p-80) outliers start: 1 outliers final: 1 residues processed: 137 average time/residue: 0.7700 time to fit residues: 170.7362 Evaluate side-chains 95 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 3.308 ------------------------------------------------------------------------------- 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: 5.9990 chunk 74 optimal weight: 20.0000 chunk 221 optimal weight: 8.9990 chunk 93 optimal weight: 30.0000 chunk 378 optimal weight: 10.0000 chunk 314 optimal weight: 30.0000 chunk 175 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 overall best weight: 10.3994 ------------------------------------------------------------------------------- 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 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 ASN ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN ** l 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 68 ASN ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 5 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** t 62 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 56844 Z= 0.379 Angle : 0.898 18.472 84343 Z= 0.441 Chirality : 0.045 0.360 10696 Planarity : 0.007 0.098 4990 Dihedral : 26.924 179.635 26638 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 75.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 0.05 % Allowed : 4.12 % Favored : 95.83 % 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: -2.83 (0.16), residues: 2418 helix: -0.69 (0.17), residues: 879 sheet: -2.75 (0.27), residues: 310 loop : -2.58 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP g 103 HIS 0.011 0.002 HIS s 14 PHE 0.019 0.002 PHE h 63 TYR 0.030 0.003 TYR f 4 ARG 0.017 0.001 ARG r 48 *********************** 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 124 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 3.956 Fit side-chains 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: b 90 PHE cc_start: 0.6212 (p90) cc_final: 0.5834 (p90) REVERT: b 154 MET cc_start: 0.7473 (pmm) cc_final: 0.6648 (pmm) REVERT: d 63 MET cc_start: 0.8210 (ppp) cc_final: 0.6826 (ppp) REVERT: e 136 MET cc_start: 0.6808 (ptt) cc_final: 0.6387 (ptt) REVERT: g 70 MET cc_start: 0.6559 (mmp) cc_final: 0.6314 (mmp) REVERT: h 19 MET cc_start: 0.8344 (ppp) cc_final: 0.7948 (ppp) REVERT: k 61 PHE cc_start: 0.9646 (t80) cc_final: 0.9044 (t80) REVERT: k 65 MET cc_start: 0.9384 (ptt) cc_final: 0.8925 (ptt) REVERT: l 39 ASN cc_start: 0.9717 (m-40) cc_final: 0.9386 (t0) REVERT: p 81 MET cc_start: 0.9046 (mmp) cc_final: 0.8742 (mmm) REVERT: r 25 HIS cc_start: 0.6442 (p-80) cc_final: 0.6095 (p-80) REVERT: r 40 GLU cc_start: 0.9512 (pm20) cc_final: 0.9136 (pm20) REVERT: r 41 ARG cc_start: 0.8923 (mmp-170) cc_final: 0.7793 (mmm160) REVERT: t 79 MET cc_start: 0.7595 (ptm) cc_final: 0.7267 (ptm) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.7615 time to fit residues: 156.4096 Evaluate side-chains 91 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 3.036 ------------------------------------------------------------------------------- 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: 0.0570 chunk 42 optimal weight: 20.0000 chunk 215 optimal weight: 8.9990 chunk 276 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 318 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 376 optimal weight: 20.0000 chunk 235 optimal weight: 0.0040 chunk 229 optimal weight: 30.0000 chunk 173 optimal weight: 8.9990 overall best weight: 5.2116 ------------------------------------------------------------------------------- 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 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** f 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 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 37 ASN ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 62 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3241 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= 0.235 Angle : 0.752 17.815 84343 Z= 0.378 Chirality : 0.041 0.342 10696 Planarity : 0.005 0.058 4990 Dihedral : 26.662 179.087 26638 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 53.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.54 % 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: -2.68 (0.16), residues: 2418 helix: -0.56 (0.17), residues: 883 sheet: -2.55 (0.26), residues: 327 loop : -2.52 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP f 43 HIS 0.007 0.001 HIS s 14 PHE 0.027 0.002 PHE b 56 TYR 0.026 0.002 TYR f 4 ARG 0.010 0.001 ARG h 119 *********************** 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 127 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 3.720 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: b 90 PHE cc_start: 0.5854 (p90) cc_final: 0.5473 (p90) REVERT: d 63 MET cc_start: 0.7963 (ppp) cc_final: 0.6719 (ppp) REVERT: e 136 MET cc_start: 0.6660 (ptt) cc_final: 0.6309 (ptt) REVERT: g 31 MET cc_start: 0.7464 (tmm) cc_final: 0.7210 (tmm) REVERT: h 19 MET cc_start: 0.8378 (ppp) cc_final: 0.8153 (ppp) REVERT: k 61 PHE cc_start: 0.9687 (t80) cc_final: 0.9261 (t80) REVERT: k 65 MET cc_start: 0.9426 (ptt) cc_final: 0.9026 (ptt) REVERT: l 39 ASN cc_start: 0.9702 (m-40) cc_final: 0.9337 (t0) REVERT: p 81 MET cc_start: 0.8901 (mmp) cc_final: 0.8566 (mmm) REVERT: r 25 HIS cc_start: 0.6293 (p-80) cc_final: 0.6076 (p-80) REVERT: r 40 GLU cc_start: 0.9509 (pm20) cc_final: 0.9062 (pm20) REVERT: r 41 ARG cc_start: 0.8923 (mmp-170) cc_final: 0.8072 (mmm160) REVERT: r 70 MET cc_start: 0.9194 (tpt) cc_final: 0.8844 (tpp) REVERT: t 79 MET cc_start: 0.7472 (ptm) cc_final: 0.7260 (ptm) outliers start: 1 outliers final: 1 residues processed: 127 average time/residue: 0.7101 time to fit residues: 148.6745 Evaluate side-chains 96 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 3.398 ------------------------------------------------------------------------------- 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: 7.9990 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: 9.9990 chunk 256 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 296 optimal weight: 1.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** f 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** 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 62 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3411 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= 0.300 Angle : 0.805 18.232 84343 Z= 0.401 Chirality : 0.042 0.350 10696 Planarity : 0.006 0.060 4990 Dihedral : 26.776 179.814 26638 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 64.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 0.05 % Allowed : 1.66 % Favored : 98.29 % 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: -2.75 (0.16), residues: 2418 helix: -0.64 (0.17), residues: 884 sheet: -2.72 (0.27), residues: 310 loop : -2.51 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP c 18 HIS 0.008 0.002 HIS s 14 PHE 0.021 0.002 PHE b 69 TYR 0.028 0.002 TYR f 4 ARG 0.018 0.001 ARG m 14 *********************** 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 127 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0.6012 (p90) cc_final: 0.5657 (p90) REVERT: e 136 MET cc_start: 0.6696 (ptt) cc_final: 0.6301 (ptt) REVERT: h 19 MET cc_start: 0.8396 (ppp) cc_final: 0.7968 (ppp) REVERT: k 61 PHE cc_start: 0.9686 (t80) cc_final: 0.9098 (t80) REVERT: k 65 MET cc_start: 0.9362 (ptt) cc_final: 0.8811 (ptt) REVERT: l 39 ASN cc_start: 0.9711 (m-40) cc_final: 0.9354 (t0) REVERT: p 81 MET cc_start: 0.8970 (mmp) cc_final: 0.8665 (mmm) REVERT: r 25 HIS cc_start: 0.6290 (p-80) cc_final: 0.6088 (p-80) REVERT: r 40 GLU cc_start: 0.9562 (pm20) cc_final: 0.9228 (pm20) REVERT: r 41 ARG cc_start: 0.8973 (mmp-170) cc_final: 0.7809 (mmm160) REVERT: r 70 MET cc_start: 0.9218 (tpt) cc_final: 0.8965 (tpp) REVERT: t 79 MET cc_start: 0.7516 (ptm) cc_final: 0.7249 (ptm) outliers start: 1 outliers final: 1 residues processed: 127 average time/residue: 0.7230 time to fit residues: 150.1330 Evaluate side-chains 96 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 3.334 ------------------------------------------------------------------------------- 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: 10.0000 chunk 361 optimal weight: 20.0000 chunk 329 optimal weight: 30.0000 chunk 351 optimal weight: 6.9990 chunk 360 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 275 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 317 optimal weight: 9.9990 chunk 332 optimal weight: 0.7980 overall best weight: 6.5588 ------------------------------------------------------------------------------- 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 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** f 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** 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 62 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 56844 Z= 0.261 Angle : 0.773 17.786 84343 Z= 0.387 Chirality : 0.041 0.349 10696 Planarity : 0.006 0.125 4990 Dihedral : 26.698 180.000 26638 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 59.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 0.05 % Allowed : 0.85 % Favored : 99.10 % 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: -2.73 (0.16), residues: 2418 helix: -0.63 (0.17), residues: 890 sheet: -2.52 (0.27), residues: 314 loop : -2.56 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP c 18 HIS 0.007 0.002 HIS o 42 PHE 0.030 0.002 PHE b 56 TYR 0.026 0.002 TYR f 4 ARG 0.026 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 131 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 3.403 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: b 90 PHE cc_start: 0.5907 (p90) cc_final: 0.5486 (p90) REVERT: b 113 ARG cc_start: 0.7257 (ptt180) cc_final: 0.7012 (ptt180) REVERT: d 63 MET cc_start: 0.8201 (ppp) cc_final: 0.6543 (ppp) REVERT: e 136 MET cc_start: 0.6694 (ptt) cc_final: 0.6322 (ptt) REVERT: h 19 MET cc_start: 0.8445 (ppp) cc_final: 0.8176 (ppp) REVERT: k 61 PHE cc_start: 0.9692 (t80) cc_final: 0.9237 (t80) REVERT: k 65 MET cc_start: 0.9375 (ptt) cc_final: 0.8939 (ptt) REVERT: l 39 ASN cc_start: 0.9712 (m-40) cc_final: 0.9358 (t0) REVERT: j 57 MET cc_start: 0.4635 (pmm) cc_final: 0.4395 (pmm) REVERT: p 81 MET cc_start: 0.8965 (mmp) cc_final: 0.8646 (mmm) REVERT: r 25 HIS cc_start: 0.6169 (p-80) cc_final: 0.5956 (p-80) REVERT: r 70 MET cc_start: 0.9271 (tpt) cc_final: 0.9026 (tpp) REVERT: t 79 MET cc_start: 0.7385 (ptm) cc_final: 0.7170 (ptm) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.7771 time to fit residues: 163.5428 Evaluate side-chains 104 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 3.164 ------------------------------------------------------------------------------- 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: 10.0000 chunk 230 optimal weight: 30.0000 chunk 371 optimal weight: 9.9990 chunk 226 optimal weight: 0.6980 chunk 176 optimal weight: 20.0000 chunk 258 optimal weight: 9.9990 chunk 389 optimal weight: 8.9990 chunk 358 optimal weight: 0.0870 chunk 310 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 239 optimal weight: 10.0000 overall best weight: 5.9564 ------------------------------------------------------------------------------- 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 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** f 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 70 HIS ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 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 62 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 56844 Z= 0.251 Angle : 0.765 17.518 84343 Z= 0.383 Chirality : 0.041 0.350 10696 Planarity : 0.006 0.115 4990 Dihedral : 26.631 179.735 26638 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 57.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 0.05 % Allowed : 0.66 % Favored : 99.29 % 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: -2.68 (0.16), residues: 2418 helix: -0.60 (0.17), residues: 888 sheet: -2.53 (0.27), residues: 316 loop : -2.50 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 18 HIS 0.007 0.002 HIS r 69 PHE 0.026 0.002 PHE b 69 TYR 0.027 0.002 TYR f 4 ARG 0.025 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 131 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 3.341 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: b 90 PHE cc_start: 0.5928 (p90) cc_final: 0.5647 (p90) REVERT: b 113 ARG cc_start: 0.7318 (ptt180) cc_final: 0.7108 (ptt180) REVERT: b 170 ARG cc_start: 0.9658 (ttp80) cc_final: 0.9444 (mmm160) REVERT: d 63 MET cc_start: 0.8133 (ppp) cc_final: 0.6403 (ppp) REVERT: d 87 MET cc_start: 0.9630 (mpp) cc_final: 0.9214 (mpp) REVERT: e 136 MET cc_start: 0.6611 (ptt) cc_final: 0.6244 (ptt) REVERT: g 31 MET cc_start: 0.7541 (tmm) cc_final: 0.7328 (tmm) REVERT: h 19 MET cc_start: 0.8433 (ppp) cc_final: 0.8153 (ppp) REVERT: k 61 PHE cc_start: 0.9694 (t80) cc_final: 0.9238 (t80) REVERT: k 65 MET cc_start: 0.9378 (ptt) cc_final: 0.8945 (ptt) REVERT: l 39 ASN cc_start: 0.9718 (m-40) cc_final: 0.9366 (t0) REVERT: j 57 MET cc_start: 0.4521 (pmm) cc_final: 0.4309 (pmm) REVERT: p 81 MET cc_start: 0.8946 (mmp) cc_final: 0.8629 (mmm) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.7493 time to fit residues: 156.7913 Evaluate side-chains 103 residues out of total 2110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 3.278 ------------------------------------------------------------------------------- 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: 0.9980 chunk 246 optimal weight: 4.9990 chunk 330 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 286 optimal weight: 30.0000 chunk 45 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 chunk 319 optimal weight: 40.0000 chunk 39 optimal weight: 20.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- 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 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 166 GLN ** f 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 73 ASN ** i 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 GLN ** 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 41 ASN t 62 GLN ** t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.034101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.025809 restraints weight = 1114154.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.026374 restraints weight = 690607.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.026778 restraints weight = 514819.706| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 56844 Z= 0.262 Angle : 0.774 17.727 84343 Z= 0.386 Chirality : 0.041 0.353 10696 Planarity : 0.006 0.111 4990 Dihedral : 26.637 179.822 26638 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 58.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 0.05 % Allowed : 0.52 % Favored : 99.43 % 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: -2.73 (0.16), residues: 2418 helix: -0.63 (0.17), residues: 890 sheet: -2.59 (0.26), residues: 338 loop : -2.53 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP k 44 HIS 0.009 0.002 HIS r 69 PHE 0.025 0.002 PHE f 26 TYR 0.033 0.002 TYR r 28 ARG 0.022 0.001 ARG r 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7466.83 seconds wall clock time: 142 minutes 42.00 seconds (8562.00 seconds total)