Starting phenix.real_space_refine on Thu Dec 7 16:09:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2l_31655/12_2023/7v2l_31655.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2l_31655/12_2023/7v2l_31655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2l_31655/12_2023/7v2l_31655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2l_31655/12_2023/7v2l_31655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2l_31655/12_2023/7v2l_31655.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2l_31655/12_2023/7v2l_31655.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1507 5.49 5 S 55 5.16 5 C 27668 2.51 5 N 10043 2.21 5 O 14135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 31": "OE1" <-> "OE2" Residue "F TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H GLU 132": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I GLU 2": "OE1" <-> "OE2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "M GLU 8": "OE1" <-> "OE2" Residue "M GLU 50": "OE1" <-> "OE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P GLU 54": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 86": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "S GLU 43": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T GLU 93": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 53410 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 32392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1507, 32392 Classifications: {'RNA': 1507} Modifications used: {'rna2p_pur': 131, 'rna2p_pyr': 102, 'rna3p_pur': 723, 'rna3p_pyr': 551} Link IDs: {'rna2p': 233, 'rna3p': 1273} Chain: "B" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1802 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain: "C" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "D" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "E" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1146 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "F" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "G" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1257 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "H" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "I" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "J" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 794 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "K" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 885 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 970 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "M" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 905 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "N" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "O" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "P" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 682 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "Q" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 834 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "R" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 565 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "S" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 647 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "T" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 763 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "V" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 208 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "W" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2048 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 12, 'TRANS': 248} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 35865 SG CYS D 9 85.613 72.270 95.464 1.00 41.81 S ATOM 35890 SG CYS D 12 86.967 75.326 97.989 1.00 41.65 S ATOM 36008 SG CYS D 26 88.894 71.268 96.557 1.00 44.83 S ATOM 36048 SG CYS D 31 89.831 73.944 94.958 1.00 45.74 S ATOM 46626 SG CYS N 24 59.325 125.258 49.202 1.00 39.58 S ATOM 46650 SG CYS N 27 57.408 123.803 51.889 1.00 38.99 S ATOM 46757 SG CYS N 40 58.505 127.319 52.335 1.00 37.14 S ATOM 46782 SG CYS N 43 61.110 124.783 52.255 1.00 36.97 S Time building chain proxies: 20.97, per 1000 atoms: 0.39 Number of scatterers: 53410 At special positions: 0 Unit cell: (139.38, 213.9, 227.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 55 16.00 P 1507 15.00 O 14135 8.00 N 10043 7.00 C 27668 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: 19.67 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 31 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 9 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 12 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " Number of angles added : 12 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4850 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 22 sheets defined 43.2% alpha, 18.1% beta 470 base pairs and 748 stacking pairs defined. Time for finding SS restraints: 18.38 Creating SS restraints... Processing helix chain 'B' and resid 25 through 30 removed outlier: 4.609A pdb=" N ARG B 30 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 65 Processing helix chain 'B' and resid 76 through 87 removed outlier: 4.391A pdb=" N ILE B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 123 removed outlier: 3.701A pdb=" N ARG B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 149 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 170 through 180 Processing helix chain 'B' and resid 193 through 197 removed outlier: 3.570A pdb=" N LEU B 196 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 225 Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 47 through 51 removed outlier: 4.014A pdb=" N GLY C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 51' Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.867A pdb=" N VAL C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 108 through 111 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 144 removed outlier: 3.696A pdb=" N SER C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 4.150A pdb=" N GLY C 159 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 52 through 69 removed outlier: 3.859A pdb=" N TYR D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 113 through 124 removed outlier: 3.709A pdb=" N GLN D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 153 Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 199 through 207 removed outlier: 4.039A pdb=" N VAL D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR D 207 " --> pdb=" O VAL D 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 65 Processing helix chain 'E' and resid 103 through 112 removed outlier: 3.596A pdb=" N LEU E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 141 Processing helix chain 'E' and resid 144 through 153 Processing helix chain 'F' and resid 15 through 33 Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 71 through 80 Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.689A pdb=" N THR G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 54 Processing helix chain 'G' and resid 57 through 69 removed outlier: 3.587A pdb=" N VAL G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 132 through 145 Processing helix chain 'G' and resid 148 through 153 removed outlier: 4.110A pdb=" N HIS G 153 " --> pdb=" O ALA G 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 19 removed outlier: 3.619A pdb=" N VAL H 19 " --> pdb=" O ASN H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 42 Processing helix chain 'H' and resid 103 through 107 Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'I' and resid 33 through 37 removed outlier: 3.684A pdb=" N PHE I 37 " --> pdb=" O PHE I 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 33 through 37' Processing helix chain 'I' and resid 40 through 46 removed outlier: 3.998A pdb=" N VAL I 44 " --> pdb=" O VAL I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 53 removed outlier: 3.650A pdb=" N ARG I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL I 53 " --> pdb=" O PRO I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 89 Processing helix chain 'I' and resid 92 through 97 Processing helix chain 'J' and resid 12 through 30 Processing helix chain 'J' and resid 78 through 85 Processing helix chain 'K' and resid 45 through 49 removed outlier: 3.706A pdb=" N GLY K 49 " --> pdb=" O GLY K 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 45 through 49' Processing helix chain 'K' and resid 51 through 56 removed outlier: 3.635A pdb=" N ARG K 54 " --> pdb=" O LYS K 51 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS K 55 " --> pdb=" O GLY K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 74 Processing helix chain 'K' and resid 90 through 100 removed outlier: 3.590A pdb=" N ALA K 100 " --> pdb=" O ARG K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 126 Processing helix chain 'L' and resid 3 through 11 Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'M' and resid 14 through 20 removed outlier: 3.925A pdb=" N THR M 20 " --> pdb=" O ASP M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 44 through 48 removed outlier: 3.619A pdb=" N LEU M 48 " --> pdb=" O VAL M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 64 removed outlier: 3.667A pdb=" N TRP M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.925A pdb=" N ILE M 84 " --> pdb=" O ARG M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 95 Processing helix chain 'M' and resid 107 through 112 Processing helix chain 'N' and resid 3 through 10 Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.662A pdb=" N HIS O 53 " --> pdb=" O ASP O 49 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 67 through 77 Processing helix chain 'Q' and resid 81 through 94 removed outlier: 4.302A pdb=" N VAL Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 98 Processing helix chain 'R' and resid 36 through 41 Processing helix chain 'R' and resid 42 through 44 No H-bonds generated for 'chain 'R' and resid 42 through 44' Processing helix chain 'R' and resid 52 through 57 Processing helix chain 'R' and resid 59 through 77 Processing helix chain 'S' and resid 12 through 24 removed outlier: 4.487A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 70 through 75 removed outlier: 3.572A pdb=" N PHE S 74 " --> pdb=" O LEU S 71 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA S 75 " --> pdb=" O GLY S 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 47 removed outlier: 3.661A pdb=" N ARG T 17 " --> pdb=" O LEU T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 69 removed outlier: 3.764A pdb=" N GLY T 69 " --> pdb=" O LYS T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 92 Processing helix chain 'V' and resid 8 through 16 removed outlier: 3.696A pdb=" N LYS V 12 " --> pdb=" O THR V 8 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 45 Processing helix chain 'W' and resid 60 through 70 removed outlier: 4.069A pdb=" N GLN W 65 " --> pdb=" O ALA W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 90 Processing helix chain 'W' and resid 107 through 116 removed outlier: 3.855A pdb=" N VAL W 111 " --> pdb=" O ASP W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 133 through 143 removed outlier: 3.540A pdb=" N GLU W 143 " --> pdb=" O LYS W 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 157 through 160 removed outlier: 4.223A pdb=" N GLU W 160 " --> pdb=" O GLU W 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 157 through 160' Processing helix chain 'W' and resid 172 through 181 Processing helix chain 'W' and resid 220 through 232 Processing helix chain 'W' and resid 238 through 245 Processing helix chain 'W' and resid 253 through 264 Processing helix chain 'W' and resid 276 through 292 removed outlier: 3.965A pdb=" N ALA W 290 " --> pdb=" O GLY W 286 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 20 removed outlier: 5.135A pdb=" N HIS B 40 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 34 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 93 removed outlier: 8.368A pdb=" N VAL B 93 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE B 70 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 69 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 21 removed outlier: 6.666A pdb=" N HIS C 69 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR C 67 " --> pdb=" O VAL C 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'D' and resid 126 through 128 Processing sheet with id=AA6, first strand: chain 'E' and resid 7 through 20 removed outlier: 5.314A pdb=" N GLU E 8 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLY E 35 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N MET E 10 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL E 33 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 12 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY E 23 " --> pdb=" O GLN E 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 80 through 84 Processing sheet with id=AA8, first strand: chain 'F' and resid 36 through 52 removed outlier: 6.988A pdb=" N GLN F 64 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL F 40 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TRP F 62 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU F 42 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE F 60 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY F 44 " --> pdb=" O GLY F 58 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY F 58 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ARG F 46 " --> pdb=" O PRO F 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 98 through 99 removed outlier: 3.506A pdb=" N PHE R 29 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 74 through 80 Processing sheet with id=AB2, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AB3, first strand: chain 'H' and resid 94 through 95 removed outlier: 6.322A pdb=" N LEU H 133 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER H 113 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS H 135 " --> pdb=" O ILE H 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'J' and resid 40 through 49 removed outlier: 5.249A pdb=" N ASN J 69 " --> pdb=" O PRO J 41 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY J 10 " --> pdb=" O HIS J 68 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU J 8 " --> pdb=" O ARG J 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 40 through 49 removed outlier: 5.249A pdb=" N ASN J 69 " --> pdb=" O PRO J 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 39 through 44 removed outlier: 6.732A pdb=" N ILE K 32 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TRP K 42 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL K 30 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER K 44 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR K 28 " --> pdb=" O SER K 44 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA K 19 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ARG K 85 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE K 21 " --> pdb=" O ARG K 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 29 through 40 removed outlier: 5.608A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL L 36 " --> pdb=" O LYS L 54 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 49 through 51 removed outlier: 6.588A pdb=" N ILE P 19 " --> pdb=" O ILE P 36 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR P 17 " --> pdb=" O TYR P 38 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL P 2 " --> pdb=" O GLN P 65 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Q' and resid 5 through 15 removed outlier: 14.673A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.948A pdb=" N GLN Q 26 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR Q 7 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU Q 24 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL Q 9 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR Q 20 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASP Q 13 " --> pdb=" O THR Q 18 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR Q 18 " --> pdb=" O ASP Q 13 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N LYS Q 69 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU Q 43 " --> pdb=" O LYS Q 69 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE Q 71 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU Q 76 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL Q 56 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 31 through 33 Processing sheet with id=AC4, first strand: chain 'W' and resid 96 through 98 removed outlier: 6.603A pdb=" N GLY W 51 " --> pdb=" O MET W 123 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL W 125 " --> pdb=" O GLY W 51 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE W 53 " --> pdb=" O VAL W 125 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ASN W 127 " --> pdb=" O ILE W 53 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE W 55 " --> pdb=" O ASN W 127 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE W 122 " --> pdb=" O GLY W 149 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N VAL W 151 " --> pdb=" O ILE W 122 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL W 124 " --> pdb=" O VAL W 151 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N MET W 153 " --> pdb=" O VAL W 124 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA W 126 " --> pdb=" O MET W 153 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N GLN W 155 " --> pdb=" O ALA W 126 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU W 154 " --> pdb=" O ALA W 204 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER W 203 " --> pdb=" O ILE W 189 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE W 189 " --> pdb=" O SER W 203 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL W 205 " --> pdb=" O VAL W 187 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2754 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1250 hydrogen bonds 2052 hydrogen bond angles 0 basepair planarities 470 basepair parallelities 748 stacking parallelities Total time for adding SS restraints: 31.99 Time building geometry restraints manager: 21.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8469 1.34 - 1.46: 24957 1.46 - 1.58: 21071 1.58 - 1.70: 3013 1.70 - 1.82: 96 Bond restraints: 57606 Sorted by residual: bond pdb=" C SER W 91 " pdb=" N PRO W 92 " ideal model delta sigma weight residual 1.334 1.360 -0.026 8.40e-03 1.42e+04 9.69e+00 bond pdb=" C ASP H 73 " pdb=" N PRO H 74 " ideal model delta sigma weight residual 1.331 1.355 -0.023 7.90e-03 1.60e+04 8.50e+00 bond pdb=" C ASP F 55 " pdb=" N PRO F 56 " ideal model delta sigma weight residual 1.332 1.356 -0.024 8.90e-03 1.26e+04 7.10e+00 bond pdb=" N GLY D 2 " pdb=" CA GLY D 2 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.51e+00 bond pdb=" N GLY C 2 " pdb=" CA GLY C 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.40e+00 ... (remaining 57601 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.23: 9244 106.23 - 113.29: 31768 113.29 - 120.35: 24934 120.35 - 127.41: 16142 127.41 - 134.47: 3167 Bond angle restraints: 85255 Sorted by residual: angle pdb=" O3' U A 735 " pdb=" C3' U A 735 " pdb=" C2' U A 735 " ideal model delta sigma weight residual 113.70 125.51 -11.81 1.50e+00 4.44e-01 6.20e+01 angle pdb=" C4' G A1426 " pdb=" C3' G A1426 " pdb=" O3' G A1426 " ideal model delta sigma weight residual 109.40 117.36 -7.96 1.50e+00 4.44e-01 2.81e+01 angle pdb=" O3' G A 409 " pdb=" C3' G A 409 " pdb=" C2' G A 409 " ideal model delta sigma weight residual 109.50 116.91 -7.41 1.50e+00 4.44e-01 2.44e+01 angle pdb=" C2' A A 547 " pdb=" C1' A A 547 " pdb=" N9 A A 547 " ideal model delta sigma weight residual 112.00 118.97 -6.97 1.50e+00 4.44e-01 2.16e+01 angle pdb=" CA ASP M 16 " pdb=" CB ASP M 16 " pdb=" CG ASP M 16 " ideal model delta sigma weight residual 112.60 116.96 -4.36 1.00e+00 1.00e+00 1.90e+01 ... (remaining 85250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 32425 35.90 - 71.80: 3339 71.80 - 107.70: 537 107.70 - 143.60: 5 143.60 - 179.50: 27 Dihedral angle restraints: 36333 sinusoidal: 28796 harmonic: 7537 Sorted by residual: dihedral pdb=" O4' C A 950 " pdb=" C1' C A 950 " pdb=" N1 C A 950 " pdb=" C2 C A 950 " ideal model delta sinusoidal sigma weight residual 200.00 20.50 179.50 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A1176 " pdb=" C1' U A1176 " pdb=" N1 U A1176 " pdb=" C2 U A1176 " ideal model delta sinusoidal sigma weight residual 200.00 21.04 178.96 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A 339 " pdb=" C1' U A 339 " pdb=" N1 U A 339 " pdb=" C2 U A 339 " ideal model delta sinusoidal sigma weight residual -160.00 15.57 -175.57 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 36330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 6706 0.092 - 0.184: 3254 0.184 - 0.276: 719 0.276 - 0.368: 12 0.368 - 0.460: 2 Chirality restraints: 10693 Sorted by residual: chirality pdb=" C3' G A 409 " pdb=" C4' G A 409 " pdb=" O3' G A 409 " pdb=" C2' G A 409 " both_signs ideal model delta sigma weight residual False -2.74 -2.28 -0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CA ASP M 16 " pdb=" N ASP M 16 " pdb=" C ASP M 16 " pdb=" CB ASP M 16 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA GLU G 146 " pdb=" N GLU G 146 " pdb=" C GLU G 146 " pdb=" CB GLU G 146 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 10690 not shown) Planarity restraints: 5213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 53 " -0.017 2.00e-02 2.50e+03 1.99e-02 1.19e+01 pdb=" N9 G A 53 " 0.005 2.00e-02 2.50e+03 pdb=" C8 G A 53 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A 53 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G A 53 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A 53 " 0.013 2.00e-02 2.50e+03 pdb=" O6 G A 53 " -0.003 2.00e-02 2.50e+03 pdb=" N1 G A 53 " -0.046 2.00e-02 2.50e+03 pdb=" C2 G A 53 " 0.045 2.00e-02 2.50e+03 pdb=" N2 G A 53 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A 53 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A 53 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 762 " -0.005 2.00e-02 2.50e+03 1.83e-02 1.01e+01 pdb=" N9 G A 762 " -0.006 2.00e-02 2.50e+03 pdb=" C8 G A 762 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G A 762 " 0.009 2.00e-02 2.50e+03 pdb=" C5 G A 762 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G A 762 " 0.021 2.00e-02 2.50e+03 pdb=" O6 G A 762 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G A 762 " -0.043 2.00e-02 2.50e+03 pdb=" C2 G A 762 " 0.038 2.00e-02 2.50e+03 pdb=" N2 G A 762 " -0.000 2.00e-02 2.50e+03 pdb=" N3 G A 762 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G A 762 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 864 " -0.001 2.00e-02 2.50e+03 1.72e-02 8.84e+00 pdb=" N9 G A 864 " 0.005 2.00e-02 2.50e+03 pdb=" C8 G A 864 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A 864 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G A 864 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G A 864 " -0.018 2.00e-02 2.50e+03 pdb=" O6 G A 864 " -0.000 2.00e-02 2.50e+03 pdb=" N1 G A 864 " 0.040 2.00e-02 2.50e+03 pdb=" C2 G A 864 " -0.038 2.00e-02 2.50e+03 pdb=" N2 G A 864 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A 864 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G A 864 " 0.004 2.00e-02 2.50e+03 ... (remaining 5210 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5939 2.75 - 3.29: 47053 3.29 - 3.83: 106225 3.83 - 4.36: 130314 4.36 - 4.90: 182448 Nonbonded interactions: 471979 Sorted by model distance: nonbonded pdb=" O SER Q 66 " pdb=" NH1 ARG Q 70 " model vdw 2.214 2.520 nonbonded pdb=" O GLN J 84 " pdb=" OG1 THR J 87 " model vdw 2.224 2.440 nonbonded pdb=" O6 G A 980 " pdb=" N6 A A1024 " model vdw 2.225 2.520 nonbonded pdb=" NH1 ARG I 104 " pdb=" O ASP I 105 " model vdw 2.230 2.520 nonbonded pdb=" O2 U A 661 " pdb=" O2' A A 761 " model vdw 2.233 2.440 ... (remaining 471974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 8.840 Check model and map are aligned: 0.630 Set scattering table: 0.370 Process input model: 141.110 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 0.008 0.041 57606 Z= 0.480 Angle : 1.075 11.810 85255 Z= 0.677 Chirality : 0.099 0.460 10693 Planarity : 0.004 0.020 5213 Dihedral : 23.179 179.500 31483 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.71 % Favored : 93.14 % Rotamer: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2579 helix: 0.88 (0.16), residues: 1032 sheet: -0.14 (0.26), residues: 417 loop : -1.75 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 167 HIS 0.008 0.002 HIS P 13 PHE 0.014 0.002 PHE D 79 TYR 0.018 0.002 TYR H 65 ARG 0.008 0.001 ARG E 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 434 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 435 average time/residue: 0.5973 time to fit residues: 422.7563 Evaluate side-chains 366 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 365 time to evaluate : 2.591 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4497 time to fit residues: 3.7236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 340 optimal weight: 5.9990 chunk 305 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 315 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 365 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN J 33 GLN P 76 GLN Q 26 GLN T 90 GLN W 117 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 57606 Z= 0.292 Angle : 0.598 9.344 85255 Z= 0.305 Chirality : 0.037 0.230 10693 Planarity : 0.005 0.055 5213 Dihedral : 23.728 179.842 26040 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.86 % Favored : 93.02 % Rotamer: Outliers : 1.54 % Allowed : 10.63 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2579 helix: 1.13 (0.16), residues: 1061 sheet: -0.44 (0.25), residues: 453 loop : -1.60 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 64 HIS 0.008 0.001 HIS N 49 PHE 0.022 0.002 PHE H 31 TYR 0.019 0.002 TYR C 193 ARG 0.006 0.001 ARG N 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 367 time to evaluate : 2.619 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 26 residues processed: 380 average time/residue: 0.5530 time to fit residues: 346.3149 Evaluate side-chains 374 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 348 time to evaluate : 2.595 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3879 time to fit residues: 21.9750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 203 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 304 optimal weight: 8.9990 chunk 249 optimal weight: 5.9990 chunk 100 optimal weight: 40.0000 chunk 366 optimal weight: 7.9990 chunk 396 optimal weight: 10.0000 chunk 326 optimal weight: 0.9990 chunk 363 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 294 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN P 76 GLN Q 26 GLN T 42 GLN W 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 57606 Z= 0.261 Angle : 0.572 9.367 85255 Z= 0.292 Chirality : 0.036 0.230 10693 Planarity : 0.004 0.049 5213 Dihedral : 23.693 179.647 26040 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.86 % Favored : 93.02 % Rotamer: Outliers : 1.09 % Allowed : 13.40 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2579 helix: 1.18 (0.16), residues: 1065 sheet: -0.47 (0.25), residues: 453 loop : -1.59 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 167 HIS 0.006 0.001 HIS N 49 PHE 0.020 0.001 PHE H 31 TYR 0.019 0.002 TYR M 59 ARG 0.008 0.000 ARG K 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 359 time to evaluate : 2.619 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 375 average time/residue: 0.5548 time to fit residues: 342.5085 Evaluate side-chains 353 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 344 time to evaluate : 2.594 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3848 time to fit residues: 9.5347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 362 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 chunk 246 optimal weight: 1.9990 chunk 367 optimal weight: 5.9990 chunk 389 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 348 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 GLN ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN G 109 ASN P 76 GLN Q 26 GLN W 117 GLN W 234 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 57606 Z= 0.184 Angle : 0.527 9.535 85255 Z= 0.270 Chirality : 0.034 0.219 10693 Planarity : 0.004 0.045 5213 Dihedral : 23.639 179.567 26040 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.17 % Favored : 93.72 % Rotamer: Outliers : 1.04 % Allowed : 14.86 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2579 helix: 1.40 (0.16), residues: 1060 sheet: -0.30 (0.25), residues: 445 loop : -1.56 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 167 HIS 0.004 0.001 HIS H 82 PHE 0.015 0.001 PHE H 31 TYR 0.013 0.001 TYR P 32 ARG 0.005 0.000 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 364 time to evaluate : 2.630 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 375 average time/residue: 0.5525 time to fit residues: 341.9015 Evaluate side-chains 361 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 349 time to evaluate : 2.646 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3851 time to fit residues: 11.8132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 324 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 290 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 332 optimal weight: 9.9990 chunk 269 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 349 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN P 76 GLN Q 26 GLN W 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 57606 Z= 0.399 Angle : 0.667 9.236 85255 Z= 0.336 Chirality : 0.041 0.255 10693 Planarity : 0.005 0.054 5213 Dihedral : 23.762 179.814 26040 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.44 % Favored : 92.44 % Rotamer: Outliers : 1.50 % Allowed : 16.67 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2579 helix: 0.99 (0.16), residues: 1071 sheet: -0.56 (0.25), residues: 443 loop : -1.63 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 24 HIS 0.011 0.002 HIS J 56 PHE 0.023 0.002 PHE H 31 TYR 0.024 0.002 TYR I 125 ARG 0.008 0.001 ARG N 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 352 time to evaluate : 2.612 Fit side-chains outliers start: 33 outliers final: 19 residues processed: 375 average time/residue: 0.5601 time to fit residues: 347.1445 Evaluate side-chains 359 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 340 time to evaluate : 2.609 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4812 time to fit residues: 19.6101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 131 optimal weight: 10.0000 chunk 350 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 228 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 389 optimal weight: 0.8980 chunk 323 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN G 109 ASN J 33 GLN P 76 GLN Q 26 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 57606 Z= 0.168 Angle : 0.522 9.506 85255 Z= 0.267 Chirality : 0.034 0.219 10693 Planarity : 0.004 0.041 5213 Dihedral : 23.611 179.812 26040 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.78 % Favored : 94.11 % Rotamer: Outliers : 1.09 % Allowed : 17.40 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2579 helix: 1.45 (0.16), residues: 1056 sheet: -0.28 (0.26), residues: 438 loop : -1.57 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 167 HIS 0.009 0.001 HIS S 14 PHE 0.014 0.001 PHE G 62 TYR 0.019 0.001 TYR I 125 ARG 0.004 0.000 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 362 time to evaluate : 2.579 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 374 average time/residue: 0.5501 time to fit residues: 340.1954 Evaluate side-chains 352 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 342 time to evaluate : 2.602 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3792 time to fit residues: 10.1833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 375 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 222 optimal weight: 0.5980 chunk 284 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 328 optimal weight: 5.9990 chunk 217 optimal weight: 0.7980 chunk 388 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 chunk 236 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN J 33 GLN P 76 GLN W 117 GLN W 246 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 57606 Z= 0.143 Angle : 0.502 9.655 85255 Z= 0.258 Chirality : 0.032 0.216 10693 Planarity : 0.004 0.048 5213 Dihedral : 23.566 179.707 26040 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.13 % Favored : 93.76 % Rotamer: Outliers : 0.73 % Allowed : 18.40 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2579 helix: 1.59 (0.16), residues: 1055 sheet: -0.25 (0.26), residues: 449 loop : -1.52 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 167 HIS 0.004 0.001 HIS S 14 PHE 0.014 0.001 PHE G 62 TYR 0.022 0.001 TYR I 125 ARG 0.006 0.000 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 358 time to evaluate : 2.626 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 369 average time/residue: 0.5632 time to fit residues: 344.5332 Evaluate side-chains 361 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 350 time to evaluate : 2.578 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3887 time to fit residues: 11.0672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 240 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 chunk 264 optimal weight: 9.9990 chunk 192 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 109 ASN J 33 GLN P 76 GLN W 117 GLN W 246 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 57606 Z= 0.319 Angle : 0.612 9.418 85255 Z= 0.310 Chirality : 0.038 0.230 10693 Planarity : 0.005 0.048 5213 Dihedral : 23.668 179.601 26040 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.29 % Favored : 92.59 % Rotamer: Outliers : 0.64 % Allowed : 18.36 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2579 helix: 1.21 (0.16), residues: 1069 sheet: -0.35 (0.26), residues: 430 loop : -1.59 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 24 HIS 0.008 0.001 HIS J 56 PHE 0.018 0.002 PHE H 31 TYR 0.023 0.002 TYR I 125 ARG 0.006 0.001 ARG N 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 349 time to evaluate : 2.607 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 357 average time/residue: 0.5601 time to fit residues: 331.5116 Evaluate side-chains 349 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 341 time to evaluate : 2.599 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3832 time to fit residues: 8.8539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 353 optimal weight: 10.0000 chunk 372 optimal weight: 9.9990 chunk 339 optimal weight: 1.9990 chunk 361 optimal weight: 20.0000 chunk 217 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 284 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 chunk 327 optimal weight: 9.9990 chunk 342 optimal weight: 0.9990 chunk 360 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN J 33 GLN P 76 GLN Q 26 GLN T 42 GLN W 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 57606 Z= 0.186 Angle : 0.533 9.465 85255 Z= 0.273 Chirality : 0.034 0.219 10693 Planarity : 0.004 0.047 5213 Dihedral : 23.600 179.504 26040 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.13 % Favored : 93.76 % Rotamer: Outliers : 0.41 % Allowed : 18.63 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2579 helix: 1.42 (0.16), residues: 1061 sheet: -0.28 (0.26), residues: 437 loop : -1.50 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 167 HIS 0.006 0.001 HIS S 14 PHE 0.020 0.001 PHE G 62 TYR 0.023 0.001 TYR I 125 ARG 0.006 0.000 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 348 time to evaluate : 2.612 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 354 average time/residue: 0.5565 time to fit residues: 325.7065 Evaluate side-chains 350 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 345 time to evaluate : 2.918 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3747 time to fit residues: 6.5880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 237 optimal weight: 0.0670 chunk 382 optimal weight: 0.6980 chunk 233 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 266 optimal weight: 8.9990 chunk 401 optimal weight: 6.9990 chunk 369 optimal weight: 10.0000 chunk 319 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 246 optimal weight: 0.8980 chunk 196 optimal weight: 20.0000 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN J 33 GLN P 76 GLN Q 26 GLN T 42 GLN W 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 57606 Z= 0.126 Angle : 0.518 9.706 85255 Z= 0.266 Chirality : 0.033 0.220 10693 Planarity : 0.004 0.046 5213 Dihedral : 23.621 179.760 26040 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.28 % Favored : 93.60 % Rotamer: Outliers : 0.32 % Allowed : 18.81 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2579 helix: 1.50 (0.16), residues: 1061 sheet: -0.18 (0.26), residues: 438 loop : -1.46 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 167 HIS 0.006 0.001 HIS S 14 PHE 0.010 0.001 PHE R 29 TYR 0.031 0.001 TYR W 288 ARG 0.008 0.000 ARG C 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5158 Ramachandran restraints generated. 2579 Oldfield, 0 Emsley, 2579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 355 time to evaluate : 2.687 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 358 average time/residue: 0.5626 time to fit residues: 332.0147 Evaluate side-chains 351 residues out of total 2201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 347 time to evaluate : 2.595 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3739 time to fit residues: 5.8218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 253 optimal weight: 4.9990 chunk 340 optimal weight: 0.0050 chunk 97 optimal weight: 20.0000 chunk 294 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 320 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 328 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 overall best weight: 6.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN J 33 GLN P 76 GLN W 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.079756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.058412 restraints weight = 136961.637| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 1.09 r_work: 0.2657 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 57606 Z= 0.386 Angle : 0.664 9.164 85255 Z= 0.334 Chirality : 0.040 0.249 10693 Planarity : 0.005 0.053 5213 Dihedral : 23.710 179.589 26040 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.87 % Favored : 92.01 % Rotamer: Outliers : 0.36 % Allowed : 18.72 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2579 helix: 1.08 (0.16), residues: 1065 sheet: -0.45 (0.25), residues: 439 loop : -1.62 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 24 HIS 0.010 0.002 HIS J 56 PHE 0.021 0.002 PHE H 31 TYR 0.031 0.002 TYR C 193 ARG 0.008 0.001 ARG L 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7940.69 seconds wall clock time: 143 minutes 29.42 seconds (8609.42 seconds total)