Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 16:49:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9l_10415/04_2023/6t9l_10415.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9l_10415/04_2023/6t9l_10415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9l_10415/04_2023/6t9l_10415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9l_10415/04_2023/6t9l_10415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9l_10415/04_2023/6t9l_10415.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t9l_10415/04_2023/6t9l_10415.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 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 8 6.06 5 P 288 5.49 5 S 58 5.16 5 C 10515 2.51 5 N 3304 2.21 5 O 3984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K ASP 312": "OD1" <-> "OD2" Residue "K PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 374": "NH1" <-> "NH2" Residue "K ASP 408": "OD1" <-> "OD2" Residue "K GLU 453": "OE1" <-> "OE2" Residue "K TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 23": "OE1" <-> "OE2" Residue "L ASP 40": "OD1" <-> "OD2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L GLU 90": "OE1" <-> "OE2" Residue "M ASP 9": "OD1" <-> "OD2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N ASP 30": "OD1" <-> "OD2" Residue "N ASP 47": "OD1" <-> "OD2" Residue "N ASP 67": "OD1" <-> "OD2" Residue "N ASP 70": "OD1" <-> "OD2" Residue "O ASP 52": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18157 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3560 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 431} Chain breaks: 3 Chain: "L" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 719 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "M" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 718 Classifications: {'peptide': 90} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 86} Chain: "N" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 663 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 7, 'TRANS': 74} Chain breaks: 1 Chain: "O" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' ZN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" 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 12247 SG CYS K 46 20.335 121.114 83.464 1.00559.10 S ATOM 12264 SG CYS K 49 21.461 124.114 81.327 1.00552.89 S ATOM 12400 SG CYS K 68 24.337 123.088 84.113 1.00570.25 S ATOM 12346 SG CYS K 60 18.493 111.899 91.515 1.00554.36 S ATOM 12369 SG CYS K 63 15.108 112.316 90.947 1.00539.82 S ATOM 12627 SG CYS K 96 29.738 112.405 98.879 1.00559.36 S ATOM 12653 SG CYS K 99 32.641 112.804 101.346 1.00562.68 S ATOM 13245 SG CYS K 174 44.447 71.445 76.629 1.00460.20 S ATOM 13308 SG CYS K 182 48.138 73.639 73.714 1.00406.32 S ATOM 13331 SG CYS K 185 47.354 73.231 77.816 1.00408.46 S ATOM 13914 SG CYS K 271 40.324 79.219 64.060 1.00469.68 S ATOM 13929 SG CYS K 273 42.915 81.466 65.469 1.00458.01 S ATOM 14065 SG CYS K 292 38.642 99.115 26.685 1.00613.19 S ATOM 14456 SG CYS K 339 42.734 96.444 25.849 1.00634.00 S ATOM 16715 SG CYS M 73 66.148 69.407 83.582 1.00343.41 S ATOM 16738 SG CYS M 76 68.791 66.531 84.276 1.00347.20 S ATOM 17397 SG CYS N 78 41.792 80.510 94.198 1.00404.65 S ATOM 17421 SG CYS N 81 43.482 78.935 91.255 1.00394.45 S ATOM 17548 SG CYS N 98 40.348 76.993 93.985 1.00457.16 S Time building chain proxies: 9.44, per 1000 atoms: 0.52 Number of scatterers: 18157 At special positions: 0 Unit cell: (146.59, 146.59, 123.3, 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 8 29.99 S 58 16.00 P 288 15.00 O 3984 8.00 N 3304 7.00 C 10515 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: 8.48 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 501 " pdb="ZN ZN K 501 " - pdb=" SG CYS K 46 " pdb="ZN ZN K 501 " - pdb=" SG CYS K 68 " pdb="ZN ZN K 501 " - pdb=" SG CYS K 49 " pdb="ZN ZN K 501 " - pdb=" ND1 HIS K 73 " pdb=" ZN K 502 " pdb="ZN ZN K 502 " - pdb=" NE2 HIS K 83 " pdb="ZN ZN K 502 " - pdb=" SG CYS K 60 " pdb="ZN ZN K 502 " - pdb=" SG CYS K 63 " pdb="ZN ZN K 502 " - pdb=" NE2 HIS K 77 " pdb=" ZN K 503 " pdb="ZN ZN K 503 " - pdb=" ND1 HIS K 6 " pdb="ZN ZN K 503 " - pdb=" SG CYS K 99 " pdb="ZN ZN K 503 " - pdb=" SG CYS K 96 " pdb=" ZN K 504 " pdb="ZN ZN K 504 " - pdb=" NE2 HIS K 170 " pdb="ZN ZN K 504 " - pdb=" SG CYS K 185 " pdb="ZN ZN K 504 " - pdb=" SG CYS K 182 " pdb="ZN ZN K 504 " - pdb=" SG CYS K 174 " pdb=" ZN K 505 " pdb="ZN ZN K 505 " - pdb=" ND1 HIS K 250 " pdb="ZN ZN K 505 " - pdb=" ND1 HIS K 276 " pdb="ZN ZN K 505 " - pdb=" SG CYS K 273 " pdb="ZN ZN K 505 " - pdb=" SG CYS K 271 " pdb=" ZN K 506 " pdb="ZN ZN K 506 " - pdb=" SG CYS K 339 " pdb="ZN ZN K 506 " - pdb=" SG CYS K 292 " pdb=" ZN M 101 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 76 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 73 " pdb=" ZN N 701 " pdb="ZN ZN N 701 " - pdb=" NE2 HIS N 93 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 81 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 98 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 78 " Number of angles added : 13 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2892 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 16 sheets defined 58.4% alpha, 7.8% beta 145 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 6.97 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.006A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.565A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.631A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.440A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.038A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.549A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.708A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.488A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.615A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.547A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.906A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.973A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.911A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.730A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.565A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.639A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 4 through 11 removed outlier: 3.675A pdb=" N VAL K 10 " --> pdb=" O HIS K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 32 removed outlier: 3.791A pdb=" N ASN K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 43 removed outlier: 3.846A pdb=" N PHE K 40 " --> pdb=" O PRO K 36 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU K 41 " --> pdb=" O LYS K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.596A pdb=" N SER K 78 " --> pdb=" O PHE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 111 removed outlier: 3.524A pdb=" N ASN K 110 " --> pdb=" O ILE K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 115 Processing helix chain 'K' and resid 117 through 124 removed outlier: 3.526A pdb=" N VAL K 121 " --> pdb=" O TYR K 117 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS K 122 " --> pdb=" O TRP K 118 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR K 123 " --> pdb=" O ASP K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 157 removed outlier: 3.778A pdb=" N SER K 150 " --> pdb=" O CYS K 146 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE K 151 " --> pdb=" O PHE K 147 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS K 154 " --> pdb=" O SER K 150 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU K 155 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS K 157 " --> pdb=" O GLN K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 167 Processing helix chain 'K' and resid 182 through 196 removed outlier: 3.549A pdb=" N LYS K 189 " --> pdb=" O CYS K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 227 removed outlier: 3.681A pdb=" N ILE K 217 " --> pdb=" O GLN K 213 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR K 218 " --> pdb=" O THR K 214 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU K 219 " --> pdb=" O GLY K 215 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU K 220 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS K 225 " --> pdb=" O THR K 221 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE K 226 " --> pdb=" O CYS K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 231 Processing helix chain 'K' and resid 238 through 256 removed outlier: 3.541A pdb=" N ASN K 247 " --> pdb=" O GLN K 243 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS K 250 " --> pdb=" O ILE K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 325 Processing helix chain 'K' and resid 388 through 392 removed outlier: 3.779A pdb=" N TYR K 391 " --> pdb=" O MET K 388 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS K 392 " --> pdb=" O LYS K 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 388 through 392' Processing helix chain 'K' and resid 451 through 456 removed outlier: 3.865A pdb=" N VAL K 455 " --> pdb=" O SER K 451 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU K 456 " --> pdb=" O GLN K 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 451 through 456' Processing helix chain 'L' and resid 7 through 19 removed outlier: 3.574A pdb=" N VAL L 17 " --> pdb=" O GLN L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 36 removed outlier: 4.209A pdb=" N LEU L 24 " --> pdb=" O GLY L 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER L 26 " --> pdb=" O TYR L 22 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 54 removed outlier: 3.620A pdb=" N ASN L 51 " --> pdb=" O LYS L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 69 removed outlier: 3.882A pdb=" N THR L 64 " --> pdb=" O GLN L 60 " (cutoff:3.500A) Proline residue: L 67 - end of helix Processing helix chain 'L' and resid 74 through 90 removed outlier: 3.770A pdb=" N THR L 80 " --> pdb=" O SER L 76 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL L 81 " --> pdb=" O THR L 77 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU L 87 " --> pdb=" O LYS L 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 42 removed outlier: 4.158A pdb=" N ILE M 11 " --> pdb=" O THR M 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY M 14 " --> pdb=" O SER M 10 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG M 30 " --> pdb=" O ASP M 26 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 93 removed outlier: 3.714A pdb=" N GLN M 90 " --> pdb=" O ALA M 86 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG M 91 " --> pdb=" O ALA M 87 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU M 93 " --> pdb=" O LEU M 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 18 removed outlier: 3.997A pdb=" N GLU N 18 " --> pdb=" O LYS N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 34 Processing helix chain 'N' and resid 35 through 40 Processing helix chain 'N' and resid 51 through 58 removed outlier: 3.859A pdb=" N LYS N 55 " --> pdb=" O ARG N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 88 No H-bonds generated for 'chain 'N' and resid 86 through 88' Processing helix chain 'N' and resid 89 through 97 removed outlier: 3.645A pdb=" N HIS N 93 " --> pdb=" O ALA N 89 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU N 95 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN N 96 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 35 removed outlier: 3.900A pdb=" N VAL O 26 " --> pdb=" O THR O 22 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN O 31 " --> pdb=" O LYS O 27 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS O 33 " --> pdb=" O LYS O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 60 removed outlier: 3.555A pdb=" N ASN O 60 " --> pdb=" O SER O 57 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.865A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.956A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.974A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.772A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.598A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 66 through 67 removed outlier: 3.619A pdb=" N GLY K 67 " --> pdb=" O PHE K 58 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE K 58 " --> pdb=" O GLY K 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 125 through 126 Processing sheet with id=AB2, first strand: chain 'K' and resid 236 through 237 removed outlier: 3.813A pdb=" N GLN K 236 " --> pdb=" O GLY O 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 299 through 303 removed outlier: 3.743A pdb=" N THR K 299 " --> pdb=" O SER K 285 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER K 282 " --> pdb=" O HIS K 352 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 306 through 309 removed outlier: 6.292A pdb=" N LEU K 306 " --> pdb=" O GLN K 361 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LYS K 363 " --> pdb=" O LEU K 306 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU K 308 " --> pdb=" O LYS K 363 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR K 461 " --> pdb=" O LEU K 362 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL K 417 " --> pdb=" O TYR K 461 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU K 463 " --> pdb=" O GLY K 415 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY K 415 " --> pdb=" O LEU K 463 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR K 465 " --> pdb=" O LEU K 413 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU K 413 " --> pdb=" O TYR K 465 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE K 467 " --> pdb=" O TYR K 411 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR K 411 " --> pdb=" O ILE K 467 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLN K 469 " --> pdb=" O ILE K 409 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE K 409 " --> pdb=" O GLN K 469 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE K 414 " --> pdb=" O LYS K 433 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS K 432 " --> pdb=" O PHE K 440 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN K 438 " --> pdb=" O ILE K 434 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TRP K 439 " --> pdb=" O ILE K 450 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 365 through 367 Processing sheet with id=AB6, first strand: chain 'M' and resid 70 through 72 Processing sheet with id=AB7, first strand: chain 'O' and resid 12 through 16 removed outlier: 9.476A pdb=" N LEU O 67 " --> pdb=" O GLN O 2 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N PHE O 4 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU O 69 " --> pdb=" O PHE O 4 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS O 6 " --> pdb=" O LEU O 69 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 7.84 Time building geometry restraints manager: 8.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4421 1.34 - 1.45: 4827 1.45 - 1.57: 9157 1.57 - 1.69: 576 1.69 - 1.81: 82 Bond restraints: 19063 Sorted by residual: bond pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 9.77e-01 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.451 -0.029 3.00e-02 1.11e+03 9.44e-01 bond pdb=" N PRO G 109 " pdb=" CA PRO G 109 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 8.72e-01 bond pdb=" O4' DC I -20 " pdb=" C1' DC I -20 " ideal model delta sigma weight residual 1.414 1.396 0.018 2.00e-02 2.50e+03 8.15e-01 bond pdb=" C3' DC I -48 " pdb=" C2' DC I -48 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 7.92e-01 ... (remaining 19058 not shown) Histogram of bond angle deviations from ideal: 98.71 - 105.76: 1617 105.76 - 112.82: 10538 112.82 - 119.87: 6356 119.87 - 126.93: 7673 126.93 - 133.99: 797 Bond angle restraints: 26981 Sorted by residual: angle pdb=" N ILE L 92 " pdb=" CA ILE L 92 " pdb=" C ILE L 92 " ideal model delta sigma weight residual 113.53 109.97 3.56 9.80e-01 1.04e+00 1.32e+01 angle pdb=" C4' DC I -20 " pdb=" O4' DC I -20 " pdb=" C1' DC I -20 " ideal model delta sigma weight residual 109.70 106.41 3.29 1.50e+00 4.44e-01 4.80e+00 angle pdb=" C ASN K 295 " pdb=" N SER K 296 " pdb=" CA SER K 296 " ideal model delta sigma weight residual 121.70 125.39 -3.69 1.80e+00 3.09e-01 4.19e+00 angle pdb=" N ILE K 226 " pdb=" CA ILE K 226 " pdb=" C ILE K 226 " ideal model delta sigma weight residual 111.67 109.77 1.90 9.50e-01 1.11e+00 4.01e+00 angle pdb=" C3' DA J -38 " pdb=" C2' DA J -38 " pdb=" C1' DA J -38 " ideal model delta sigma weight residual 101.60 104.60 -3.00 1.50e+00 4.44e-01 3.99e+00 ... (remaining 26976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.07: 8721 24.07 - 48.15: 1187 48.15 - 72.22: 595 72.22 - 96.29: 8 96.29 - 120.36: 1 Dihedral angle restraints: 10512 sinusoidal: 6048 harmonic: 4464 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 -19.64 -120.36 1 3.50e+01 8.16e-04 1.18e+01 dihedral pdb=" CB MET D 56 " pdb=" CG MET D 56 " pdb=" SD MET D 56 " pdb=" CE MET D 56 " ideal model delta sinusoidal sigma weight residual -180.00 -124.37 -55.63 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" CB MET H 56 " pdb=" CG MET H 56 " pdb=" SD MET H 56 " pdb=" CE MET H 56 " ideal model delta sinusoidal sigma weight residual -60.00 -110.16 50.16 3 1.50e+01 4.44e-03 8.87e+00 ... (remaining 10509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2078 0.027 - 0.054: 706 0.054 - 0.081: 174 0.081 - 0.108: 74 0.108 - 0.135: 28 Chirality restraints: 3060 Sorted by residual: chirality pdb=" CB ILE K 409 " pdb=" CA ILE K 409 " pdb=" CG1 ILE K 409 " pdb=" CG2 ILE K 409 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE K 351 " pdb=" N ILE K 351 " pdb=" C ILE K 351 " pdb=" CB ILE K 351 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA ILE K 429 " pdb=" N ILE K 429 " pdb=" C ILE K 429 " pdb=" CB ILE K 429 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 3057 not shown) Planarity restraints: 2427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I -20 " -0.008 2.00e-02 2.50e+03 1.59e-02 5.72e+00 pdb=" N1 DC I -20 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DC I -20 " -0.037 2.00e-02 2.50e+03 pdb=" O2 DC I -20 " 0.022 2.00e-02 2.50e+03 pdb=" N3 DC I -20 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DC I -20 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC I -20 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DC I -20 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC I -20 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 42 " -0.016 2.00e-02 2.50e+03 7.88e-03 1.71e+00 pdb=" N9 DA J 42 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DA J 42 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA J 42 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA J 42 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA J 42 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA J 42 " -0.003 2.00e-02 2.50e+03 pdb=" N1 DA J 42 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA J 42 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA J 42 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA J 42 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL K 35 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO K 36 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO K 36 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO K 36 " 0.016 5.00e-02 4.00e+02 ... (remaining 2424 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 522 2.69 - 3.24: 16222 3.24 - 3.79: 31699 3.79 - 4.35: 40360 4.35 - 4.90: 60105 Nonbonded interactions: 148908 Sorted by model distance: nonbonded pdb=" O2 DC I -46 " pdb=" N2 DG J 46 " model vdw 2.136 2.496 nonbonded pdb=" O2 DC I -51 " pdb=" N2 DG J 51 " model vdw 2.186 2.496 nonbonded pdb=" O2 DC I 19 " pdb=" N2 DG J -19 " model vdw 2.190 2.496 nonbonded pdb=" O VAL K 121 " pdb=" OG1 THR K 125 " model vdw 2.205 2.440 nonbonded pdb=" O ILE K 30 " pdb=" OG SER K 34 " model vdw 2.255 2.440 ... (remaining 148903 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = (chain 'E' and resid 40 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.010 Extract box with map and model: 14.360 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 57.360 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 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 : 0.002 0.030 19063 Z= 0.125 Angle : 0.468 5.365 26981 Z= 0.303 Chirality : 0.032 0.135 3060 Planarity : 0.002 0.029 2427 Dihedral : 22.541 120.364 7620 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: -1.63 (0.19), residues: 1498 helix: -0.43 (0.17), residues: 802 sheet: -1.23 (0.44), residues: 121 loop : -1.88 (0.21), residues: 575 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 473 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 474 average time/residue: 0.3777 time to fit residues: 250.0219 Evaluate side-chains 279 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.723 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 53 optimal weight: 0.0570 chunk 83 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN C 73 ASN D 44 GLN D 92 GLN F 93 GLN G 24 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 236 GLN K 367 HIS K 459 GLN ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN O 2 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 19063 Z= 0.261 Angle : 0.590 9.492 26981 Z= 0.338 Chirality : 0.038 0.283 3060 Planarity : 0.004 0.055 2427 Dihedral : 28.003 106.943 4577 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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 (0.21), residues: 1498 helix: 0.89 (0.18), residues: 829 sheet: -0.59 (0.46), residues: 115 loop : -1.50 (0.23), residues: 554 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 271 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 30 residues processed: 296 average time/residue: 0.3299 time to fit residues: 142.7851 Evaluate side-chains 255 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 225 time to evaluate : 1.672 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1813 time to fit residues: 11.8127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 159 optimal weight: 0.6980 chunk 171 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 157 optimal weight: 0.4980 chunk 54 optimal weight: 0.0270 chunk 127 optimal weight: 3.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 19063 Z= 0.191 Angle : 0.536 11.557 26981 Z= 0.309 Chirality : 0.036 0.210 3060 Planarity : 0.003 0.041 2427 Dihedral : 28.000 103.887 4577 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.22), residues: 1498 helix: 1.60 (0.19), residues: 821 sheet: -0.20 (0.48), residues: 115 loop : -1.19 (0.24), residues: 562 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 242 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 256 average time/residue: 0.3252 time to fit residues: 124.5135 Evaluate side-chains 234 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 221 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1668 time to fit residues: 6.1881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN H 64 ASN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 19063 Z= 0.251 Angle : 0.578 12.155 26981 Z= 0.330 Chirality : 0.037 0.181 3060 Planarity : 0.004 0.036 2427 Dihedral : 28.349 95.846 4577 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 0.76 (0.22), residues: 1498 helix: 1.63 (0.19), residues: 831 sheet: -0.22 (0.47), residues: 122 loop : -1.09 (0.24), residues: 545 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 244 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 20 residues processed: 260 average time/residue: 0.3193 time to fit residues: 122.8404 Evaluate side-chains 242 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 222 time to evaluate : 1.720 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1637 time to fit residues: 8.3176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.0060 chunk 144 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 75 HIS D 81 ASN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 236 GLN ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 19063 Z= 0.201 Angle : 0.540 9.378 26981 Z= 0.312 Chirality : 0.036 0.156 3060 Planarity : 0.003 0.037 2427 Dihedral : 28.213 96.158 4577 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 0.98 (0.22), residues: 1498 helix: 1.81 (0.19), residues: 831 sheet: -0.12 (0.48), residues: 122 loop : -1.01 (0.25), residues: 545 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 241 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 246 average time/residue: 0.3276 time to fit residues: 121.2396 Evaluate side-chains 240 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 228 time to evaluate : 1.655 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1600 time to fit residues: 5.7603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 169 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 199 ASN ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 19063 Z= 0.222 Angle : 0.557 9.521 26981 Z= 0.321 Chirality : 0.036 0.179 3060 Planarity : 0.003 0.036 2427 Dihedral : 28.311 91.202 4577 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.07 (0.22), residues: 1498 helix: 1.85 (0.19), residues: 828 sheet: -0.03 (0.48), residues: 122 loop : -0.90 (0.26), residues: 548 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 232 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 238 average time/residue: 0.3160 time to fit residues: 113.7031 Evaluate side-chains 235 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 224 time to evaluate : 1.674 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1674 time to fit residues: 5.7523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 105 optimal weight: 0.0000 chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 53 ASN ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 2 GLN O 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 19063 Z= 0.204 Angle : 0.550 10.029 26981 Z= 0.317 Chirality : 0.036 0.168 3060 Planarity : 0.003 0.052 2427 Dihedral : 28.281 92.419 4577 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.10 (0.22), residues: 1498 helix: 1.91 (0.19), residues: 829 sheet: 0.07 (0.48), residues: 119 loop : -0.98 (0.25), residues: 550 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 231 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 238 average time/residue: 0.3065 time to fit residues: 110.1395 Evaluate side-chains 228 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 223 time to evaluate : 1.634 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1611 time to fit residues: 3.5837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 199 ASN ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 19063 Z= 0.207 Angle : 0.558 10.131 26981 Z= 0.322 Chirality : 0.037 0.422 3060 Planarity : 0.003 0.048 2427 Dihedral : 28.276 93.192 4577 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.13 (0.22), residues: 1498 helix: 1.93 (0.19), residues: 823 sheet: -0.00 (0.48), residues: 121 loop : -0.90 (0.25), residues: 554 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 228 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 234 average time/residue: 0.3118 time to fit residues: 110.3361 Evaluate side-chains 233 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 222 time to evaluate : 1.630 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1888 time to fit residues: 5.5218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 19063 Z= 0.250 Angle : 0.591 10.526 26981 Z= 0.337 Chirality : 0.038 0.383 3060 Planarity : 0.004 0.045 2427 Dihedral : 28.360 92.839 4577 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.00 (0.22), residues: 1498 helix: 1.81 (0.19), residues: 827 sheet: 0.05 (0.48), residues: 120 loop : -0.97 (0.26), residues: 551 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 223 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 228 average time/residue: 0.3166 time to fit residues: 109.4450 Evaluate side-chains 225 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 220 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2756 time to fit residues: 4.3329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 160 optimal weight: 0.0770 chunk 138 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 19063 Z= 0.220 Angle : 0.585 16.373 26981 Z= 0.332 Chirality : 0.037 0.370 3060 Planarity : 0.004 0.046 2427 Dihedral : 28.288 93.634 4577 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 0.97 (0.22), residues: 1498 helix: 1.84 (0.19), residues: 827 sheet: -0.13 (0.46), residues: 130 loop : -1.06 (0.25), residues: 541 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 231 average time/residue: 0.3091 time to fit residues: 108.0288 Evaluate side-chains 223 residues out of total 1342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 221 time to evaluate : 1.711 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1581 time to fit residues: 2.7563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 128 optimal weight: 0.0020 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.0980 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.098361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.074049 restraints weight = 51897.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.074718 restraints weight = 30322.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075638 restraints weight = 21180.974| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 19063 Z= 0.182 Angle : 0.564 15.528 26981 Z= 0.323 Chirality : 0.037 0.372 3060 Planarity : 0.003 0.041 2427 Dihedral : 28.157 95.284 4577 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.14 (0.22), residues: 1498 helix: 1.93 (0.19), residues: 829 sheet: 0.19 (0.49), residues: 115 loop : -0.94 (0.25), residues: 554 =============================================================================== Job complete usr+sys time: 3391.95 seconds wall clock time: 62 minutes 30.26 seconds (3750.26 seconds total)