Starting phenix.real_space_refine on Sat Dec 16 07:21:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5h_12736/12_2023/7o5h_12736.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5h_12736/12_2023/7o5h_12736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5h_12736/12_2023/7o5h_12736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5h_12736/12_2023/7o5h_12736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5h_12736/12_2023/7o5h_12736.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5h_12736/12_2023/7o5h_12736.pdb" } resolution = 3.1 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= 0.006 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 P 964 5.49 5 Mg 167 5.21 5 S 59 5.16 5 C 17729 2.51 5 N 6377 2.21 5 O 9140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "V PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 34436 Number of models: 1 Model: "" Number of chains: 22 Chain: "V" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1955 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 231} Chain: "A" Number of atoms: 20726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 20726 Classifications: {'RNA': 964} Modifications used: {'rna2p_pur': 78, 'rna2p_pyr': 44, 'rna3p_pur': 485, 'rna3p_pyr': 357} Link IDs: {'rna2p': 121, 'rna3p': 842} Chain breaks: 7 Chain: "B" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1165 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "O" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 252 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Unusual residues: {' MG': 161} Classifications: {'undetermined': 161} Link IDs: {None: 160} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29871 SG CYS K 121 97.455 45.225 110.621 1.00 55.55 S Time building chain proxies: 18.07, per 1000 atoms: 0.52 Number of scatterers: 34436 At special positions: 0 Unit cell: (168.19, 191.82, 159.85, 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) S 59 16.00 P 964 15.00 Mg 167 11.99 O 9140 8.00 N 6377 7.00 C 17729 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: 18.54 Conformation dependent library (CDL) restraints added in 3.0 seconds 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3214 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 15 sheets defined 46.6% alpha, 18.9% beta 317 base pairs and 590 stacking pairs defined. Time for finding SS restraints: 17.26 Creating SS restraints... Processing helix chain 'V' and resid 22 through 34 Processing helix chain 'V' and resid 51 through 56 removed outlier: 3.846A pdb=" N VAL V 55 " --> pdb=" O LEU V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 77 Processing helix chain 'V' and resid 96 through 105 removed outlier: 4.495A pdb=" N LEU V 100 " --> pdb=" O ASN V 96 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA V 101 " --> pdb=" O PHE V 97 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU V 102 " --> pdb=" O GLY V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 115 through 128 removed outlier: 4.439A pdb=" N THR V 120 " --> pdb=" O TYR V 116 " (cutoff:3.500A) Proline residue: V 121 - end of helix Processing helix chain 'V' and resid 141 through 150 Processing helix chain 'V' and resid 158 through 167 removed outlier: 4.308A pdb=" N TYR V 167 " --> pdb=" O MET V 163 " (cutoff:3.500A) Processing helix chain 'V' and resid 177 through 179 No H-bonds generated for 'chain 'V' and resid 177 through 179' Processing helix chain 'V' and resid 206 through 218 Processing helix chain 'V' and resid 219 through 221 No H-bonds generated for 'chain 'V' and resid 219 through 221' Processing helix chain 'V' and resid 224 through 229 Processing helix chain 'V' and resid 234 through 241 Processing helix chain 'V' and resid 248 through 252 Processing helix chain 'V' and resid 253 through 268 Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 24 through 29 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 42 through 63 removed outlier: 3.587A pdb=" N THR B 46 " --> pdb=" O ASN B 42 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 73 through 87 removed outlier: 4.359A pdb=" N GLU B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 123 removed outlier: 3.621A pdb=" N SER B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 149 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.626A pdb=" N GLY B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 227 removed outlier: 3.762A pdb=" N THR B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.207A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.778A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 43 removed outlier: 4.456A pdb=" N ALA D 43 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 147 through 150 Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.752A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 206 Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.597A pdb=" N ARG E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.676A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 146 removed outlier: 3.712A pdb=" N ASN E 146 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 157 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 12 through 16 removed outlier: 4.934A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 32 removed outlier: 3.518A pdb=" N ARG F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 80 removed outlier: 3.551A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.524A pdb=" N ASP H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 94 through 99 removed outlier: 3.679A pdb=" N ALA H 97 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'K' and resid 48 through 51 removed outlier: 3.879A pdb=" N GLY K 51 " --> pdb=" O GLY K 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 48 through 51' Processing helix chain 'K' and resid 59 through 75 removed outlier: 3.615A pdb=" N ALA K 63 " --> pdb=" O THR K 59 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 78 No H-bonds generated for 'chain 'K' and resid 76 through 78' Processing helix chain 'K' and resid 92 through 103 removed outlier: 3.574A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 113 through 117 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 4.263A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.750A 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 53 through 63 Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'Q' and resid 49 through 52 removed outlier: 3.929A pdb=" N GLU Q 52 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 49 through 52' Processing helix chain 'R' and resid 25 through 31 removed outlier: 3.805A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.587A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.506A pdb=" N ARG T 24 " --> pdb=" O HIS T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 removed outlier: 3.622A pdb=" N ALA T 47 " --> pdb=" O ASP T 43 " (cutoff:3.500A) Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 Processing helix chain 'U' and resid 29 through 36 removed outlier: 3.578A pdb=" N ARG U 33 " --> pdb=" O LEU U 29 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG U 34 " --> pdb=" O ALA U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 55 Processing sheet with id=AA1, first strand: chain 'V' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'V' and resid 85 through 89 removed outlier: 3.546A pdb=" N PHE V 111 " --> pdb=" O VAL V 42 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE V 44 " --> pdb=" O PHE V 111 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU V 108 " --> pdb=" O ASP V 135 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N HIS V 137 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL V 110 " --> pdb=" O HIS V 137 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N MET V 139 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA V 134 " --> pdb=" O PRO V 196 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG V 193 " --> pdb=" O PRO V 172 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL V 195 " --> pdb=" O VAL V 170 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL V 170 " --> pdb=" O VAL V 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 16 through 19 removed outlier: 5.552A pdb=" N PHE B 16 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE B 41 " --> pdb=" O PHE B 16 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N HIS B 18 " --> pdb=" O HIS B 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.268A pdb=" N LEU B 68 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE B 164 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 70 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 183 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE B 200 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA B 185 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.849A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 12 through 24 removed outlier: 5.001A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 88 removed outlier: 6.465A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 35 through 51 removed outlier: 5.000A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG F 38 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG F 44 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA F 57 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLN F 46 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N HIS F 55 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 24 through 28 Processing sheet with id=AB1, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AB2, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.845A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 41 through 46 removed outlier: 6.681A pdb=" N ILE K 34 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TRP K 44 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL K 32 " --> pdb=" O TRP K 44 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR K 46 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR K 30 " --> pdb=" O THR K 46 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU K 82 " --> pdb=" O ILE K 107 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN K 109 " --> pdb=" O LEU K 82 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 62 through 66 removed outlier: 3.545A pdb=" N ARG L 36 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS L 30 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER L 78 " --> pdb=" O CYS L 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 50 through 52 removed outlier: 6.638A pdb=" N VAL P 19 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR P 17 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 8 through 14 removed outlier: 7.521A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N LYS Q 71 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N HIS Q 45 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU Q 75 " --> pdb=" O HIS Q 47 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU Q 75 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ARG Q 62 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG Q 77 " --> pdb=" O GLU Q 60 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1899 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 778 hydrogen bonds 1242 hydrogen bond angles 0 basepair planarities 317 basepair parallelities 590 stacking parallelities Total time for adding SS restraints: 27.31 Time building geometry restraints manager: 19.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6692 1.33 - 1.45: 13488 1.45 - 1.57: 14758 1.57 - 1.69: 1920 1.69 - 1.81: 105 Bond restraints: 36963 Sorted by residual: bond pdb=" C3' A A 411 " pdb=" O3' A A 411 " ideal model delta sigma weight residual 1.427 1.445 -0.018 1.50e-02 4.44e+03 1.37e+00 bond pdb=" CA VAL F 18 " pdb=" CB VAL F 18 " ideal model delta sigma weight residual 1.539 1.545 -0.006 5.40e-03 3.43e+04 1.21e+00 bond pdb=" CA VAL B 47 " pdb=" CB VAL B 47 " ideal model delta sigma weight residual 1.539 1.544 -0.005 5.40e-03 3.43e+04 1.03e+00 bond pdb=" C VAL V 110 " pdb=" N PHE V 111 " ideal model delta sigma weight residual 1.333 1.345 -0.012 1.30e-02 5.92e+03 8.83e-01 bond pdb=" CA VAL H 72 " pdb=" CB VAL H 72 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 6.75e-01 ... (remaining 36958 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.95: 6048 106.95 - 113.70: 22319 113.70 - 120.45: 13449 120.45 - 127.20: 10709 127.20 - 133.95: 2182 Bond angle restraints: 54707 Sorted by residual: angle pdb=" C3' A A 411 " pdb=" O3' A A 411 " pdb=" P A A 412 " ideal model delta sigma weight residual 120.20 125.15 -4.95 1.50e+00 4.44e-01 1.09e+01 angle pdb=" C4' A A 411 " pdb=" C3' A A 411 " pdb=" O3' A A 411 " ideal model delta sigma weight residual 109.40 113.03 -3.63 1.50e+00 4.44e-01 5.84e+00 angle pdb=" O3' A A 411 " pdb=" C3' A A 411 " pdb=" C2' A A 411 " ideal model delta sigma weight residual 109.50 113.02 -3.52 1.50e+00 4.44e-01 5.50e+00 angle pdb=" C3' C A1107 " pdb=" O3' C A1107 " pdb=" P G A1108 " ideal model delta sigma weight residual 120.20 123.42 -3.22 1.50e+00 4.44e-01 4.60e+00 angle pdb=" O3' C A1107 " pdb=" C3' C A1107 " pdb=" C2' C A1107 " ideal model delta sigma weight residual 113.70 116.70 -3.00 1.50e+00 4.44e-01 4.01e+00 ... (remaining 54702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 20674 35.58 - 71.16: 1892 71.16 - 106.74: 250 106.74 - 142.32: 0 142.32 - 177.89: 7 Dihedral angle restraints: 22823 sinusoidal: 17850 harmonic: 4973 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 53.36 146.64 1 1.50e+01 4.44e-03 7.83e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 57.36 142.64 1 1.50e+01 4.44e-03 7.66e+01 dihedral pdb=" O4' C A 183 " pdb=" C1' C A 183 " pdb=" N1 C A 183 " pdb=" C2 C A 183 " ideal model delta sinusoidal sigma weight residual 232.00 54.11 177.89 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 22820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 6324 0.041 - 0.081: 399 0.081 - 0.122: 163 0.122 - 0.163: 12 0.163 - 0.204: 1 Chirality restraints: 6899 Sorted by residual: chirality pdb=" C3' A A 411 " pdb=" C4' A A 411 " pdb=" O3' A A 411 " pdb=" C2' A A 411 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C3' C A1107 " pdb=" C4' C A1107 " pdb=" O3' C A1107 " pdb=" C2' C A1107 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" C1' U A 365 " pdb=" O4' U A 365 " pdb=" C2' U A 365 " pdb=" N1 U A 365 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 6896 not shown) Planarity restraints: 3369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 44 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO L 45 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO L 45 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 45 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 138 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO D 139 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 139 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 139 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 80 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO H 81 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO H 81 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 81 " 0.016 5.00e-02 4.00e+02 ... (remaining 3366 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 4 1.99 - 2.72: 2835 2.72 - 3.44: 46149 3.44 - 4.17: 112281 4.17 - 4.90: 155292 Nonbonded interactions: 316561 Sorted by model distance: nonbonded pdb="MG MG A1632 " pdb="MG MG A1696 " model vdw 1.262 1.300 nonbonded pdb=" OP1 C A 504 " pdb="MG MG A1725 " model vdw 1.933 2.170 nonbonded pdb=" OP2 A A 195 " pdb="MG MG A1642 " model vdw 1.976 2.170 nonbonded pdb=" OP1 A A 59 " pdb="MG MG A1621 " model vdw 1.983 2.170 nonbonded pdb=" O4' G A 713 " pdb="MG MG A1708 " model vdw 2.009 2.170 ... (remaining 316556 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: 1.610 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: 0.040 Extract box with map and model: 8.490 Check model and map are aligned: 0.510 Set scattering table: 0.350 Process input model: 116.070 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 0.035 36963 Z= 0.108 Angle : 0.328 5.327 54707 Z= 0.176 Chirality : 0.025 0.204 6899 Planarity : 0.003 0.030 3369 Dihedral : 20.732 177.894 19609 Min Nonbonded Distance : 1.262 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.98 % Allowed : 3.07 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 1.09 (0.21), residues: 1702 helix: 1.77 (0.20), residues: 682 sheet: 0.14 (0.31), residues: 301 loop : 0.07 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 23 HIS 0.003 0.001 HIS E 89 PHE 0.008 0.001 PHE V 111 TYR 0.007 0.001 TYR L 95 ARG 0.003 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 413 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 427 average time/residue: 0.5897 time to fit residues: 377.0224 Evaluate side-chains 295 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 291 time to evaluate : 2.295 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3112 time to fit residues: 5.0617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 237 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 78 HIS ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 19 GLN B 36 ASN B 120 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS F 52 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN O 62 GLN P 18 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 ASN T 20 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 36963 Z= 0.363 Angle : 0.640 8.548 54707 Z= 0.324 Chirality : 0.039 0.223 6899 Planarity : 0.005 0.050 3369 Dihedral : 22.087 176.798 16230 Min Nonbonded Distance : 1.096 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.93 % Allowed : 10.96 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.21), residues: 1702 helix: 1.45 (0.20), residues: 694 sheet: 0.11 (0.32), residues: 291 loop : -0.26 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 23 HIS 0.005 0.001 HIS E 89 PHE 0.017 0.002 PHE K 61 TYR 0.013 0.002 TYR L 66 ARG 0.006 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 309 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 29 residues processed: 328 average time/residue: 0.5742 time to fit residues: 284.5649 Evaluate side-chains 300 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 271 time to evaluate : 2.279 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3276 time to fit residues: 20.1743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 202 HIS B 36 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS K 22 HIS ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 ASN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN T 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36963 Z= 0.161 Angle : 0.510 8.705 54707 Z= 0.265 Chirality : 0.033 0.216 6899 Planarity : 0.004 0.041 3369 Dihedral : 22.036 178.586 16230 Min Nonbonded Distance : 1.169 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.33 % Allowed : 12.50 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.96 (0.21), residues: 1702 helix: 1.68 (0.20), residues: 697 sheet: 0.26 (0.32), residues: 283 loop : -0.15 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 60 HIS 0.003 0.001 HIS E 89 PHE 0.010 0.001 PHE F 8 TYR 0.018 0.001 TYR V 157 ARG 0.009 0.000 ARG K 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 312 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 325 average time/residue: 0.5530 time to fit residues: 275.3486 Evaluate side-chains 284 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 275 time to evaluate : 2.295 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3565 time to fit residues: 8.4121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 0.3980 chunk 179 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 chunk 26 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 36 ASN B 120 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 36963 Z= 0.193 Angle : 0.516 9.399 54707 Z= 0.267 Chirality : 0.033 0.218 6899 Planarity : 0.004 0.040 3369 Dihedral : 22.014 178.114 16230 Min Nonbonded Distance : 1.132 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.03 % Allowed : 13.69 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.92 (0.21), residues: 1702 helix: 1.64 (0.20), residues: 696 sheet: 0.28 (0.32), residues: 283 loop : -0.19 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 42 HIS 0.004 0.001 HIS E 89 PHE 0.009 0.001 PHE B 90 TYR 0.031 0.001 TYR V 157 ARG 0.014 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 288 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 302 average time/residue: 0.5807 time to fit residues: 271.8243 Evaluate side-chains 291 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 272 time to evaluate : 2.226 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3299 time to fit residues: 14.4614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 227 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 202 HIS B 36 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36963 Z= 0.204 Angle : 0.521 9.976 54707 Z= 0.270 Chirality : 0.034 0.220 6899 Planarity : 0.004 0.040 3369 Dihedral : 22.009 178.073 16230 Min Nonbonded Distance : 1.118 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.26 % Allowed : 15.43 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.86 (0.21), residues: 1702 helix: 1.61 (0.20), residues: 696 sheet: 0.27 (0.32), residues: 278 loop : -0.26 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 23 HIS 0.004 0.001 HIS E 89 PHE 0.020 0.001 PHE K 61 TYR 0.018 0.001 TYR V 157 ARG 0.006 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 290 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 294 average time/residue: 0.5556 time to fit residues: 250.0239 Evaluate side-chains 279 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 267 time to evaluate : 2.385 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4435 time to fit residues: 11.2552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 5.9990 chunk 228 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS E 148 ASN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 36963 Z= 0.275 Angle : 0.575 10.386 54707 Z= 0.297 Chirality : 0.036 0.236 6899 Planarity : 0.005 0.041 3369 Dihedral : 22.061 178.117 16230 Min Nonbonded Distance : 1.089 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.58 % Allowed : 16.06 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.70 (0.20), residues: 1702 helix: 1.52 (0.20), residues: 690 sheet: 0.13 (0.32), residues: 283 loop : -0.35 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 42 HIS 0.005 0.001 HIS E 89 PHE 0.021 0.002 PHE K 61 TYR 0.016 0.002 TYR V 257 ARG 0.007 0.001 ARG O 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 275 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 30 residues processed: 290 average time/residue: 0.5476 time to fit residues: 245.5745 Evaluate side-chains 297 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 267 time to evaluate : 2.283 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3330 time to fit residues: 21.1474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 213 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 252 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS B 19 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36963 Z= 0.199 Angle : 0.540 10.374 54707 Z= 0.280 Chirality : 0.034 0.230 6899 Planarity : 0.004 0.052 3369 Dihedral : 22.067 178.365 16230 Min Nonbonded Distance : 1.106 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.77 % Allowed : 16.83 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.72 (0.21), residues: 1702 helix: 1.52 (0.20), residues: 696 sheet: 0.16 (0.32), residues: 283 loop : -0.35 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 42 HIS 0.009 0.001 HIS B 168 PHE 0.023 0.001 PHE K 61 TYR 0.019 0.002 TYR V 263 ARG 0.013 0.001 ARG V 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 286 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 290 average time/residue: 0.5423 time to fit residues: 243.7055 Evaluate side-chains 275 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 267 time to evaluate : 2.114 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3602 time to fit residues: 7.6646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 HIS ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS E 148 ASN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 36963 Z= 0.476 Angle : 0.727 10.952 54707 Z= 0.369 Chirality : 0.044 0.243 6899 Planarity : 0.006 0.072 3369 Dihedral : 22.218 177.610 16230 Min Nonbonded Distance : 1.036 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.89 % Allowed : 17.32 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.04 (0.20), residues: 1702 helix: 1.00 (0.20), residues: 695 sheet: -0.29 (0.30), residues: 294 loop : -0.73 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 23 HIS 0.006 0.002 HIS E 89 PHE 0.018 0.002 PHE K 61 TYR 0.020 0.002 TYR V 157 ARG 0.011 0.001 ARG V 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 266 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 22 residues processed: 275 average time/residue: 0.5610 time to fit residues: 237.6999 Evaluate side-chains 283 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 261 time to evaluate : 2.434 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3263 time to fit residues: 16.2010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 0.9980 chunk 241 optimal weight: 0.8980 chunk 220 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 234 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN F 94 HIS L 20 ASN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36963 Z= 0.159 Angle : 0.531 14.038 54707 Z= 0.275 Chirality : 0.034 0.256 6899 Planarity : 0.004 0.045 3369 Dihedral : 22.067 178.833 16230 Min Nonbonded Distance : 1.148 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.14 % Allowed : 18.37 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1702 helix: 1.54 (0.20), residues: 701 sheet: -0.08 (0.32), residues: 271 loop : -0.40 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 60 HIS 0.006 0.001 HIS B 168 PHE 0.029 0.001 PHE B 90 TYR 0.019 0.001 TYR V 263 ARG 0.012 0.000 ARG V 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 294 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 295 average time/residue: 0.5520 time to fit residues: 252.0000 Evaluate side-chains 264 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.295 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 6.9990 chunk 248 optimal weight: 0.0770 chunk 151 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 172 optimal weight: 0.5980 chunk 261 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 36963 Z= 0.139 Angle : 0.508 10.657 54707 Z= 0.264 Chirality : 0.032 0.214 6899 Planarity : 0.004 0.037 3369 Dihedral : 21.941 178.832 16230 Min Nonbonded Distance : 1.161 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.49 % Allowed : 20.25 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.80 (0.21), residues: 1702 helix: 1.62 (0.20), residues: 702 sheet: 0.19 (0.33), residues: 266 loop : -0.35 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 60 HIS 0.004 0.001 HIS B 168 PHE 0.029 0.001 PHE B 90 TYR 0.013 0.001 TYR V 263 ARG 0.009 0.000 ARG V 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 287 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 289 average time/residue: 0.5764 time to fit residues: 254.1550 Evaluate side-chains 273 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 268 time to evaluate : 2.161 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3369 time to fit residues: 5.5313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 208 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 213 optimal weight: 0.3980 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 HIS H 118 GLN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.064064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.051097 restraints weight = 141179.591| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.37 r_work: 0.2941 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36963 Z= 0.245 Angle : 0.562 10.643 54707 Z= 0.290 Chirality : 0.035 0.251 6899 Planarity : 0.004 0.039 3369 Dihedral : 21.980 178.892 16230 Min Nonbonded Distance : 1.107 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.56 % Allowed : 20.39 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.60 (0.21), residues: 1702 helix: 1.43 (0.20), residues: 712 sheet: -0.00 (0.32), residues: 278 loop : -0.43 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 42 HIS 0.005 0.001 HIS E 89 PHE 0.028 0.002 PHE B 90 TYR 0.021 0.002 TYR F 59 ARG 0.014 0.001 ARG B 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7001.70 seconds wall clock time: 128 minutes 54.00 seconds (7734.00 seconds total)