Starting phenix.real_space_refine on Fri Nov 17 17:31:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/11_2023/7xg0_33181_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/11_2023/7xg0_33181.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/11_2023/7xg0_33181_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/11_2023/7xg0_33181_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/11_2023/7xg0_33181_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/11_2023/7xg0_33181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/11_2023/7xg0_33181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/11_2023/7xg0_33181_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xg0_33181/11_2023/7xg0_33181_updated.pdb" } resolution = 2.6 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= 0.002 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 1 6.06 5 P 118 5.49 5 S 86 5.16 5 C 12157 2.51 5 N 3537 2.21 5 O 3994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E GLU 285": "OE1" <-> "OE2" Residue "E GLU 308": "OE1" <-> "OE2" Residue "E GLU 328": "OE1" <-> "OE2" Residue "E GLU 337": "OE1" <-> "OE2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F GLU 157": "OE1" <-> "OE2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F GLU 308": "OE1" <-> "OE2" Residue "F GLU 339": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "G GLU 285": "OE1" <-> "OE2" Residue "G GLU 308": "OE1" <-> "OE2" Residue "G GLU 320": "OE1" <-> "OE2" Residue "G GLU 328": "OE1" <-> "OE2" Residue "G GLU 337": "OE1" <-> "OE2" Residue "H PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 19893 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1897 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain: "B" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1709 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 17, 'TRANS': 201} Chain: "C" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2488 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain breaks: 1 Chain: "D" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2503 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 18, 'TRANS': 312} Chain breaks: 1 Chain: "E" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2442 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain breaks: 1 Chain: "F" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2442 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain breaks: 1 Chain: "G" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2131 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 17, 'TRANS': 262} Chain breaks: 1 Chain: "H" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain: "I" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1317 Classifications: {'RNA': 61} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 27, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 39} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "J" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 365 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 798 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "A" 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 226 SG CYS A 30 71.954 39.770 21.644 1.00 48.83 S ATOM 248 SG CYS A 33 75.711 41.962 22.539 1.00 60.11 S ATOM 495 SG CYS A 66 75.352 38.925 19.938 1.00 61.46 S ATOM 526 SG CYS A 69 75.981 39.246 24.284 1.00 67.58 S Time building chain proxies: 10.80, per 1000 atoms: 0.54 Number of scatterers: 19893 At special positions: 0 Unit cell: (110, 145.2, 178.2, 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 1 29.99 S 86 16.00 P 118 15.00 O 3994 8.00 N 3537 7.00 C 12157 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: 8.78 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 33 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 66 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 69 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 30 " Number of angles added : 6 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4106 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 30 sheets defined 29.7% alpha, 15.7% beta 30 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 9.12 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 removed outlier: 3.933A pdb=" N ILE A 7 " --> pdb=" O PRO A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 150 through 163 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 209 through 218 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'C' and resid 67 through 81 Processing helix chain 'C' and resid 83 through 89 Processing helix chain 'C' and resid 96 through 104 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.800A pdb=" N GLU C 157 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ARG C 158 " --> pdb=" O ASN C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 194 No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 201 through 222 Processing helix chain 'C' and resid 269 through 280 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'D' and resid 67 through 81 Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 96 through 104 Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 154 through 160 removed outlier: 5.097A pdb=" N ARG D 158 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 160 " --> pdb=" O GLU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 194 No H-bonds generated for 'chain 'D' and resid 191 through 194' Processing helix chain 'D' and resid 201 through 222 Processing helix chain 'D' and resid 269 through 282 Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'E' and resid 67 through 81 Processing helix chain 'E' and resid 83 through 89 Processing helix chain 'E' and resid 96 through 103 Processing helix chain 'E' and resid 118 through 126 Processing helix chain 'E' and resid 128 through 132 Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'E' and resid 201 through 216 Processing helix chain 'E' and resid 269 through 281 removed outlier: 3.621A pdb=" N LYS E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 330 Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 96 through 104 Processing helix chain 'F' and resid 118 through 126 Processing helix chain 'F' and resid 154 through 160 removed outlier: 4.796A pdb=" N ARG F 158 " --> pdb=" O ASN F 155 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU F 160 " --> pdb=" O GLU F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' Processing helix chain 'F' and resid 201 through 216 Processing helix chain 'F' and resid 269 through 280 Processing helix chain 'F' and resid 282 through 284 No H-bonds generated for 'chain 'F' and resid 282 through 284' Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'G' and resid 67 through 87 removed outlier: 5.315A pdb=" N GLU G 84 " --> pdb=" O LYS G 80 " (cutoff:3.500A) Proline residue: G 85 - end of helix Processing helix chain 'G' and resid 96 through 103 Processing helix chain 'G' and resid 118 through 125 Processing helix chain 'G' and resid 157 through 160 No H-bonds generated for 'chain 'G' and resid 157 through 160' Processing helix chain 'G' and resid 269 through 281 Processing helix chain 'G' and resid 320 through 331 Processing helix chain 'G' and resid 336 through 342 Processing helix chain 'H' and resid 16 through 26 Processing helix chain 'H' and resid 32 through 38 Processing helix chain 'H' and resid 70 through 94 Proline residue: H 82 - end of helix Processing helix chain 'H' and resid 132 through 139 Processing helix chain 'H' and resid 141 through 163 removed outlier: 3.937A pdb=" N VAL H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE H 147 " --> pdb=" O THR H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 230 No H-bonds generated for 'chain 'H' and resid 227 through 230' Processing sheet with id= A, first strand: chain 'A' and resid 43 through 45 Processing sheet with id= B, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.832A pdb=" N VAL A 114 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 72 through 75 removed outlier: 5.990A pdb=" N ALA B 128 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU B 10 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 80 through 86 Processing sheet with id= E, first strand: chain 'B' and resid 196 through 200 Processing sheet with id= F, first strand: chain 'C' and resid 144 through 146 removed outlier: 6.501A pdb=" N ARG C 8 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE C 300 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.855A pdb=" N ASN C 21 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 45 through 50 Processing sheet with id= I, first strand: chain 'C' and resid 149 through 151 Processing sheet with id= J, first strand: chain 'C' and resid 174 through 181 Processing sheet with id= K, first strand: chain 'D' and resid 144 through 146 removed outlier: 6.195A pdb=" N ARG D 8 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE D 300 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.981A pdb=" N ASN D 21 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 45 through 51 Processing sheet with id= N, first strand: chain 'D' and resid 149 through 151 Processing sheet with id= O, first strand: chain 'D' and resid 174 through 181 Processing sheet with id= P, first strand: chain 'E' and resid 144 through 146 removed outlier: 6.255A pdb=" N ARG E 8 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE E 300 " --> pdb=" O ARG E 8 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 45 through 51 Processing sheet with id= R, first strand: chain 'E' and resid 149 through 151 Processing sheet with id= S, first strand: chain 'E' and resid 174 through 181 Processing sheet with id= T, first strand: chain 'F' and resid 144 through 146 removed outlier: 6.449A pdb=" N ARG F 8 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE F 300 " --> pdb=" O ARG F 8 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 21 through 23 removed outlier: 3.790A pdb=" N ASN F 21 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 174 through 180 Processing sheet with id= W, first strand: chain 'F' and resid 45 through 53 removed outlier: 7.036A pdb=" N VAL F 56 " --> pdb=" O VAL F 52 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 298 through 300 removed outlier: 3.535A pdb=" N LEU G 256 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 45 through 51 removed outlier: 3.702A pdb=" N LEU G 62 " --> pdb=" O MET G 46 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 174 through 177 Processing sheet with id= AA, first strand: chain 'H' and resid 102 through 109 removed outlier: 3.596A pdb=" N GLY H 63 " --> pdb=" O PHE H 60 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE H 60 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA H 65 " --> pdb=" O SER H 58 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.843A pdb=" N GLY H 177 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU H 203 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N PHE H 175 " --> pdb=" O GLU H 203 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 180 through 184 Processing sheet with id= AD, first strand: chain 'H' and resid 211 through 213 removed outlier: 3.502A pdb=" N ILE H 225 " --> pdb=" O TRP H 212 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1695 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 6.72 Time building geometry restraints manager: 9.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5106 1.33 - 1.46: 5073 1.46 - 1.58: 9985 1.58 - 1.70: 233 1.70 - 1.83: 162 Bond restraints: 20559 Sorted by residual: bond pdb=" O3' 23G I 61 " pdb=" PC 23G I 61 " ideal model delta sigma weight residual 1.334 1.603 -0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C4' 23G I 61 " pdb=" O4' 23G I 61 " ideal model delta sigma weight residual 1.663 1.431 0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C4' 23G I 61 " pdb=" C3' 23G I 61 " ideal model delta sigma weight residual 1.302 1.518 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C2' 23G I 61 " pdb=" O2' 23G I 61 " ideal model delta sigma weight residual 1.250 1.427 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N3 23G I 61 " pdb=" C4 23G I 61 " ideal model delta sigma weight residual 1.502 1.354 0.148 2.00e-02 2.50e+03 5.46e+01 ... (remaining 20554 not shown) Histogram of bond angle deviations from ideal: 93.72 - 102.20: 154 102.20 - 110.68: 6875 110.68 - 119.16: 10722 119.16 - 127.64: 10294 127.64 - 136.12: 376 Bond angle restraints: 28421 Sorted by residual: angle pdb=" O3' DT K 37 " pdb=" C3' DT K 37 " pdb=" C2' DT K 37 " ideal model delta sigma weight residual 111.50 100.67 10.83 1.50e+00 4.44e-01 5.21e+01 angle pdb=" CA GLU G 328 " pdb=" CB GLU G 328 " pdb=" CG GLU G 328 " ideal model delta sigma weight residual 114.10 124.34 -10.24 2.00e+00 2.50e-01 2.62e+01 angle pdb=" O3' DT K 28 " pdb=" C3' DT K 28 " pdb=" C2' DT K 28 " ideal model delta sigma weight residual 111.50 103.87 7.63 1.50e+00 4.44e-01 2.59e+01 angle pdb=" CB MET A 77 " pdb=" CG MET A 77 " pdb=" SD MET A 77 " ideal model delta sigma weight residual 112.70 126.03 -13.33 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C GLU G 89 " pdb=" N LYS G 90 " pdb=" CA LYS G 90 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 ... (remaining 28416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 11276 35.66 - 71.32: 627 71.32 - 106.98: 35 106.98 - 142.64: 0 142.64 - 178.30: 5 Dihedral angle restraints: 11943 sinusoidal: 5514 harmonic: 6429 Sorted by residual: dihedral pdb=" O4' C I 20 " pdb=" C1' C I 20 " pdb=" N1 C I 20 " pdb=" C2 C I 20 " ideal model delta sinusoidal sigma weight residual -128.00 44.66 -172.66 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C I 17 " pdb=" C1' C I 17 " pdb=" N1 C I 17 " pdb=" C2 C I 17 " ideal model delta sinusoidal sigma weight residual -160.00 -82.52 -77.48 1 1.50e+01 4.44e-03 3.34e+01 dihedral pdb=" O4' C I 46 " pdb=" C2' C I 46 " pdb=" C1' C I 46 " pdb=" C3' C I 46 " ideal model delta sinusoidal sigma weight residual 25.00 -11.25 36.25 1 8.00e+00 1.56e-02 2.90e+01 ... (remaining 11940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2511 0.065 - 0.131: 559 0.131 - 0.196: 117 0.196 - 0.262: 22 0.262 - 0.327: 4 Chirality restraints: 3213 Sorted by residual: chirality pdb=" C3' DT K 37 " pdb=" C4' DT K 37 " pdb=" O3' DT K 37 " pdb=" C2' DT K 37 " both_signs ideal model delta sigma weight residual False -2.66 -2.99 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C2' G I 13 " pdb=" C3' G I 13 " pdb=" O2' G I 13 " pdb=" C1' G I 13 " both_signs ideal model delta sigma weight residual False -2.52 -2.24 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CB VAL G 310 " pdb=" CA VAL G 310 " pdb=" CG1 VAL G 310 " pdb=" CG2 VAL G 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 3210 not shown) Planarity restraints: 3271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 289 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.21e+00 pdb=" C GLY F 289 " -0.052 2.00e-02 2.50e+03 pdb=" O GLY F 289 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY F 290 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 317 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C THR G 317 " 0.049 2.00e-02 2.50e+03 pdb=" O THR G 317 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY G 318 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 28 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C THR F 28 " -0.048 2.00e-02 2.50e+03 pdb=" O THR F 28 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE F 29 " 0.016 2.00e-02 2.50e+03 ... (remaining 3268 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 93 2.43 - 3.05: 11155 3.05 - 3.67: 33461 3.67 - 4.28: 50222 4.28 - 4.90: 80040 Nonbonded interactions: 174971 Sorted by model distance: nonbonded pdb=" N4 C I 47 " pdb=" O6 G I 60 " model vdw 1.817 2.520 nonbonded pdb=" OD1 ASP A 6 " pdb=" NH2 ARG A 35 " model vdw 1.866 2.520 nonbonded pdb=" O VAL A 8 " pdb=" O LEU A 12 " model vdw 1.869 3.040 nonbonded pdb=" N3 C I 47 " pdb=" N1 G I 60 " model vdw 1.878 2.600 nonbonded pdb=" CE1 PHE H 60 " pdb=" OP2 G I 37 " model vdw 1.939 3.340 ... (remaining 174966 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 'C' and (resid 1 through 217 or resid 240 through 344)) selection = (chain 'D' and (resid 1 through 217 or resid 240 through 344)) selection = (chain 'E' and resid 1 through 344) selection = (chain 'F' and resid 1 through 344) } 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: 2.470 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: 0.020 Extract box with map and model: 10.230 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 62.760 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.080 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:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.007 0.269 20559 Z= 0.412 Angle : 0.976 13.332 28421 Z= 0.565 Chirality : 0.059 0.327 3213 Planarity : 0.008 0.079 3271 Dihedral : 19.588 178.295 7837 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.76 % Allowed : 21.98 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.15), residues: 2254 helix: -1.50 (0.16), residues: 745 sheet: -0.81 (0.26), residues: 327 loop : -1.38 (0.16), residues: 1182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 331 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 37 residues processed: 371 average time/residue: 1.4275 time to fit residues: 592.3918 Evaluate side-chains 326 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 289 time to evaluate : 1.980 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 32 residues processed: 6 average time/residue: 0.6507 time to fit residues: 7.5573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 184 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 99 ASN ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 GLN B 150 GLN C 2 GLN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 HIS F 343 GLN G 30 ASN G 280 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 20559 Z= 0.358 Angle : 0.665 6.571 28421 Z= 0.346 Chirality : 0.045 0.254 3213 Planarity : 0.005 0.048 3271 Dihedral : 18.219 177.974 3753 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 5.36 % Allowed : 19.11 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.16), residues: 2254 helix: -0.26 (0.18), residues: 748 sheet: -0.75 (0.24), residues: 367 loop : -1.04 (0.17), residues: 1139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 300 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 50 residues processed: 365 average time/residue: 1.3980 time to fit residues: 572.2513 Evaluate side-chains 342 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 292 time to evaluate : 1.868 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 41 residues processed: 10 average time/residue: 0.8529 time to fit residues: 12.6082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 177 optimal weight: 9.9990 chunk 145 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 230 optimal weight: 20.0000 chunk 190 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 171 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN D 2 GLN ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN F 343 GLN G 30 ASN G 63 GLN G 280 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20559 Z= 0.274 Angle : 0.605 7.057 28421 Z= 0.315 Chirality : 0.043 0.186 3213 Planarity : 0.004 0.046 3271 Dihedral : 18.068 179.279 3753 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.58 % Allowed : 18.90 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2254 helix: 0.37 (0.19), residues: 751 sheet: -0.78 (0.25), residues: 361 loop : -0.92 (0.18), residues: 1142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 299 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 59 residues processed: 369 average time/residue: 1.4646 time to fit residues: 604.3589 Evaluate side-chains 333 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 274 time to evaluate : 2.197 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 46 residues processed: 14 average time/residue: 0.9502 time to fit residues: 18.7233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 1.9990 chunk 160 optimal weight: 0.0030 chunk 110 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 chunk 214 optimal weight: 20.0000 chunk 227 optimal weight: 2.9990 chunk 112 optimal weight: 0.0770 chunk 203 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 3 ASN C 340 GLN ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN F 30 ASN F 343 GLN H 224 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20559 Z= 0.203 Angle : 0.575 10.280 28421 Z= 0.298 Chirality : 0.041 0.167 3213 Planarity : 0.004 0.046 3271 Dihedral : 17.938 178.703 3753 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.31 % Allowed : 19.49 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2254 helix: 0.74 (0.19), residues: 751 sheet: -0.86 (0.24), residues: 355 loop : -0.83 (0.18), residues: 1148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 285 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 55 residues processed: 355 average time/residue: 1.3935 time to fit residues: 556.1286 Evaluate side-chains 332 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 277 time to evaluate : 2.006 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 49 residues processed: 7 average time/residue: 0.7334 time to fit residues: 8.9317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 0.9980 chunk 128 optimal weight: 0.0870 chunk 3 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 203 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN E 209 GLN F 343 GLN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN G 63 GLN G 280 ASN H 224 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20559 Z= 0.247 Angle : 0.588 7.625 28421 Z= 0.304 Chirality : 0.042 0.236 3213 Planarity : 0.004 0.046 3271 Dihedral : 17.889 178.227 3753 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.98 % Allowed : 19.71 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2254 helix: 0.83 (0.19), residues: 756 sheet: -0.88 (0.24), residues: 355 loop : -0.79 (0.18), residues: 1143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 287 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 57 residues processed: 353 average time/residue: 1.4205 time to fit residues: 561.8725 Evaluate side-chains 341 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 284 time to evaluate : 1.965 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 46 residues processed: 12 average time/residue: 0.8826 time to fit residues: 15.1925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 0.8980 chunk 204 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 133 optimal weight: 0.1980 chunk 56 optimal weight: 0.6980 chunk 227 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 119 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 3 ASN C 284 ASN C 340 GLN D 2 GLN D 247 ASN F 30 ASN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN G 63 GLN G 280 ASN G 340 GLN H 134 HIS H 224 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20559 Z= 0.231 Angle : 0.583 11.068 28421 Z= 0.300 Chirality : 0.041 0.151 3213 Planarity : 0.004 0.046 3271 Dihedral : 17.838 178.828 3753 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.82 % Allowed : 20.19 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2254 helix: 0.88 (0.19), residues: 762 sheet: -0.87 (0.24), residues: 355 loop : -0.74 (0.18), residues: 1137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 286 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 55 residues processed: 348 average time/residue: 1.4457 time to fit residues: 564.0413 Evaluate side-chains 338 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 283 time to evaluate : 2.055 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 45 residues processed: 11 average time/residue: 1.1385 time to fit residues: 17.1314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 191 optimal weight: 0.0870 chunk 126 optimal weight: 0.0040 chunk 226 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 104 optimal weight: 0.7980 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN C 284 ASN C 340 GLN D 247 ASN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN G 63 GLN G 280 ASN H 224 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20559 Z= 0.202 Angle : 0.569 8.811 28421 Z= 0.293 Chirality : 0.041 0.143 3213 Planarity : 0.004 0.046 3271 Dihedral : 17.790 179.550 3753 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.44 % Allowed : 20.90 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2254 helix: 1.00 (0.19), residues: 760 sheet: -0.84 (0.25), residues: 354 loop : -0.70 (0.18), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 286 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 53 residues processed: 348 average time/residue: 1.4632 time to fit residues: 573.3457 Evaluate side-chains 328 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 275 time to evaluate : 2.075 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 45 residues processed: 9 average time/residue: 0.7830 time to fit residues: 11.5653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 0.0170 chunk 43 optimal weight: 0.3980 chunk 144 optimal weight: 0.2980 chunk 154 optimal weight: 0.9980 chunk 111 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 3 ASN C 340 GLN D 247 ASN F 175 GLN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 280 ASN H 224 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20559 Z= 0.194 Angle : 0.579 12.021 28421 Z= 0.297 Chirality : 0.041 0.139 3213 Planarity : 0.004 0.046 3271 Dihedral : 17.746 179.978 3753 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.01 % Allowed : 21.93 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2254 helix: 1.07 (0.19), residues: 757 sheet: -0.81 (0.25), residues: 354 loop : -0.66 (0.18), residues: 1143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 298 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 52 residues processed: 353 average time/residue: 1.4969 time to fit residues: 589.8648 Evaluate side-chains 340 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 288 time to evaluate : 2.032 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 43 residues processed: 10 average time/residue: 0.7514 time to fit residues: 11.6745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 206 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 91 optimal weight: 0.0980 chunk 165 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 chunk 210 optimal weight: 20.0000 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 284 ASN C 340 GLN D 2 GLN D 247 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN H 224 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20559 Z= 0.282 Angle : 0.617 8.399 28421 Z= 0.318 Chirality : 0.042 0.180 3213 Planarity : 0.004 0.045 3271 Dihedral : 17.795 179.278 3753 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.74 % Allowed : 21.93 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2254 helix: 0.99 (0.19), residues: 755 sheet: -0.86 (0.24), residues: 370 loop : -0.67 (0.18), residues: 1129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 284 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 45 residues processed: 338 average time/residue: 1.5118 time to fit residues: 573.1966 Evaluate side-chains 316 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 271 time to evaluate : 2.171 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 42 residues processed: 4 average time/residue: 0.6922 time to fit residues: 6.2664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 138 optimal weight: 0.0670 chunk 223 optimal weight: 0.0870 chunk 136 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 234 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 186 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 144 optimal weight: 0.2980 chunk 114 optimal weight: 0.6980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 167 GLN ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN D 2 GLN D 247 ASN F 30 ASN G 280 ASN H 224 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20559 Z= 0.197 Angle : 0.599 14.311 28421 Z= 0.305 Chirality : 0.041 0.139 3213 Planarity : 0.004 0.046 3271 Dihedral : 17.740 179.020 3753 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.82 % Allowed : 23.01 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2254 helix: 1.03 (0.19), residues: 762 sheet: -0.77 (0.25), residues: 354 loop : -0.65 (0.19), residues: 1138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 281 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 45 residues processed: 326 average time/residue: 1.4346 time to fit residues: 523.9375 Evaluate side-chains 318 residues out of total 1847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 273 time to evaluate : 1.876 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 42 residues processed: 4 average time/residue: 0.4424 time to fit residues: 5.0110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 148 optimal weight: 0.3980 chunk 198 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 186 optimal weight: 0.2980 chunk 78 optimal weight: 0.0980 chunk 191 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 167 GLN ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 2 GLN D 247 ASN F 30 ASN G 280 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.171518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119007 restraints weight = 23833.245| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.89 r_work: 0.3100 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20559 Z= 0.190 Angle : 0.589 12.946 28421 Z= 0.301 Chirality : 0.041 0.184 3213 Planarity : 0.004 0.046 3271 Dihedral : 17.722 178.940 3753 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.09 % Allowed : 22.79 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2254 helix: 1.10 (0.19), residues: 760 sheet: -0.77 (0.25), residues: 354 loop : -0.63 (0.19), residues: 1140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9225.18 seconds wall clock time: 163 minutes 46.16 seconds (9826.16 seconds total)