Starting phenix.real_space_refine (version: dev) on Fri Dec 16 04:49:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiu_9998/12_2022/6kiu_9998_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiu_9998/12_2022/6kiu_9998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiu_9998/12_2022/6kiu_9998.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiu_9998/12_2022/6kiu_9998.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiu_9998/12_2022/6kiu_9998_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiu_9998/12_2022/6kiu_9998_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8540 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 3885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 3916": "NH1" <-> "NH2" Residue "K ARG 3936": "NH1" <-> "NH2" Residue "K ARG 3965": "NH1" <-> "NH2" Residue "N TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 76": "NH1" <-> "NH2" Residue "N ARG 103": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "N ARG 190": "NH1" <-> "NH2" Residue "N ARG 228": "NH1" <-> "NH2" Residue "N ARG 272": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 20503 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 738 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1436 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "N" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2768 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain breaks: 1 Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2326 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain: "T" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1399 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 12, 'TRANS': 163} Chain breaks: 1 Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {' ZN': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 2} Not linked: pdbres="SAH K4001 " pdbres=" ZN K4002 " Not linked: pdbres=" ZN K4002 " pdbres="LYS K4003 " List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13282 SG CYS K3959 91.570 70.702 20.892 1.00 54.95 S Time building chain proxies: 11.83, per 1000 atoms: 0.58 Number of scatterers: 20503 At special positions: 0 Unit cell: (158.05, 147.15, 129.71, 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 62 16.00 P 290 15.00 O 4401 8.00 N 3724 7.00 C 12025 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.92 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K4002 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3959 " 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3434 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 22 sheets defined 27.8% alpha, 12.5% beta 144 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 8.37 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 87 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 33 through 41 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.930A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 47 through 72 removed outlier: 4.059A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 119 removed outlier: 3.854A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 87 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 removed outlier: 4.055A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.800A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 119 Processing helix chain 'K' and resid 3816 through 3830 removed outlier: 3.519A pdb=" N ARG K3821 " --> pdb=" O PRO K3817 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS K3822 " --> pdb=" O MET K3818 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS K3824 " --> pdb=" O PHE K3820 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS K3825 " --> pdb=" O ARG K3821 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS K3828 " --> pdb=" O LYS K3824 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU K3829 " --> pdb=" O LYS K3825 " (cutoff:3.500A) Processing helix chain 'K' and resid 3867 through 3877 Processing helix chain 'N' and resid 229 through 233 Processing helix chain 'O' and resid 24 through 33 Processing sheet with id= A, first strand: chain 'K' and resid 3831 through 3835 Processing sheet with id= B, first strand: chain 'K' and resid 3861 through 3864 Processing sheet with id= C, first strand: chain 'K' and resid 3915 through 3920 removed outlier: 3.530A pdb=" N VAL K3927 " --> pdb=" O ARG K3916 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN K3923 " --> pdb=" O ILE K3920 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE K3856 " --> pdb=" O ILE K3928 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'N' and resid 38 through 42 removed outlier: 4.006A pdb=" N LEU N 39 " --> pdb=" O TRP N 51 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASP N 52 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE N 58 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'N' and resid 72 through 74 Processing sheet with id= F, first strand: chain 'N' and resid 122 through 126 removed outlier: 3.658A pdb=" N VAL N 123 " --> pdb=" O LEU N 135 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'N' and resid 156 through 159 removed outlier: 3.976A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LYS N 179 " --> pdb=" O LEU N 185 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU N 185 " --> pdb=" O LYS N 179 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'N' and resid 243 through 246 removed outlier: 5.275A pdb=" N ILE N 221 " --> pdb=" O THR N 217 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR N 217 " --> pdb=" O ILE N 221 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE N 213 " --> pdb=" O TYR N 225 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU N 205 " --> pdb=" O LEU N 214 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER N 203 " --> pdb=" O ASN N 216 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 254 through 259 removed outlier: 6.941A pdb=" N GLY N 269 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS N 257 " --> pdb=" O VAL N 267 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL N 267 " --> pdb=" O CYS N 257 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE N 259 " --> pdb=" O TYR N 265 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR N 265 " --> pdb=" O PHE N 259 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS N 288 " --> pdb=" O ILE N 278 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU N 280 " --> pdb=" O LEU N 286 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU N 286 " --> pdb=" O GLU N 280 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 317 through 321 removed outlier: 3.547A pdb=" N TRP N 321 " --> pdb=" O ILE N 310 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE N 310 " --> pdb=" O TRP N 321 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP N 300 " --> pdb=" O ILE N 313 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 40 through 42 Processing sheet with id= L, first strand: chain 'R' and resid 123 through 125 removed outlier: 3.796A pdb=" N LYS R 123 " --> pdb=" O ILE R 113 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS R 112 " --> pdb=" O SER R 104 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'R' and resid 132 through 137 removed outlier: 7.015A pdb=" N GLY R 147 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS R 135 " --> pdb=" O VAL R 145 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL R 145 " --> pdb=" O CYS R 135 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE R 137 " --> pdb=" O LEU R 143 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU R 143 " --> pdb=" O PHE R 137 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG R 154 " --> pdb=" O SER R 146 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER R 148 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N SER R 152 " --> pdb=" O SER R 148 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL R 153 " --> pdb=" O LEU R 167 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE R 155 " --> pdb=" O LYS R 165 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASP R 157 " --> pdb=" O CYS R 163 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS R 163 " --> pdb=" O ASP R 157 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'R' and resid 176 through 179 removed outlier: 4.050A pdb=" N ALA R 176 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS R 178 " --> pdb=" O VAL R 187 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'R' and resid 228 through 233 removed outlier: 3.560A pdb=" N ILE R 229 " --> pdb=" O TRP R 241 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR R 233 " --> pdb=" O THR R 237 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR R 237 " --> pdb=" O THR R 233 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'R' and resid 273 through 276 removed outlier: 3.611A pdb=" N LEU R 297 " --> pdb=" O VAL R 283 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'R' and resid 306 through 309 removed outlier: 3.851A pdb=" N SER R 306 " --> pdb=" O ALA R 319 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA R 308 " --> pdb=" O ALA R 317 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'R' and resid 69 through 72 removed outlier: 3.893A pdb=" N LYS R 81 " --> pdb=" O ILE R 71 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'R' and resid 194 through 198 removed outlier: 3.815A pdb=" N CYS R 195 " --> pdb=" O LEU R 209 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS R 207 " --> pdb=" O ILE R 197 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'T' and resid 306 through 308 removed outlier: 3.840A pdb=" N ASN T 483 " --> pdb=" O GLU T 330 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU T 330 " --> pdb=" O ASN T 483 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'T' and resid 342 through 347 removed outlier: 3.837A pdb=" N SER T 473 " --> pdb=" O ARG T 343 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY T 345 " --> pdb=" O ALA T 471 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA T 471 " --> pdb=" O GLY T 345 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.948A pdb=" N VAL O 5 " --> pdb=" O ILE O 13 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 369 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 9.31 Time building geometry restraints manager: 9.39 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: 4596 1.33 - 1.45: 6066 1.45 - 1.58: 10165 1.58 - 1.70: 578 1.70 - 1.82: 90 Bond restraints: 21495 Sorted by residual: bond pdb=" C2 SAH K4001 " pdb=" N3 SAH K4001 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.25e+00 bond pdb=" C8 SAH K4001 " pdb=" N7 SAH K4001 " ideal model delta sigma weight residual 1.299 1.348 -0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" C2 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.330 1.378 -0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.492 -0.070 3.00e-02 1.11e+03 5.50e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.32e+00 ... (remaining 21490 not shown) Histogram of bond angle deviations from ideal: 94.81 - 102.67: 458 102.67 - 110.53: 7867 110.53 - 118.39: 9681 118.39 - 126.25: 11212 126.25 - 134.11: 1069 Bond angle restraints: 30287 Sorted by residual: angle pdb=" N VAL G 27 " pdb=" CA VAL G 27 " pdb=" C VAL G 27 " ideal model delta sigma weight residual 112.96 107.56 5.40 1.00e+00 1.00e+00 2.92e+01 angle pdb=" N VAL C 27 " pdb=" CA VAL C 27 " pdb=" C VAL C 27 " ideal model delta sigma weight residual 112.96 108.03 4.93 1.00e+00 1.00e+00 2.43e+01 angle pdb=" C ASN N 250 " pdb=" N ARG N 251 " pdb=" CA ARG N 251 " ideal model delta sigma weight residual 121.54 130.93 -9.39 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C ASN N 12 " pdb=" N TYR N 13 " pdb=" CA TYR N 13 " ideal model delta sigma weight residual 120.51 127.38 -6.87 1.45e+00 4.76e-01 2.25e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 123.58 -10.40 2.37e+00 1.78e-01 1.92e+01 ... (remaining 30282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.07: 10490 35.07 - 70.15: 1382 70.15 - 105.22: 12 105.22 - 140.30: 2 140.30 - 175.37: 2 Dihedral angle restraints: 11888 sinusoidal: 6564 harmonic: 5324 Sorted by residual: dihedral pdb=" CA LYS B 31 " pdb=" C LYS B 31 " pdb=" N PRO B 32 " pdb=" CA PRO B 32 " ideal model delta harmonic sigma weight residual 180.00 135.05 44.95 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" CA ALA N 322 " pdb=" C ALA N 322 " pdb=" N GLN N 323 " pdb=" CA GLN N 323 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ARG N 251 " pdb=" C ARG N 251 " pdb=" N THR N 252 " pdb=" CA THR N 252 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 11885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2396 0.049 - 0.098: 770 0.098 - 0.147: 203 0.147 - 0.196: 32 0.196 - 0.245: 4 Chirality restraints: 3405 Sorted by residual: chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA SER N 108 " pdb=" N SER N 108 " pdb=" C SER N 108 " pdb=" CB SER N 108 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE T 482 " pdb=" CA ILE T 482 " pdb=" CG1 ILE T 482 " pdb=" CG2 ILE T 482 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3402 not shown) Planarity restraints: 2831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.081 5.00e-02 4.00e+02 1.23e-01 2.44e+01 pdb=" N PRO B 32 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 108 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO N 109 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO N 109 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 109 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 51 " 0.017 2.00e-02 2.50e+03 1.96e-02 7.67e+00 pdb=" CG TYR B 51 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 51 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 51 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 51 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 51 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 51 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 51 " -0.002 2.00e-02 2.50e+03 ... (remaining 2828 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1222 2.72 - 3.27: 16800 3.27 - 3.81: 33716 3.81 - 4.36: 43556 4.36 - 4.90: 66008 Nonbonded interactions: 161302 Sorted by model distance: nonbonded pdb=" O CYS K3957 " pdb="ZN ZN K4002 " model vdw 2.178 2.230 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.241 2.440 nonbonded pdb=" O ILE K3905 " pdb=" OH TYR K3944 " model vdw 2.280 2.440 nonbonded pdb=" O TYR K3874 " pdb=" OG SER K3877 " model vdw 2.291 2.440 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.295 2.440 ... (remaining 161297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 120) selection = (chain 'H' and resid 28 through 120) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 290 5.49 5 S 62 5.16 5 C 12025 2.51 5 N 3724 2.21 5 O 4401 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 6.000 Check model and map are aligned: 0.280 Convert atoms to be neutral: 0.180 Process input model: 65.740 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 0.085 21495 Z= 0.435 Angle : 0.863 10.396 30287 Z= 0.494 Chirality : 0.052 0.245 3405 Planarity : 0.007 0.123 2831 Dihedral : 21.948 175.371 8454 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.16), residues: 1802 helix: -1.23 (0.18), residues: 582 sheet: -2.84 (0.28), residues: 270 loop : -3.19 (0.16), residues: 950 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.4466 time to fit residues: 219.0472 Evaluate side-chains 190 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.972 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 53 optimal weight: 0.0270 chunk 104 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 97 optimal weight: 7.9990 chunk 119 optimal weight: 0.2980 chunk 186 optimal weight: 0.0060 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN G 73 ASN K3822 HIS ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 376 GLN T 381 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 21495 Z= 0.152 Angle : 0.568 14.307 30287 Z= 0.326 Chirality : 0.039 0.180 3405 Planarity : 0.005 0.096 2831 Dihedral : 27.130 174.074 4923 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -2.25 (0.18), residues: 1802 helix: 0.78 (0.21), residues: 576 sheet: -2.41 (0.28), residues: 285 loop : -2.78 (0.17), residues: 941 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 224 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 232 average time/residue: 0.3675 time to fit residues: 125.3328 Evaluate side-chains 192 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 184 time to evaluate : 1.886 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2191 time to fit residues: 5.5246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 201 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN D 46 HIS G 73 ASN G 82 HIS G 84 GLN H 46 HIS N 323 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 21495 Z= 0.288 Angle : 0.612 9.751 30287 Z= 0.348 Chirality : 0.042 0.157 3405 Planarity : 0.005 0.102 2831 Dihedral : 27.259 173.678 4923 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -2.01 (0.19), residues: 1802 helix: 1.08 (0.22), residues: 572 sheet: -2.16 (0.28), residues: 293 loop : -2.73 (0.17), residues: 937 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 198 time to evaluate : 1.929 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 206 average time/residue: 0.3678 time to fit residues: 112.3168 Evaluate side-chains 188 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 1.920 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2205 time to fit residues: 7.3289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 30.0000 chunk 140 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 198 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS ** N 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 21495 Z= 0.380 Angle : 0.661 7.974 30287 Z= 0.374 Chirality : 0.044 0.170 3405 Planarity : 0.006 0.107 2831 Dihedral : 27.451 174.909 4923 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.06 % 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: -2.10 (0.18), residues: 1802 helix: 0.87 (0.21), residues: 570 sheet: -2.05 (0.29), residues: 275 loop : -2.74 (0.17), residues: 957 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 198 average time/residue: 0.3705 time to fit residues: 108.0102 Evaluate side-chains 183 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 1.886 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3162 time to fit residues: 4.9473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 136 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 65 HIS N 323 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 21495 Z= 0.264 Angle : 0.584 7.508 30287 Z= 0.335 Chirality : 0.041 0.152 3405 Planarity : 0.005 0.103 2831 Dihedral : 27.308 173.176 4923 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -1.81 (0.19), residues: 1802 helix: 1.21 (0.22), residues: 567 sheet: -2.00 (0.28), residues: 289 loop : -2.58 (0.17), residues: 946 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 201 average time/residue: 0.3747 time to fit residues: 110.7614 Evaluate side-chains 191 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 182 time to evaluate : 1.911 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1807 time to fit residues: 5.5211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 0.6980 chunk 178 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 chunk 164 optimal weight: 30.0000 chunk 91 optimal weight: 6.9990 chunk 16 optimal weight: 0.0570 chunk 65 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 21495 Z= 0.157 Angle : 0.544 7.384 30287 Z= 0.315 Chirality : 0.039 0.153 3405 Planarity : 0.004 0.097 2831 Dihedral : 27.205 172.264 4923 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -1.39 (0.19), residues: 1802 helix: 1.73 (0.22), residues: 567 sheet: -1.69 (0.30), residues: 275 loop : -2.47 (0.18), residues: 960 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 206 average time/residue: 0.3772 time to fit residues: 114.1190 Evaluate side-chains 188 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 1.785 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1985 time to fit residues: 3.7538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN G 84 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 21495 Z= 0.390 Angle : 0.650 7.370 30287 Z= 0.368 Chirality : 0.044 0.153 3405 Planarity : 0.006 0.103 2831 Dihedral : 27.408 174.283 4923 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -1.76 (0.19), residues: 1802 helix: 1.11 (0.22), residues: 569 sheet: -1.79 (0.29), residues: 287 loop : -2.52 (0.18), residues: 946 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 190 average time/residue: 0.3917 time to fit residues: 109.9984 Evaluate side-chains 189 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 181 time to evaluate : 2.020 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1831 time to fit residues: 5.3544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 chunk 179 optimal weight: 30.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 21495 Z= 0.192 Angle : 0.554 8.981 30287 Z= 0.319 Chirality : 0.039 0.151 3405 Planarity : 0.004 0.099 2831 Dihedral : 27.210 172.541 4923 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -1.39 (0.19), residues: 1802 helix: 1.59 (0.22), residues: 565 sheet: -1.53 (0.31), residues: 273 loop : -2.42 (0.18), residues: 964 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 191 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 192 average time/residue: 0.3655 time to fit residues: 103.3935 Evaluate side-chains 188 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 1.871 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1830 time to fit residues: 3.7750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 0.3980 chunk 172 optimal weight: 0.9980 chunk 184 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 21495 Z= 0.321 Angle : 0.617 9.219 30287 Z= 0.350 Chirality : 0.042 0.149 3405 Planarity : 0.005 0.101 2831 Dihedral : 27.326 173.646 4923 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -1.58 (0.19), residues: 1802 helix: 1.28 (0.22), residues: 567 sheet: -1.54 (0.31), residues: 262 loop : -2.46 (0.17), residues: 973 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 187 time to evaluate : 1.951 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 193 average time/residue: 0.3912 time to fit residues: 110.9012 Evaluate side-chains 176 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.982 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1774 time to fit residues: 2.9357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 204 optimal weight: 30.0000 chunk 187 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN N 67 HIS N 88 ASN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.084 21495 Z= 0.565 Angle : 0.765 13.380 30287 Z= 0.426 Chirality : 0.050 0.226 3405 Planarity : 0.007 0.107 2831 Dihedral : 27.671 176.709 4923 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -2.14 (0.18), residues: 1802 helix: 0.49 (0.21), residues: 572 sheet: -1.77 (0.31), residues: 265 loop : -2.63 (0.17), residues: 965 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 171 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 174 average time/residue: 0.3957 time to fit residues: 100.3527 Evaluate side-chains 171 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1896 time to fit residues: 4.5182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.191421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142916 restraints weight = 28934.511| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.52 r_work: 0.3272 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 21495 Z= 0.176 Angle : 0.563 13.086 30287 Z= 0.322 Chirality : 0.039 0.158 3405 Planarity : 0.004 0.098 2831 Dihedral : 27.252 171.758 4923 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -1.42 (0.19), residues: 1802 helix: 1.48 (0.22), residues: 566 sheet: -1.50 (0.31), residues: 265 loop : -2.40 (0.18), residues: 971 =============================================================================== Job complete usr+sys time: 3462.91 seconds wall clock time: 64 minutes 13.88 seconds (3853.88 seconds total)