Starting phenix.real_space_refine (version: dev) on Sun May 15 23:10:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kix_0694/05_2022/6kix_0694_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kix_0694/05_2022/6kix_0694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kix_0694/05_2022/6kix_0694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kix_0694/05_2022/6kix_0694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kix_0694/05_2022/6kix_0694_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kix_0694/05_2022/6kix_0694_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" 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" Residue "K ARG 3916": "NH1" <-> "NH2" Residue "K ARG 3936": "NH1" <-> "NH2" Residue "K ARG 3965": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 19900 Number of models: 1 Model: "" Number of chains: 15 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: "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: "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: "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: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1, 'peptide': 3} Modifications used: {'COO': 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 16036 SG CYS K3957 95.433 67.783 25.595 1.00104.51 S ATOM 16050 SG CYS K3959 93.563 70.018 23.360 1.00110.33 S Time building chain proxies: 11.37, per 1000 atoms: 0.57 Number of scatterers: 19900 At special positions: 0 Unit cell: (162.8, 150.7, 121, 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 60 16.00 P 290 15.00 O 4284 8.00 N 3619 7.00 C 11646 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: 9.05 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN K4002 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3959 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3957 " 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 17 sheets defined 28.3% alpha, 9.3% beta 145 base pairs and 238 stacking pairs defined. Time for finding SS restraints: 8.33 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 86 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 76 removed outlier: 4.732A 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 28 through 35 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.939A 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 92 through 96 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: 4.028A 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 86 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: 4.560A 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: 4.023A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 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 'N' and resid 229 through 233 Processing helix chain 'K' and resid 3816 through 3827 removed outlier: 3.878A pdb=" N HIS K3822 " --> pdb=" O MET K3818 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS K3824 " --> pdb=" O PHE K3820 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS K3825 " --> pdb=" O ARG K3821 " (cutoff:3.500A) Processing helix chain 'K' and resid 3867 through 3878 Processing helix chain 'K' and resid 3901 through 3903 No H-bonds generated for 'chain 'K' and resid 3901 through 3903' Processing helix chain 'T' and resid 369 through 371 No H-bonds generated for 'chain 'T' and resid 369 through 371' Processing sheet with id= A, first strand: chain 'N' and resid 40 through 42 Processing sheet with id= B, first strand: chain 'N' and resid 112 through 115 removed outlier: 3.909A pdb=" N LYS N 112 " --> pdb=" O CYS N 126 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET N 134 " --> pdb=" O VAL N 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'N' and resid 156 through 159 removed outlier: 3.668A pdb=" N PHE N 189 " --> pdb=" O ILE N 175 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'N' and resid 212 through 216 removed outlier: 3.669A pdb=" N GLN N 243 " --> pdb=" O VAL N 224 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'N' and resid 288 through 290 removed outlier: 3.659A pdb=" N LYS N 288 " --> pdb=" O ILE N 278 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU N 276 " --> pdb=" O LEU N 290 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR N 277 " --> pdb=" O ALA N 268 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE N 266 " --> pdb=" O TRP N 279 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL N 267 " --> pdb=" O CYS N 258 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS N 258 " --> pdb=" O VAL N 267 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS N 256 " --> pdb=" O GLY N 269 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'N' and resid 300 through 303 removed outlier: 3.721A pdb=" N ASP N 300 " --> pdb=" O ILE N 313 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE N 310 " --> pdb=" O TRP N 321 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP N 321 " --> pdb=" O ILE N 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER N 312 " --> pdb=" O SER N 319 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL N 317 " --> pdb=" O SER N 314 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 3862 through 3864 Processing sheet with id= H, first strand: chain 'R' and resid 101 through 103 Processing sheet with id= I, first strand: chain 'R' and resid 166 through 168 removed outlier: 5.152A pdb=" N SER R 152 " --> pdb=" O SER R 148 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N SER R 148 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN R 136 " --> pdb=" O VAL R 145 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY R 147 " --> pdb=" O CYS R 134 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS R 134 " --> pdb=" O GLY R 147 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'R' and resid 196 through 199 removed outlier: 3.678A pdb=" N ARG R 196 " --> pdb=" O SER R 188 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N HIS R 178 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER R 189 " --> pdb=" O ALA R 176 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA R 176 " --> pdb=" O SER R 189 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 228 through 231 removed outlier: 3.583A pdb=" N ILE R 229 " --> pdb=" O TRP R 241 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'R' and resid 273 through 276 removed outlier: 3.608A pdb=" N TRP R 286 " --> pdb=" O ILE R 274 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'R' and resid 48 through 53 removed outlier: 7.257A pdb=" N SER R 63 " --> pdb=" O SER R 49 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL R 51 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA R 61 " --> pdb=" O VAL R 51 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'R' and resid 90 through 93 removed outlier: 6.543A pdb=" N ALA R 105 " --> pdb=" O SER R 91 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'R' and resid 304 through 309 removed outlier: 3.766A pdb=" N ILE R 305 " --> pdb=" O ALA R 319 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA R 319 " --> pdb=" O ILE R 305 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR R 307 " --> pdb=" O ALA R 317 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA R 317 " --> pdb=" O THR R 307 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'T' and resid 343 through 346 removed outlier: 3.759A pdb=" N ARG T 343 " --> pdb=" O SER T 473 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER T 473 " --> pdb=" O ARG T 343 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY T 345 " --> pdb=" O ALA T 471 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA T 471 " --> pdb=" O GLY T 345 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'T' and resid 447 through 449 removed outlier: 4.249A pdb=" N ILE T 447 " --> pdb=" O TYR T 460 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE T 449 " --> pdb=" O VAL T 458 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL T 458 " --> pdb=" O PHE T 449 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 238 stacking parallelities Total time for adding SS restraints: 8.66 Time building geometry restraints manager: 9.56 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: 4120 1.33 - 1.45: 5971 1.45 - 1.57: 10130 1.57 - 1.69: 578 1.69 - 1.81: 87 Bond restraints: 20886 Sorted by residual: bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.58e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.09e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.86e+00 bond pdb=" C LEU E 65 " pdb=" N PRO E 66 " ideal model delta sigma weight residual 1.336 1.357 -0.022 1.23e-02 6.61e+03 3.12e+00 bond pdb=" C LEU A 65 " pdb=" N PRO A 66 " ideal model delta sigma weight residual 1.336 1.357 -0.022 1.23e-02 6.61e+03 3.06e+00 ... (remaining 20881 not shown) Histogram of bond angle deviations from ideal: 92.93 - 101.17: 198 101.17 - 109.40: 4943 109.40 - 117.63: 11705 117.63 - 125.86: 11516 125.86 - 134.09: 1106 Bond angle restraints: 29468 Sorted by residual: angle pdb=" N ILE K3866 " pdb=" CA ILE K3866 " pdb=" C ILE K3866 " ideal model delta sigma weight residual 113.47 108.30 5.17 1.01e+00 9.80e-01 2.62e+01 angle pdb=" C PRO N 107 " pdb=" N SER N 108 " pdb=" CA SER N 108 " ideal model delta sigma weight residual 120.58 126.88 -6.30 1.32e+00 5.74e-01 2.27e+01 angle pdb=" C ASP B 24 " pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.27e+01 angle pdb=" N SER N 108 " pdb=" CA SER N 108 " pdb=" C SER N 108 " ideal model delta sigma weight residual 113.45 119.31 -5.86 1.39e+00 5.18e-01 1.78e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 122.58 -9.40 2.37e+00 1.78e-01 1.57e+01 ... (remaining 29463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 10102 34.20 - 68.40: 1382 68.40 - 102.60: 29 102.60 - 136.80: 1 136.80 - 171.00: 3 Dihedral angle restraints: 11517 sinusoidal: 6411 harmonic: 5106 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 180.00 134.57 45.43 0 5.00e+00 4.00e-02 8.25e+01 dihedral pdb=" CA ARG K3864 " pdb=" C ARG K3864 " pdb=" N SER K3865 " pdb=" CA SER K3865 " ideal model delta harmonic sigma weight residual -180.00 -143.11 -36.89 0 5.00e+00 4.00e-02 5.44e+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 180.00 146.80 33.20 0 5.00e+00 4.00e-02 4.41e+01 ... (remaining 11514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2287 0.046 - 0.093: 780 0.093 - 0.139: 204 0.139 - 0.185: 29 0.185 - 0.232: 7 Chirality restraints: 3307 Sorted by residual: 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 1.34e+00 chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3304 not shown) Planarity restraints: 2726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO B 32 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 223 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO R 224 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 224 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 224 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 30 " 0.034 2.00e-02 2.50e+03 1.54e-02 6.51e+00 pdb=" N9 DA I 30 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 30 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 30 " -0.017 2.00e-02 2.50e+03 pdb=" C5 DA I 30 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 30 " 0.010 2.00e-02 2.50e+03 pdb=" N6 DA I 30 " 0.016 2.00e-02 2.50e+03 pdb=" N1 DA I 30 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA I 30 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 30 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DA I 30 " -0.006 2.00e-02 2.50e+03 ... (remaining 2723 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2375 2.75 - 3.29: 16781 3.29 - 3.83: 34842 3.83 - 4.36: 39321 4.36 - 4.90: 61547 Nonbonded interactions: 154866 Sorted by model distance: nonbonded pdb=" N CYS K3959 " pdb="ZN ZN K4002 " model vdw 2.219 2.310 nonbonded pdb=" OD1 ASP R 108 " pdb=" OG1 THR R 110 " model vdw 2.257 2.440 nonbonded pdb=" O TYR R 131 " pdb=" OG SER R 148 " model vdw 2.263 2.440 nonbonded pdb=" OG SER R 278 " pdb=" OD1 ASP R 280 " model vdw 2.298 2.440 nonbonded pdb=" OG SER R 223 " pdb=" OD1 ASN R 225 " model vdw 2.301 2.440 ... (remaining 154861 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 60 5.16 5 C 11646 2.51 5 N 3619 2.21 5 O 4284 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 6.350 Check model and map are aligned: 0.320 Convert atoms to be neutral: 0.180 Process input model: 63.180 Find NCS groups from input model: 0.760 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 : 0.006 0.071 20886 Z= 0.334 Angle : 0.835 9.897 29468 Z= 0.480 Chirality : 0.050 0.232 3307 Planarity : 0.007 0.111 2726 Dihedral : 22.575 171.004 8225 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.12 % 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: -3.74 (0.17), residues: 1728 helix: -1.12 (0.18), residues: 556 sheet: -3.16 (0.28), residues: 246 loop : -3.27 (0.16), residues: 926 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.3915 time to fit residues: 230.6104 Evaluate side-chains 205 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.042 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 24 GLN C 73 ASN D 81 ASN E 68 GLN E 76 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 81 ASN N 65 HIS N 88 ASN N 92 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 ASN N 216 ASN N 243 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 348 GLN T 354 GLN ** T 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 381 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 20886 Z= 0.171 Angle : 0.574 9.582 29468 Z= 0.328 Chirality : 0.039 0.185 3307 Planarity : 0.005 0.096 2726 Dihedral : 27.639 168.461 4855 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -2.38 (0.19), residues: 1728 helix: 0.93 (0.22), residues: 552 sheet: -2.73 (0.29), residues: 266 loop : -2.96 (0.17), residues: 910 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3415 time to fit residues: 150.9643 Evaluate side-chains 200 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.886 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 180 optimal weight: 40.0000 chunk 194 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 24 GLN C 31 HIS D 79 HIS D 81 ASN G 73 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3958 ASN R 86 HIS T 348 GLN ** T 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 354 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 20886 Z= 0.310 Angle : 0.660 8.746 29468 Z= 0.370 Chirality : 0.042 0.164 3307 Planarity : 0.005 0.093 2726 Dihedral : 27.642 164.380 4855 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -2.22 (0.19), residues: 1728 helix: 1.06 (0.22), residues: 548 sheet: -2.51 (0.31), residues: 238 loop : -2.90 (0.17), residues: 942 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3265 time to fit residues: 120.0192 Evaluate side-chains 175 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.758 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 191 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 38 ASN D 46 HIS D 79 HIS G 73 ASN N 65 HIS ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 20886 Z= 0.289 Angle : 0.646 8.239 29468 Z= 0.363 Chirality : 0.042 0.164 3307 Planarity : 0.005 0.093 2726 Dihedral : 27.609 166.035 4855 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -2.13 (0.19), residues: 1728 helix: 1.02 (0.22), residues: 549 sheet: -2.35 (0.32), residues: 241 loop : -2.81 (0.18), residues: 938 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.3312 time to fit residues: 114.6169 Evaluate side-chains 175 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.970 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS E 113 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 HIS N 121 ASN N 274 HIS K3848 ASN ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 20886 Z= 0.349 Angle : 0.697 7.782 29468 Z= 0.390 Chirality : 0.044 0.181 3307 Planarity : 0.005 0.093 2726 Dihedral : 27.759 164.695 4855 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -2.33 (0.19), residues: 1728 helix: 0.83 (0.22), residues: 540 sheet: -2.57 (0.31), residues: 256 loop : -2.83 (0.17), residues: 932 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.3356 time to fit residues: 109.7404 Evaluate side-chains 163 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.934 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 7.9990 chunk 172 optimal weight: 0.0770 chunk 37 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 0.0000 chunk 191 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 overall best weight: 1.2148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3848 ASN ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 20886 Z= 0.162 Angle : 0.564 8.661 29468 Z= 0.321 Chirality : 0.039 0.198 3307 Planarity : 0.004 0.091 2726 Dihedral : 27.433 172.983 4855 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -1.67 (0.20), residues: 1728 helix: 1.71 (0.23), residues: 551 sheet: -2.29 (0.31), residues: 261 loop : -2.67 (0.18), residues: 916 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.3133 time to fit residues: 114.8272 Evaluate side-chains 182 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 161 optimal weight: 0.2980 chunk 106 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3848 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 20886 Z= 0.240 Angle : 0.609 8.964 29468 Z= 0.342 Chirality : 0.041 0.172 3307 Planarity : 0.004 0.089 2726 Dihedral : 27.461 170.205 4855 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -1.69 (0.20), residues: 1728 helix: 1.50 (0.22), residues: 549 sheet: -2.19 (0.33), residues: 245 loop : -2.58 (0.18), residues: 934 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.3114 time to fit residues: 105.8872 Evaluate side-chains 175 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.969 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 40.0000 chunk 76 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 121 optimal weight: 0.0470 chunk 130 optimal weight: 0.1980 chunk 94 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3848 ASN ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 20886 Z= 0.172 Angle : 0.562 8.454 29468 Z= 0.318 Chirality : 0.039 0.168 3307 Planarity : 0.004 0.092 2726 Dihedral : 27.252 172.957 4855 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -1.41 (0.20), residues: 1728 helix: 1.79 (0.23), residues: 552 sheet: -1.99 (0.34), residues: 250 loop : -2.48 (0.18), residues: 926 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.3150 time to fit residues: 110.4327 Evaluate side-chains 176 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.871 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.3980 chunk 182 optimal weight: 10.0000 chunk 166 optimal weight: 30.0000 chunk 177 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 20886 Z= 0.361 Angle : 0.703 8.469 29468 Z= 0.390 Chirality : 0.044 0.251 3307 Planarity : 0.005 0.091 2726 Dihedral : 27.523 169.328 4855 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -1.97 (0.19), residues: 1728 helix: 1.01 (0.22), residues: 544 sheet: -2.11 (0.34), residues: 228 loop : -2.64 (0.18), residues: 956 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 197 average time/residue: 0.3026 time to fit residues: 93.3246 Evaluate side-chains 159 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.959 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2176 time to fit residues: 2.8458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 197 optimal weight: 0.0040 chunk 181 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 121 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 20886 Z= 0.268 Angle : 0.635 8.735 29468 Z= 0.355 Chirality : 0.041 0.217 3307 Planarity : 0.004 0.087 2726 Dihedral : 27.399 171.889 4855 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -1.88 (0.19), residues: 1728 helix: 1.15 (0.22), residues: 546 sheet: -2.09 (0.33), residues: 239 loop : -2.62 (0.18), residues: 943 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.3008 time to fit residues: 98.7514 Evaluate side-chains 165 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.022 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 157 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3848 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.127997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.100631 restraints weight = 58984.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.100175 restraints weight = 82585.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.100619 restraints weight = 76333.624| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 20886 Z= 0.156 Angle : 0.558 10.506 29468 Z= 0.313 Chirality : 0.039 0.442 3307 Planarity : 0.004 0.083 2726 Dihedral : 27.089 175.290 4855 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -1.33 (0.20), residues: 1728 helix: 1.86 (0.23), residues: 551 sheet: -1.92 (0.35), residues: 240 loop : -2.44 (0.18), residues: 937 =============================================================================== Job complete usr+sys time: 3232.33 seconds wall clock time: 60 minutes 2.34 seconds (3602.34 seconds total)