Starting phenix.real_space_refine on Wed Mar 20 19:27:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kix_0694/03_2024/6kix_0694_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kix_0694/03_2024/6kix_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_0694/03_2024/6kix_0694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kix_0694/03_2024/6kix_0694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kix_0694/03_2024/6kix_0694_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kix_0694/03_2024/6kix_0694_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 8554 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 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. 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-5265/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: {'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 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: 11.20, per 1000 atoms: 0.56 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: 9.45 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal 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: 8.66 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: 8.45 Time building geometry restraints manager: 10.14 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=" 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 8.12e+00 bond pdb=" C8 SAH K4001 " pdb=" N7 SAH K4001 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.64e+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 5.68e+00 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 ... (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: 10304 34.20 - 68.40: 1421 68.40 - 102.60: 28 102.60 - 136.80: 1 136.80 - 171.00: 3 Dihedral angle restraints: 11757 sinusoidal: 6651 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 11754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2314 0.047 - 0.095: 766 0.095 - 0.142: 195 0.142 - 0.190: 25 0.190 - 0.237: 7 Chirality restraints: 3307 Sorted by residual: chirality pdb=" C1' SAH K4001 " pdb=" C2' SAH K4001 " pdb=" N9 SAH K4001 " pdb=" O4' SAH K4001 " both_signs ideal model delta sigma weight residual False 2.35 2.58 -0.24 2.00e-01 2.50e+01 1.41e+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 1.34e+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 ... (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 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 5.440 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 64.440 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 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= 0.339 Angle : 0.845 9.897 29468 Z= 0.482 Chirality : 0.050 0.237 3307 Planarity : 0.007 0.111 2726 Dihedral : 22.722 171.004 8465 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP N 51 HIS 0.011 0.002 HIS F 75 PHE 0.017 0.002 PHE N 213 TYR 0.035 0.002 TYR B 51 ARG 0.011 0.001 ARG K3765 *********************** 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 : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8260 (mtt) cc_final: 0.7802 (mtp) REVERT: C 76 THR cc_start: 0.9205 (m) cc_final: 0.8989 (p) REVERT: D 76 ARG cc_start: 0.7746 (ttm110) cc_final: 0.6987 (mtm180) REVERT: E 56 LYS cc_start: 0.8937 (ttmt) cc_final: 0.8466 (ttmm) REVERT: F 84 MET cc_start: 0.7158 (mmm) cc_final: 0.6750 (mmm) REVERT: G 36 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8234 (mptt) REVERT: G 94 ASN cc_start: 0.9171 (t0) cc_final: 0.8784 (t0) REVERT: N 294 ARG cc_start: 0.6626 (tpt90) cc_final: 0.6342 (mtp180) REVERT: N 320 ILE cc_start: 0.8180 (mp) cc_final: 0.7856 (mm) REVERT: K 3875 TYR cc_start: 0.5074 (m-80) cc_final: 0.4808 (m-10) REVERT: K 3941 THR cc_start: 0.8567 (p) cc_final: 0.7991 (t) REVERT: R 82 THR cc_start: 0.7739 (m) cc_final: 0.7442 (p) REVERT: R 126 LYS cc_start: 0.6974 (mttm) cc_final: 0.6143 (tptp) REVERT: R 137 PHE cc_start: 0.4901 (m-80) cc_final: 0.3946 (p90) REVERT: T 500 MET cc_start: -0.0257 (mmm) cc_final: -0.0862 (mtt) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.4081 time to fit residues: 238.8175 Evaluate side-chains 211 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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: 2.9990 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: 2.9990 chunk 60 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 E 68 GLN E 76 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2363 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= 0.181 Angle : 0.581 9.592 29468 Z= 0.332 Chirality : 0.039 0.191 3307 Planarity : 0.005 0.098 2726 Dihedral : 27.359 168.185 5095 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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: -2.39 (0.19), residues: 1728 helix: 0.87 (0.22), residues: 553 sheet: -2.64 (0.30), residues: 245 loop : -2.98 (0.17), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 198 HIS 0.006 0.001 HIS K3822 PHE 0.012 0.001 PHE E 104 TYR 0.013 0.001 TYR B 88 ARG 0.006 0.000 ARG K3864 *********************** 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 296 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7644 (ttt90) REVERT: A 120 MET cc_start: 0.8181 (mtt) cc_final: 0.7759 (mtp) REVERT: B 73 THR cc_start: 0.9012 (m) cc_final: 0.8723 (p) REVERT: B 92 ARG cc_start: 0.8408 (mtp-110) cc_final: 0.8153 (mtp-110) REVERT: C 76 THR cc_start: 0.9119 (m) cc_final: 0.8834 (p) REVERT: D 76 ARG cc_start: 0.7527 (ttm110) cc_final: 0.6800 (mtm180) REVERT: E 56 LYS cc_start: 0.8958 (ttmt) cc_final: 0.8521 (ttmm) REVERT: F 59 LYS cc_start: 0.8335 (ttpt) cc_final: 0.7924 (ttpt) REVERT: F 63 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7882 (mt-10) REVERT: G 36 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8212 (mptt) REVERT: G 39 TYR cc_start: 0.8929 (m-80) cc_final: 0.8651 (m-80) REVERT: G 94 ASN cc_start: 0.9146 (t0) cc_final: 0.8883 (t0) REVERT: N 179 LYS cc_start: 0.5800 (tptp) cc_final: 0.5360 (tppt) REVERT: N 256 LYS cc_start: 0.7242 (mmpt) cc_final: 0.7002 (mmmt) REVERT: R 126 LYS cc_start: 0.6961 (mttm) cc_final: 0.6053 (tptp) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.3504 time to fit residues: 153.4037 Evaluate side-chains 211 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.778 ------------------------------------------------------------------------------- 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: 9.9990 chunk 55 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 180 optimal weight: 40.0000 chunk 194 optimal weight: 0.0270 chunk 160 optimal weight: 7.9990 chunk 178 optimal weight: 0.8980 chunk 61 optimal weight: 0.0010 chunk 144 optimal weight: 3.9990 overall best weight: 0.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 216 ASN K3958 ASN R 86 HIS ** T 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3009 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= 0.143 Angle : 0.533 9.032 29468 Z= 0.306 Chirality : 0.038 0.222 3307 Planarity : 0.004 0.087 2726 Dihedral : 27.067 171.313 5095 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: -1.78 (0.20), residues: 1728 helix: 1.61 (0.23), residues: 557 sheet: -2.41 (0.30), residues: 257 loop : -2.76 (0.17), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 198 HIS 0.011 0.001 HIS K3822 PHE 0.019 0.001 PHE K3904 TYR 0.022 0.001 TYR B 88 ARG 0.012 0.000 ARG K3871 *********************** 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 298 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8046 (tt0) cc_final: 0.7741 (tt0) REVERT: A 120 MET cc_start: 0.8069 (mtt) cc_final: 0.7608 (mtp) REVERT: B 24 ASP cc_start: 0.6650 (m-30) cc_final: 0.6413 (m-30) REVERT: B 58 LEU cc_start: 0.8812 (tp) cc_final: 0.8556 (tp) REVERT: B 88 TYR cc_start: 0.8083 (m-80) cc_final: 0.6483 (m-80) REVERT: C 76 THR cc_start: 0.9084 (m) cc_final: 0.8749 (p) REVERT: E 56 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8541 (ttmm) REVERT: E 90 MET cc_start: 0.7234 (mtm) cc_final: 0.6955 (mtt) REVERT: E 129 ARG cc_start: 0.8528 (tmt-80) cc_final: 0.8302 (tmt-80) REVERT: F 59 LYS cc_start: 0.8288 (ttpt) cc_final: 0.7779 (ttpt) REVERT: F 63 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7897 (mt-10) REVERT: F 74 GLU cc_start: 0.8194 (tt0) cc_final: 0.7761 (tt0) REVERT: F 93 GLN cc_start: 0.7370 (mm-40) cc_final: 0.6773 (mm-40) REVERT: G 36 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8111 (mptt) REVERT: G 39 TYR cc_start: 0.8795 (m-80) cc_final: 0.8490 (m-80) REVERT: G 94 ASN cc_start: 0.9080 (t0) cc_final: 0.8867 (t0) REVERT: N 179 LYS cc_start: 0.5778 (tptp) cc_final: 0.5379 (tppt) REVERT: N 294 ARG cc_start: 0.6767 (tpt90) cc_final: 0.6403 (mmm-85) REVERT: K 3845 CYS cc_start: 0.7381 (p) cc_final: 0.6873 (m) REVERT: K 3867 GLN cc_start: 0.6772 (mp10) cc_final: 0.6441 (tt0) REVERT: R 126 LYS cc_start: 0.6886 (mttm) cc_final: 0.6032 (tptp) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.3528 time to fit residues: 153.6526 Evaluate side-chains 201 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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: 8.9990 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 191 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN C 24 GLN C 31 HIS D 46 HIS D 79 HIS F 75 HIS G 73 ASN ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 354 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 20886 Z= 0.334 Angle : 0.674 7.843 29468 Z= 0.375 Chirality : 0.042 0.164 3307 Planarity : 0.005 0.090 2726 Dihedral : 27.352 167.048 5095 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: -2.02 (0.19), residues: 1728 helix: 1.18 (0.22), residues: 545 sheet: -2.36 (0.31), residues: 243 loop : -2.74 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 51 HIS 0.008 0.001 HIS F 75 PHE 0.018 0.002 PHE E 104 TYR 0.019 0.002 TYR G 50 ARG 0.012 0.001 ARG N 190 *********************** 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 230 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8592 (tt0) cc_final: 0.8359 (tt0) REVERT: A 120 MET cc_start: 0.8252 (mtt) cc_final: 0.7873 (mtp) REVERT: B 73 THR cc_start: 0.8840 (m) cc_final: 0.8535 (p) REVERT: B 88 TYR cc_start: 0.8157 (m-80) cc_final: 0.7837 (m-80) REVERT: C 56 GLU cc_start: 0.8455 (tp30) cc_final: 0.8145 (tp30) REVERT: C 76 THR cc_start: 0.9078 (m) cc_final: 0.8713 (p) REVERT: D 88 SER cc_start: 0.9059 (p) cc_final: 0.8706 (t) REVERT: E 56 LYS cc_start: 0.9095 (ttmt) cc_final: 0.8690 (ttmm) REVERT: E 90 MET cc_start: 0.7706 (mtm) cc_final: 0.7495 (mtm) REVERT: F 59 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8183 (ttpt) REVERT: F 63 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7994 (mt-10) REVERT: F 74 GLU cc_start: 0.8453 (tt0) cc_final: 0.8117 (tt0) REVERT: F 84 MET cc_start: 0.6536 (mmm) cc_final: 0.5677 (mmm) REVERT: G 39 TYR cc_start: 0.8999 (m-80) cc_final: 0.8740 (m-80) REVERT: G 94 ASN cc_start: 0.9279 (t0) cc_final: 0.8989 (t0) REVERT: H 54 LYS cc_start: 0.8951 (mppt) cc_final: 0.8742 (mmtm) REVERT: N 256 LYS cc_start: 0.7289 (mmpt) cc_final: 0.6881 (mmmt) REVERT: N 294 ARG cc_start: 0.6771 (tpt90) cc_final: 0.6134 (mtp180) REVERT: K 3845 CYS cc_start: 0.7256 (p) cc_final: 0.6834 (m) REVERT: R 126 LYS cc_start: 0.6988 (mttm) cc_final: 0.6152 (tptp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3375 time to fit residues: 116.1040 Evaluate side-chains 180 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.759 ------------------------------------------------------------------------------- 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: 9.9990 chunk 2 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 79 HIS E 113 HIS ** N 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 274 HIS ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 348 GLN ** T 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 20886 Z= 0.433 Angle : 0.755 8.850 29468 Z= 0.417 Chirality : 0.045 0.176 3307 Planarity : 0.005 0.092 2726 Dihedral : 27.600 164.330 5095 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: -2.49 (0.19), residues: 1728 helix: 0.51 (0.21), residues: 546 sheet: -2.47 (0.32), residues: 235 loop : -2.89 (0.17), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 198 HIS 0.008 0.002 HIS B 75 PHE 0.021 0.002 PHE E 104 TYR 0.018 0.003 TYR G 50 ARG 0.006 0.001 ARG C 32 *********************** 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 208 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8241 (mtt) cc_final: 0.7836 (mtp) REVERT: B 88 TYR cc_start: 0.8288 (m-80) cc_final: 0.7180 (m-80) REVERT: C 56 GLU cc_start: 0.8478 (tp30) cc_final: 0.8230 (tp30) REVERT: C 76 THR cc_start: 0.9108 (m) cc_final: 0.8760 (p) REVERT: C 99 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7716 (ptp-170) REVERT: D 80 TYR cc_start: 0.7879 (m-80) cc_final: 0.7584 (m-80) REVERT: E 56 LYS cc_start: 0.9143 (ttmt) cc_final: 0.8753 (ttmm) REVERT: F 84 MET cc_start: 0.6901 (mmm) cc_final: 0.6434 (mmm) REVERT: F 93 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7279 (mm-40) REVERT: G 94 ASN cc_start: 0.9343 (t0) cc_final: 0.9113 (t0) REVERT: H 54 LYS cc_start: 0.9035 (mppt) cc_final: 0.8701 (mmtm) REVERT: H 79 HIS cc_start: 0.8594 (t70) cc_final: 0.8329 (t-170) REVERT: N 256 LYS cc_start: 0.7278 (mmpt) cc_final: 0.6898 (mmmt) REVERT: N 294 ARG cc_start: 0.6743 (tpt90) cc_final: 0.6376 (mtp180) REVERT: K 3777 MET cc_start: 0.6357 (ptm) cc_final: 0.5706 (ttp) REVERT: K 3825 LYS cc_start: 0.7837 (ptpp) cc_final: 0.7281 (ttmm) REVERT: K 3891 GLU cc_start: 0.7035 (mp0) cc_final: 0.6739 (mp0) REVERT: T 336 MET cc_start: 0.0705 (ttt) cc_final: 0.0151 (ttm) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.3530 time to fit residues: 109.7118 Evaluate side-chains 161 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.837 ------------------------------------------------------------------------------- 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: 6.9990 chunk 172 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 191 optimal weight: 0.1980 chunk 159 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS H 81 ASN ** T 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3859 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= 0.157 Angle : 0.566 8.999 29468 Z= 0.323 Chirality : 0.039 0.204 3307 Planarity : 0.004 0.082 2726 Dihedral : 27.179 171.644 5095 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: -1.75 (0.20), residues: 1728 helix: 1.55 (0.23), residues: 551 sheet: -2.35 (0.30), residues: 272 loop : -2.66 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 198 HIS 0.009 0.001 HIS K3822 PHE 0.018 0.001 PHE K3820 TYR 0.011 0.001 TYR T 460 ARG 0.005 0.000 ARG R 154 *********************** 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 232 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8098 (mtt) cc_final: 0.7586 (mtp) REVERT: B 73 THR cc_start: 0.8823 (m) cc_final: 0.8478 (p) REVERT: B 88 TYR cc_start: 0.7971 (m-80) cc_final: 0.7648 (m-80) REVERT: C 76 THR cc_start: 0.9052 (m) cc_final: 0.8691 (p) REVERT: D 88 SER cc_start: 0.8856 (p) cc_final: 0.8400 (t) REVERT: E 56 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8622 (ttmm) REVERT: F 84 MET cc_start: 0.6361 (mmm) cc_final: 0.6073 (mmm) REVERT: G 94 ASN cc_start: 0.9286 (t0) cc_final: 0.8982 (t0) REVERT: N 256 LYS cc_start: 0.7338 (mmpt) cc_final: 0.7040 (mmmt) REVERT: N 294 ARG cc_start: 0.6801 (tpt90) cc_final: 0.6271 (mtp180) REVERT: K 3845 CYS cc_start: 0.7192 (p) cc_final: 0.6803 (m) REVERT: K 3891 GLU cc_start: 0.7002 (mp0) cc_final: 0.6740 (mp0) REVERT: T 336 MET cc_start: 0.1067 (ttt) cc_final: 0.0111 (mtp) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3142 time to fit residues: 110.9774 Evaluate side-chains 183 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.625 ------------------------------------------------------------------------------- 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: 8.9990 chunk 21 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 108 optimal weight: 0.0010 chunk 161 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 chunk 190 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 79 HIS F 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20886 Z= 0.260 Angle : 0.617 9.312 29468 Z= 0.346 Chirality : 0.040 0.171 3307 Planarity : 0.004 0.084 2726 Dihedral : 27.231 170.081 5095 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % 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: -1.82 (0.20), residues: 1728 helix: 1.42 (0.22), residues: 548 sheet: -2.37 (0.30), residues: 272 loop : -2.63 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 198 HIS 0.011 0.001 HIS K3822 PHE 0.020 0.001 PHE K3820 TYR 0.013 0.002 TYR E 54 ARG 0.006 0.000 ARG F 35 *********************** 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 208 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8243 (mt) cc_final: 0.7711 (mp) REVERT: A 74 ILE cc_start: 0.8910 (tt) cc_final: 0.8699 (tt) REVERT: A 93 GLN cc_start: 0.8255 (tt0) cc_final: 0.8022 (tt0) REVERT: A 120 MET cc_start: 0.8177 (mtt) cc_final: 0.7721 (mtp) REVERT: B 73 THR cc_start: 0.8785 (m) cc_final: 0.8480 (p) REVERT: B 88 TYR cc_start: 0.8100 (m-80) cc_final: 0.7820 (m-80) REVERT: C 76 THR cc_start: 0.9023 (m) cc_final: 0.8674 (p) REVERT: D 88 SER cc_start: 0.8891 (p) cc_final: 0.8547 (t) REVERT: E 56 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8797 (ttmm) REVERT: F 84 MET cc_start: 0.6492 (mmm) cc_final: 0.5987 (tpp) REVERT: G 94 ASN cc_start: 0.9302 (t0) cc_final: 0.9041 (t0) REVERT: N 256 LYS cc_start: 0.7444 (mmpt) cc_final: 0.7147 (mmmt) REVERT: N 294 ARG cc_start: 0.6804 (tpt90) cc_final: 0.6314 (mtp180) REVERT: K 3777 MET cc_start: 0.6145 (ptm) cc_final: 0.5542 (ttp) REVERT: K 3825 LYS cc_start: 0.8232 (pttm) cc_final: 0.7899 (pttm) REVERT: K 3845 CYS cc_start: 0.6968 (p) cc_final: 0.6671 (m) REVERT: K 3891 GLU cc_start: 0.6984 (mp0) cc_final: 0.6742 (mp0) REVERT: K 3931 MET cc_start: 0.7088 (mtt) cc_final: 0.6835 (ttm) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.3113 time to fit residues: 99.7016 Evaluate side-chains 173 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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: 8.9990 chunk 76 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 121 optimal weight: 0.4980 chunk 130 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 79 HIS H 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20886 Z= 0.321 Angle : 0.668 9.229 29468 Z= 0.373 Chirality : 0.042 0.169 3307 Planarity : 0.005 0.087 2726 Dihedral : 27.290 169.570 5095 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: -2.03 (0.19), residues: 1728 helix: 1.04 (0.22), residues: 545 sheet: -2.34 (0.33), residues: 235 loop : -2.67 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 198 HIS 0.009 0.001 HIS K3822 PHE 0.017 0.001 PHE K3885 TYR 0.014 0.002 TYR H 39 ARG 0.007 0.000 ARG F 35 *********************** 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 211 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8411 (mt) cc_final: 0.7859 (mp) REVERT: A 74 ILE cc_start: 0.8951 (tt) cc_final: 0.8750 (tt) REVERT: A 120 MET cc_start: 0.8209 (mtt) cc_final: 0.7782 (mtp) REVERT: B 73 THR cc_start: 0.8845 (m) cc_final: 0.8594 (p) REVERT: B 88 TYR cc_start: 0.8142 (m-80) cc_final: 0.7926 (m-80) REVERT: C 56 GLU cc_start: 0.8443 (tp30) cc_final: 0.8115 (tp30) REVERT: C 76 THR cc_start: 0.9002 (m) cc_final: 0.8657 (p) REVERT: D 88 SER cc_start: 0.9011 (p) cc_final: 0.8684 (t) REVERT: E 56 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8706 (ttmm) REVERT: F 84 MET cc_start: 0.6712 (mmm) cc_final: 0.6025 (tpp) REVERT: G 94 ASN cc_start: 0.9288 (t0) cc_final: 0.9046 (t0) REVERT: K 3891 GLU cc_start: 0.7004 (mp0) cc_final: 0.6656 (mp0) REVERT: T 336 MET cc_start: 0.0529 (ttt) cc_final: -0.0282 (mtp) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.3131 time to fit residues: 102.2367 Evaluate side-chains 159 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.793 ------------------------------------------------------------------------------- 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: 9.9990 chunk 182 optimal weight: 40.0000 chunk 166 optimal weight: 20.0000 chunk 177 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 160 optimal weight: 30.0000 chunk 168 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS G 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 20886 Z= 0.358 Angle : 0.703 10.349 29468 Z= 0.390 Chirality : 0.043 0.203 3307 Planarity : 0.005 0.095 2726 Dihedral : 27.380 169.107 5095 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -2.19 (0.19), residues: 1728 helix: 0.84 (0.22), residues: 545 sheet: -2.28 (0.34), residues: 215 loop : -2.78 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 198 HIS 0.011 0.001 HIS K3822 PHE 0.032 0.002 PHE E 104 TYR 0.017 0.002 TYR H 39 ARG 0.009 0.001 ARG D 30 *********************** 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 202 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8203 (mtt) cc_final: 0.7772 (mtp) REVERT: B 73 THR cc_start: 0.8929 (m) cc_final: 0.8669 (p) REVERT: B 88 TYR cc_start: 0.8146 (m-80) cc_final: 0.7909 (m-80) REVERT: C 56 GLU cc_start: 0.8463 (tp30) cc_final: 0.8136 (tp30) REVERT: C 76 THR cc_start: 0.9031 (m) cc_final: 0.8704 (p) REVERT: E 56 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8715 (ttmm) REVERT: E 120 MET cc_start: 0.8680 (mtp) cc_final: 0.8333 (mtp) REVERT: F 84 MET cc_start: 0.6683 (mmm) cc_final: 0.5857 (tpp) REVERT: G 94 ASN cc_start: 0.9293 (t0) cc_final: 0.9038 (t0) REVERT: H 80 TYR cc_start: 0.7537 (m-10) cc_final: 0.7228 (m-10) REVERT: K 3825 LYS cc_start: 0.8147 (pttm) cc_final: 0.7744 (ptmt) REVERT: K 3891 GLU cc_start: 0.7052 (mp0) cc_final: 0.6705 (mp0) REVERT: K 3923 GLN cc_start: 0.8216 (pm20) cc_final: 0.7876 (pm20) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2988 time to fit residues: 94.5454 Evaluate side-chains 163 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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: 0.0030 chunk 114 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 181 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 121 optimal weight: 0.0970 chunk 96 optimal weight: 10.0000 chunk 124 optimal weight: 0.5980 overall best weight: 1.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4599 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= 0.196 Angle : 0.586 10.536 29468 Z= 0.330 Chirality : 0.039 0.263 3307 Planarity : 0.004 0.094 2726 Dihedral : 27.040 173.577 5095 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -1.61 (0.20), residues: 1728 helix: 1.61 (0.23), residues: 547 sheet: -2.13 (0.34), residues: 229 loop : -2.57 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 198 HIS 0.013 0.001 HIS K3822 PHE 0.023 0.001 PHE K3820 TYR 0.026 0.001 TYR B 51 ARG 0.006 0.000 ARG F 35 ********************** 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 222 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8224 (mtt) cc_final: 0.7689 (mtp) REVERT: B 73 THR cc_start: 0.8801 (m) cc_final: 0.8506 (p) REVERT: B 88 TYR cc_start: 0.8012 (m-80) cc_final: 0.7619 (m-80) REVERT: C 76 THR cc_start: 0.8946 (m) cc_final: 0.8646 (p) REVERT: D 88 SER cc_start: 0.8856 (p) cc_final: 0.8471 (t) REVERT: E 56 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8748 (ttmm) REVERT: F 84 MET cc_start: 0.6422 (mmm) cc_final: 0.6074 (mmm) REVERT: F 93 GLN cc_start: 0.7378 (mm-40) cc_final: 0.6827 (mm-40) REVERT: G 56 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8514 (tm-30) REVERT: G 94 ASN cc_start: 0.9216 (t0) cc_final: 0.8955 (t0) REVERT: G 101 THR cc_start: 0.9080 (m) cc_final: 0.8627 (p) REVERT: N 279 TRP cc_start: 0.8634 (m100) cc_final: 0.8403 (m100) REVERT: K 3825 LYS cc_start: 0.8056 (pttm) cc_final: 0.7723 (ptmt) REVERT: K 3828 LYS cc_start: 0.8515 (mptt) cc_final: 0.8218 (mtpt) REVERT: K 3884 MET cc_start: 0.4342 (mmm) cc_final: 0.3817 (mtt) REVERT: K 3891 GLU cc_start: 0.7083 (mp0) cc_final: 0.6825 (mp0) REVERT: K 3923 GLN cc_start: 0.7983 (pm20) cc_final: 0.7608 (pm20) REVERT: T 336 MET cc_start: 0.0739 (ttt) cc_final: 0.0014 (mtp) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.3067 time to fit residues: 105.8005 Evaluate side-chains 172 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.767 ------------------------------------------------------------------------------- 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: 5.9990 chunk 48 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 138 optimal weight: 0.0870 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.126820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.099405 restraints weight = 58285.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098694 restraints weight = 87524.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.099179 restraints weight = 84306.843| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4753 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= 0.174 Angle : 0.570 10.182 29468 Z= 0.320 Chirality : 0.039 0.428 3307 Planarity : 0.004 0.097 2726 Dihedral : 26.857 173.910 5095 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: -1.36 (0.20), residues: 1728 helix: 1.90 (0.23), residues: 551 sheet: -2.10 (0.33), residues: 249 loop : -2.45 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 198 HIS 0.011 0.001 HIS K3822 PHE 0.023 0.001 PHE K3820 TYR 0.029 0.001 TYR B 51 ARG 0.009 0.000 ARG E 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3439.64 seconds wall clock time: 63 minutes 4.22 seconds (3784.22 seconds total)