Starting phenix.real_space_refine on Sun Mar 17 01:38:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yrg_34055/03_2024/7yrg_34055_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yrg_34055/03_2024/7yrg_34055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yrg_34055/03_2024/7yrg_34055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yrg_34055/03_2024/7yrg_34055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yrg_34055/03_2024/7yrg_34055_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yrg_34055/03_2024/7yrg_34055_updated.pdb" } resolution = 4.2 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 290 5.49 5 S 51 5.16 5 C 9376 2.51 5 N 3024 2.21 5 O 3634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "K PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 206": "OE1" <-> "OE2" Residue "K GLU 301": "OE1" <-> "OE2" Residue "K GLU 325": "OE1" <-> "OE2" Residue "K PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 206": "OE1" <-> "OE2" Residue "L GLU 301": "OE1" <-> "OE2" Residue "L GLU 325": "OE1" <-> "OE2" Residue "L PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16377 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "B" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 791 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ECX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "C" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 790 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 841 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 791 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ECX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 836 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "K" Number of atoms: 2056 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2051 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Conformer: "B" Number of residues, atoms: 259, 2051 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 bond proxies already assigned to first conformer: 2082 Chain: "L" Number of atoms: 1921 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 240, 1916 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Conformer: "B" Number of residues, atoms: 240, 1916 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 1942 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13798 SG CYS K 275 34.989 21.023 55.188 1.00 81.78 S ATOM 14142 SG CYS K 319 32.495 18.444 53.871 1.00 86.30 S ATOM 14157 SG CYS K 321 36.070 17.784 53.089 1.00 93.19 S ATOM 14182 SG CYS K 324 34.891 17.744 56.692 1.00 91.94 S ATOM 15719 SG CYS L 275 79.466 77.873 56.063 1.00 81.78 S ATOM 16063 SG CYS L 319 81.952 80.476 54.778 1.00 86.30 S ATOM 16078 SG CYS L 321 78.374 81.144 54.021 1.00 93.19 S ATOM 16103 SG CYS L 324 79.567 81.128 57.619 1.00 91.94 S Time building chain proxies: 10.82, per 1000 atoms: 0.66 Number of scatterers: 16377 At special positions: 0 Unit cell: (116, 101, 114, 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 2 29.99 S 51 16.00 P 290 15.00 O 3634 8.00 N 3024 7.00 C 9376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS K 279 " - pdb=" SG CYS K 305 " distance=2.03 Simple disulfide: pdb=" SG CYS L 279 " - pdb=" SG CYS L 305 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.54 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 324 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 319 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 321 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 275 " pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 324 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 319 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 321 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 275 " Number of angles added : 12 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 6 sheets defined 49.1% alpha, 4.0% beta 136 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 8.47 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.524A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.872A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 19 through 22 No H-bonds generated for 'chain 'C' and resid 19 through 22' Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 48 through 76 removed outlier: 3.593A pdb=" N VAL C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP C 75 " --> pdb=" O ASN C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.511A pdb=" N HIS D 109 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.113A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.871A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 19 through 22 No H-bonds generated for 'chain 'G' and resid 19 through 22' Processing helix chain 'G' and resid 29 through 36 Processing helix chain 'G' and resid 48 through 75 removed outlier: 3.626A pdb=" N VAL G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 92 Processing helix chain 'G' and resid 94 through 99 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 83 Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.514A pdb=" N HIS H 109 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR H 122 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 93 removed outlier: 4.146A pdb=" N ASP K 90 " --> pdb=" O SER K 86 " (cutoff:3.500A) Proline residue: K 91 - end of helix Processing helix chain 'K' and resid 135 through 147 removed outlier: 3.876A pdb=" N LYS K 146 " --> pdb=" O GLU K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 159 removed outlier: 3.531A pdb=" N SER K 159 " --> pdb=" O LYS K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 166 Processing helix chain 'K' and resid 172 through 185 removed outlier: 3.546A pdb=" N TYR K 185 " --> pdb=" O HIS K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 242 Processing helix chain 'K' and resid 267 through 270 Processing helix chain 'K' and resid 322 through 327 Processing helix chain 'K' and resid 355 through 362 Processing helix chain 'L' and resid 74 through 93 removed outlier: 4.145A pdb=" N ASP L 90 " --> pdb=" O SER L 86 " (cutoff:3.500A) Proline residue: L 91 - end of helix Processing helix chain 'L' and resid 135 through 147 Processing helix chain 'L' and resid 172 through 185 removed outlier: 3.546A pdb=" N TYR L 185 " --> pdb=" O HIS L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 242 Processing helix chain 'L' and resid 267 through 270 Processing helix chain 'L' and resid 322 through 327 Processing helix chain 'L' and resid 355 through 362 Processing sheet with id= A, first strand: chain 'K' and resid 195 through 199 Processing sheet with id= B, first strand: chain 'K' and resid 222 through 224 removed outlier: 3.552A pdb=" N ASP K 222 " --> pdb=" O ALA K 293 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL K 291 " --> pdb=" O ILE K 224 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS K 292 " --> pdb=" O LYS K 280 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS K 280 " --> pdb=" O LYS K 292 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 230 through 234 Processing sheet with id= D, first strand: chain 'L' and resid 195 through 199 Processing sheet with id= E, first strand: chain 'L' and resid 222 through 224 removed outlier: 3.552A pdb=" N ASP L 222 " --> pdb=" O ALA L 293 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL L 291 " --> pdb=" O ILE L 224 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS L 292 " --> pdb=" O LYS L 280 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS L 280 " --> pdb=" O LYS L 292 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 230 through 234 456 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 328 hydrogen bonds 656 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 7.07 Time building geometry restraints manager: 8.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1981 1.29 - 1.42: 5694 1.42 - 1.55: 8914 1.55 - 1.68: 594 1.68 - 1.81: 79 Bond restraints: 17262 Sorted by residual: bond pdb=" N ARG K 357 " pdb=" CA ARG K 357 " ideal model delta sigma weight residual 1.459 1.344 0.115 1.23e-02 6.61e+03 8.71e+01 bond pdb=" N ARG L 357 " pdb=" CA ARG L 357 " ideal model delta sigma weight residual 1.459 1.345 0.115 1.23e-02 6.61e+03 8.67e+01 bond pdb=" CA LYS L 362 " pdb=" C LYS L 362 " ideal model delta sigma weight residual 1.524 1.639 -0.115 1.27e-02 6.20e+03 8.19e+01 bond pdb=" CA LYS K 362 " pdb=" C LYS K 362 " ideal model delta sigma weight residual 1.524 1.638 -0.115 1.27e-02 6.20e+03 8.14e+01 bond pdb=" CA LEU L 358 " pdb=" C LEU L 358 " ideal model delta sigma weight residual 1.523 1.418 0.105 1.35e-02 5.49e+03 6.05e+01 ... (remaining 17257 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.22: 1097 104.22 - 111.65: 8860 111.65 - 119.08: 5524 119.08 - 126.51: 8075 126.51 - 133.94: 948 Bond angle restraints: 24504 Sorted by residual: angle pdb=" C LEU L 361 " pdb=" N LYS L 362 " pdb=" CA LYS L 362 " ideal model delta sigma weight residual 120.44 111.16 9.28 1.30e+00 5.92e-01 5.09e+01 angle pdb=" C LEU K 361 " pdb=" N LYS K 362 " pdb=" CA LYS K 362 " ideal model delta sigma weight residual 120.44 111.16 9.28 1.30e+00 5.92e-01 5.09e+01 angle pdb=" N LYS L 356 " pdb=" CA LYS L 356 " pdb=" C LYS L 356 " ideal model delta sigma weight residual 111.14 118.03 -6.89 1.08e+00 8.57e-01 4.07e+01 angle pdb=" N LYS K 356 " pdb=" CA LYS K 356 " pdb=" C LYS K 356 " ideal model delta sigma weight residual 111.14 118.01 -6.87 1.08e+00 8.57e-01 4.05e+01 angle pdb=" N GLY F 9 " pdb=" CA GLY F 9 " pdb=" C GLY F 9 " ideal model delta sigma weight residual 112.49 119.26 -6.77 1.21e+00 6.83e-01 3.13e+01 ... (remaining 24499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.24: 8031 31.24 - 62.49: 1669 62.49 - 93.73: 62 93.73 - 124.98: 1 124.98 - 156.22: 4 Dihedral angle restraints: 9767 sinusoidal: 5989 harmonic: 3778 Sorted by residual: dihedral pdb=" CB CYS K 279 " pdb=" SG CYS K 279 " pdb=" SG CYS K 305 " pdb=" CB CYS K 305 " ideal model delta sinusoidal sigma weight residual -86.00 -136.86 50.86 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" CB CYS L 279 " pdb=" SG CYS L 279 " pdb=" SG CYS L 305 " pdb=" CB CYS L 305 " ideal model delta sinusoidal sigma weight residual -86.00 -136.84 50.84 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" C ECX F 20 " pdb=" N ECX F 20 " pdb=" CA ECX F 20 " pdb=" CB ECX F 20 " ideal model delta harmonic sigma weight residual -122.60 -108.05 -14.55 0 2.50e+00 1.60e-01 3.39e+01 ... (remaining 9764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2641 0.103 - 0.207: 85 0.207 - 0.310: 4 0.310 - 0.414: 2 0.414 - 0.517: 4 Chirality restraints: 2736 Sorted by residual: chirality pdb=" CA VAL F 21 " pdb=" N VAL F 21 " pdb=" C VAL F 21 " pdb=" CB VAL F 21 " both_signs ideal model delta sigma weight residual False 2.44 1.92 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CA VAL B 21 " pdb=" N VAL B 21 " pdb=" C VAL B 21 " pdb=" CB VAL B 21 " both_signs ideal model delta sigma weight residual False 2.44 1.92 0.52 2.00e-01 2.50e+01 6.68e+00 chirality pdb=" CB VAL F 21 " pdb=" CA VAL F 21 " pdb=" CG1 VAL F 21 " pdb=" CG2 VAL F 21 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 2733 not shown) Planarity restraints: 2102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS K 362 " 0.025 2.00e-02 2.50e+03 5.33e-02 2.84e+01 pdb=" C LYS K 362 " -0.092 2.00e-02 2.50e+03 pdb=" O LYS K 362 " 0.036 2.00e-02 2.50e+03 pdb=" N LYS K 363 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 362 " 0.025 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C LYS L 362 " -0.092 2.00e-02 2.50e+03 pdb=" O LYS L 362 " 0.036 2.00e-02 2.50e+03 pdb=" N LYS L 363 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 21 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C VAL F 21 " -0.070 2.00e-02 2.50e+03 pdb=" O VAL F 21 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU F 22 " 0.022 2.00e-02 2.50e+03 ... (remaining 2099 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.81: 14 1.81 - 2.58: 241 2.58 - 3.35: 19948 3.35 - 4.13: 46091 4.13 - 4.90: 74408 Nonbonded interactions: 140702 Sorted by model distance: nonbonded pdb=" OE2 GLU E 73 " pdb=" CG ARG F 23 " model vdw 1.035 3.440 nonbonded pdb=" CG ASP E 77 " pdb=" NH2 ARG F 23 " model vdw 1.084 3.350 nonbonded pdb=" O LEU C 117 " pdb=" NZ LYS F 44 " model vdw 1.189 2.520 nonbonded pdb=" OD2 ASP E 77 " pdb=" NH2 ARG F 23 " model vdw 1.225 2.520 nonbonded pdb=" OD1 ASP E 77 " pdb=" O LEU F 10 " model vdw 1.254 3.040 ... (remaining 140697 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' and (resid 36 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 15 through 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 118)) selection = (chain 'G' and resid 15 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'K' and (resid 62 through 135 or resid 137 through 152 or resid 171 throu \ gh 200 or resid 202 through 363 or resid 401 through 402)) selection = (chain 'L' and (resid 62 through 151 or (resid 170 and (name N or name CA or nam \ e C or name O or name CB )) or resid 171 through 200 or resid 202 through 363 or \ resid 401 through 402)) } 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=0.50 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.760 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 57.730 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.148 17262 Z= 0.467 Angle : 0.817 11.650 24504 Z= 0.469 Chirality : 0.048 0.517 2736 Planarity : 0.006 0.073 2102 Dihedral : 25.617 156.219 7331 Min Nonbonded Distance : 1.035 Molprobity Statistics. All-atom Clashscore : 27.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.11 % Allowed : 1.20 % Favored : 97.69 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1277 helix: 0.28 (0.19), residues: 704 sheet: -1.44 (0.48), residues: 80 loop : -2.33 (0.24), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 264 HIS 0.011 0.001 HIS F 75 PHE 0.013 0.002 PHE K 154 TYR 0.012 0.001 TYR G 60 ARG 0.011 0.001 ARG L 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 451 time to evaluate : 1.267 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: symmetry clash REVERT: A 74 ILE cc_start: 0.8165 (mt) cc_final: 0.7963 (mt) REVERT: B 88 TYR cc_start: 0.6529 (m-80) cc_final: 0.6066 (m-10) REVERT: D 34 LYS cc_start: 0.7632 (ptpt) cc_final: 0.7211 (mmtt) REVERT: D 95 GLN cc_start: 0.7759 (tt0) cc_final: 0.7461 (tt0) REVERT: E 54 TYR cc_start: 0.6553 (m-80) cc_final: 0.6351 (m-10) REVERT: H 39 ILE cc_start: 0.8379 (pt) cc_final: 0.7851 (tt) REVERT: H 54 ILE cc_start: 0.8631 (tt) cc_final: 0.8395 (tt) REVERT: K 173 MET cc_start: 0.4822 (mmp) cc_final: 0.2934 (ttp) REVERT: K 195 PHE cc_start: 0.6801 (p90) cc_final: 0.6567 (p90) REVERT: K 354 THR cc_start: 0.2865 (p) cc_final: 0.2094 (p) REVERT: L 72 MET cc_start: 0.3021 (pmm) cc_final: 0.2724 (ptt) outliers start: 8 outliers final: 0 residues processed: 456 average time/residue: 0.3730 time to fit residues: 231.2204 Evaluate side-chains 237 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN L 149 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 17262 Z= 0.337 Angle : 0.780 13.294 24504 Z= 0.447 Chirality : 0.044 0.288 2736 Planarity : 0.006 0.062 2102 Dihedral : 28.692 153.865 4789 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.65 % Allowed : 4.63 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1277 helix: 0.18 (0.18), residues: 691 sheet: -1.07 (0.60), residues: 52 loop : -2.11 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 264 HIS 0.009 0.001 HIS F 75 PHE 0.030 0.002 PHE L 183 TYR 0.016 0.002 TYR B 51 ARG 0.017 0.001 ARG K 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 305 time to evaluate : 1.427 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 77 ASP cc_start: 0.7205 (t0) cc_final: 0.6994 (t0) REVERT: A 120 MET cc_start: 0.7860 (mtp) cc_final: 0.7491 (mtp) REVERT: A 126 LEU cc_start: 0.9032 (tp) cc_final: 0.8714 (tp) REVERT: A 133 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7518 (tp30) REVERT: B 88 TYR cc_start: 0.7525 (m-10) cc_final: 0.6973 (m-10) REVERT: B 96 THR cc_start: 0.8823 (m) cc_final: 0.8426 (p) REVERT: C 27 PHE cc_start: 0.8208 (m-80) cc_final: 0.7947 (m-80) REVERT: D 34 LYS cc_start: 0.7775 (ptpt) cc_final: 0.7235 (mmtt) REVERT: D 41 VAL cc_start: 0.9221 (t) cc_final: 0.8653 (p) REVERT: D 71 GLU cc_start: 0.7853 (tt0) cc_final: 0.7607 (tt0) REVERT: D 120 LYS cc_start: 0.7089 (mttt) cc_final: 0.6435 (tptp) REVERT: E 73 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: F 29 ILE cc_start: 0.9703 (mm) cc_final: 0.9488 (mm) REVERT: F 74 GLU cc_start: 0.8554 (tt0) cc_final: 0.8257 (tt0) REVERT: F 88 TYR cc_start: 0.8624 (m-10) cc_final: 0.8104 (m-10) REVERT: G 22 ARG cc_start: 0.8120 (ttt180) cc_final: 0.7916 (mtp180) REVERT: G 59 GLU cc_start: 0.8185 (tt0) cc_final: 0.7605 (tt0) REVERT: K 188 MET cc_start: 0.4055 (pmm) cc_final: 0.3792 (pmm) REVERT: K 358 LEU cc_start: 0.7330 (mt) cc_final: 0.6416 (tt) REVERT: L 72 MET cc_start: 0.3639 (pmm) cc_final: 0.3199 (ptp) REVERT: L 89 LEU cc_start: 0.7654 (mp) cc_final: 0.7409 (mp) REVERT: L 100 MET cc_start: 0.6343 (mmm) cc_final: 0.5312 (tpp) outliers start: 3 outliers final: 2 residues processed: 306 average time/residue: 0.2671 time to fit residues: 121.5206 Evaluate side-chains 223 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 220 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 48 optimal weight: 0.2980 chunk 113 optimal weight: 0.7980 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 ASN K 96 GLN K 181 HIS ** K 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17262 Z= 0.267 Angle : 0.681 11.993 24504 Z= 0.394 Chirality : 0.040 0.202 2736 Planarity : 0.005 0.064 2102 Dihedral : 28.820 169.595 4789 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.46 % Allowed : 3.05 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.22), residues: 1277 helix: 0.33 (0.19), residues: 694 sheet: -2.02 (0.64), residues: 38 loop : -1.97 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 264 HIS 0.005 0.001 HIS B 75 PHE 0.013 0.002 PHE D 70 TYR 0.036 0.002 TYR H 40 ARG 0.016 0.001 ARG F 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 1.332 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8039 (mm) cc_final: 0.7423 (mm) REVERT: A 86 SER cc_start: 0.8964 (m) cc_final: 0.8476 (t) REVERT: B 82 THR cc_start: 0.9014 (m) cc_final: 0.8637 (m) REVERT: B 88 TYR cc_start: 0.7756 (m-10) cc_final: 0.7035 (m-10) REVERT: C 52 VAL cc_start: 0.9310 (m) cc_final: 0.8942 (p) REVERT: C 87 GLN cc_start: 0.8633 (tp40) cc_final: 0.8302 (tp40) REVERT: D 34 LYS cc_start: 0.7935 (ptpt) cc_final: 0.7503 (mmtt) REVERT: D 40 TYR cc_start: 0.8029 (m-80) cc_final: 0.7700 (m-80) REVERT: D 71 GLU cc_start: 0.7696 (tt0) cc_final: 0.7447 (tt0) REVERT: D 120 LYS cc_start: 0.7546 (mttt) cc_final: 0.6519 (tptp) REVERT: E 50 GLU cc_start: 0.8333 (tt0) cc_final: 0.7994 (tt0) REVERT: E 94 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7953 (tp30) REVERT: F 59 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8591 (ttpp) REVERT: F 74 GLU cc_start: 0.8537 (tt0) cc_final: 0.8233 (tt0) REVERT: F 88 TYR cc_start: 0.8348 (m-10) cc_final: 0.7951 (m-10) REVERT: G 53 TYR cc_start: 0.9273 (t80) cc_final: 0.8935 (t80) REVERT: K 188 MET cc_start: 0.4377 (pmm) cc_final: 0.4168 (pmm) REVERT: K 195 PHE cc_start: 0.6999 (p90) cc_final: 0.6603 (p90) REVERT: K 354 THR cc_start: 0.5253 (p) cc_final: 0.4794 (p) REVERT: K 358 LEU cc_start: 0.7428 (mt) cc_final: 0.6583 (pp) REVERT: L 72 MET cc_start: 0.3281 (pmm) cc_final: 0.2908 (ptp) REVERT: L 100 MET cc_start: 0.6590 (mmm) cc_final: 0.5480 (tpp) outliers start: 1 outliers final: 1 residues processed: 304 average time/residue: 0.2720 time to fit residues: 122.1890 Evaluate side-chains 225 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 134 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN K 273 HIS L 98 HIS ** L 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.6364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17262 Z= 0.197 Angle : 0.630 9.864 24504 Z= 0.367 Chirality : 0.038 0.190 2736 Planarity : 0.004 0.043 2102 Dihedral : 28.648 171.533 4789 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.46 % Allowed : 2.13 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.22), residues: 1277 helix: 0.63 (0.20), residues: 689 sheet: -1.74 (0.65), residues: 38 loop : -1.94 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K 218 HIS 0.016 0.001 HIS L 181 PHE 0.028 0.002 PHE E 104 TYR 0.027 0.002 TYR H 40 ARG 0.014 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 307 time to evaluate : 1.532 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.9085 (m) cc_final: 0.8592 (t) REVERT: A 120 MET cc_start: 0.8216 (mtp) cc_final: 0.7640 (mtp) REVERT: B 29 ILE cc_start: 0.9128 (mm) cc_final: 0.8837 (mm) REVERT: B 88 TYR cc_start: 0.7756 (m-10) cc_final: 0.7010 (m-10) REVERT: C 87 GLN cc_start: 0.8723 (tp40) cc_final: 0.8330 (tp40) REVERT: D 34 LYS cc_start: 0.7963 (ptpt) cc_final: 0.7559 (mmtt) REVERT: D 120 LYS cc_start: 0.7586 (mttt) cc_final: 0.6392 (tptm) REVERT: E 77 ASP cc_start: 0.8218 (p0) cc_final: 0.8017 (p0) REVERT: E 94 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7949 (tp30) REVERT: F 74 GLU cc_start: 0.8528 (tt0) cc_final: 0.8181 (tt0) REVERT: F 88 TYR cc_start: 0.8220 (m-10) cc_final: 0.7965 (m-10) REVERT: G 53 TYR cc_start: 0.9351 (t80) cc_final: 0.8958 (t80) REVERT: G 87 GLN cc_start: 0.8972 (tp40) cc_final: 0.8746 (mm110) REVERT: H 90 THR cc_start: 0.8830 (m) cc_final: 0.8528 (p) REVERT: H 93 GLU cc_start: 0.9059 (mp0) cc_final: 0.8256 (mp0) REVERT: K 77 LEU cc_start: 0.7434 (mt) cc_final: 0.7186 (tp) REVERT: K 188 MET cc_start: 0.4334 (pmm) cc_final: 0.4053 (pmm) REVERT: K 309 ASP cc_start: 0.5038 (m-30) cc_final: 0.4833 (m-30) REVERT: K 354 THR cc_start: 0.5131 (p) cc_final: 0.4661 (p) REVERT: K 358 LEU cc_start: 0.7108 (mt) cc_final: 0.6344 (tt) REVERT: L 72 MET cc_start: 0.3273 (pmm) cc_final: 0.2982 (ptp) REVERT: L 100 MET cc_start: 0.6646 (mmm) cc_final: 0.5559 (tpp) REVERT: L 242 LEU cc_start: 0.7034 (mt) cc_final: 0.6818 (mt) REVERT: L 264 TRP cc_start: 0.7929 (t60) cc_final: 0.7170 (t60) REVERT: L 356 LYS cc_start: 0.5841 (pttp) cc_final: 0.5619 (tptp) outliers start: 1 outliers final: 0 residues processed: 308 average time/residue: 0.2618 time to fit residues: 123.5145 Evaluate side-chains 232 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 76 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.7813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17262 Z= 0.311 Angle : 0.741 14.889 24504 Z= 0.419 Chirality : 0.042 0.233 2736 Planarity : 0.006 0.074 2102 Dihedral : 28.925 174.914 4789 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.37 % Allowed : 3.70 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.22), residues: 1277 helix: 0.22 (0.19), residues: 696 sheet: -1.40 (0.60), residues: 60 loop : -1.98 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP K 218 HIS 0.007 0.002 HIS L 181 PHE 0.019 0.002 PHE E 104 TYR 0.031 0.002 TYR H 40 ARG 0.024 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 1.369 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 77 ASP cc_start: 0.7705 (t0) cc_final: 0.7207 (t0) REVERT: A 86 SER cc_start: 0.9104 (m) cc_final: 0.8684 (t) REVERT: A 94 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8073 (mm-30) REVERT: A 120 MET cc_start: 0.8410 (mtp) cc_final: 0.7888 (mtp) REVERT: A 126 LEU cc_start: 0.9546 (tp) cc_final: 0.8723 (tp) REVERT: B 8 LYS cc_start: 0.3955 (mppt) cc_final: 0.2932 (mmtm) REVERT: B 82 THR cc_start: 0.8815 (m) cc_final: 0.8535 (m) REVERT: B 88 TYR cc_start: 0.8209 (m-10) cc_final: 0.7585 (m-10) REVERT: C 71 ASN cc_start: 0.8276 (m-40) cc_final: 0.7996 (t0) REVERT: C 88 LEU cc_start: 0.9147 (mt) cc_final: 0.8776 (tp) REVERT: D 34 LYS cc_start: 0.7781 (ptpt) cc_final: 0.7475 (mmtt) REVERT: E 39 HIS cc_start: 0.5219 (t-90) cc_final: 0.3961 (m-70) REVERT: E 77 ASP cc_start: 0.8584 (p0) cc_final: 0.8242 (p0) REVERT: E 113 HIS cc_start: 0.9080 (t70) cc_final: 0.8723 (t-90) REVERT: F 74 GLU cc_start: 0.8470 (tt0) cc_final: 0.8210 (tt0) REVERT: F 88 TYR cc_start: 0.8317 (m-10) cc_final: 0.7879 (m-10) REVERT: H 90 THR cc_start: 0.8983 (m) cc_final: 0.8780 (p) REVERT: H 93 GLU cc_start: 0.9364 (mp0) cc_final: 0.8873 (mp0) REVERT: K 145 LYS cc_start: 0.4057 (ttmm) cc_final: 0.3852 (ptmt) REVERT: K 188 MET cc_start: 0.4572 (pmm) cc_final: 0.4197 (pmm) REVERT: K 358 LEU cc_start: 0.7454 (mt) cc_final: 0.6601 (tt) REVERT: L 72 MET cc_start: 0.3796 (pmm) cc_final: 0.3297 (ptp) REVERT: L 100 MET cc_start: 0.6714 (mmm) cc_final: 0.5659 (tpp) REVERT: L 195 PHE cc_start: 0.8154 (p90) cc_final: 0.7916 (p90) REVERT: L 242 LEU cc_start: 0.7327 (mt) cc_final: 0.7028 (mt) REVERT: L 257 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.7369 (ttp-170) REVERT: L 356 LYS cc_start: 0.6186 (pttp) cc_final: 0.5881 (tptp) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2683 time to fit residues: 119.8113 Evaluate side-chains 225 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 7.9990 chunk 135 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS G 112 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 ASN K 181 HIS ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.8203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17262 Z= 0.246 Angle : 0.666 12.713 24504 Z= 0.380 Chirality : 0.039 0.191 2736 Planarity : 0.004 0.040 2102 Dihedral : 28.856 174.127 4789 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.37 % Allowed : 1.57 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.22), residues: 1277 helix: 0.35 (0.19), residues: 699 sheet: -1.59 (0.60), residues: 58 loop : -1.98 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 264 HIS 0.007 0.001 HIS F 75 PHE 0.035 0.002 PHE L 281 TYR 0.022 0.002 TYR H 40 ARG 0.005 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7756 (t0) cc_final: 0.7479 (t0) REVERT: A 86 SER cc_start: 0.9078 (m) cc_final: 0.8647 (t) REVERT: A 94 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7823 (mm-30) REVERT: A 101 VAL cc_start: 0.9488 (t) cc_final: 0.9240 (p) REVERT: A 120 MET cc_start: 0.8269 (mtp) cc_final: 0.7838 (mtp) REVERT: B 18 HIS cc_start: 0.4798 (t70) cc_final: 0.4443 (t70) REVERT: B 25 ASN cc_start: 0.8398 (p0) cc_final: 0.8157 (p0) REVERT: B 82 THR cc_start: 0.8912 (m) cc_final: 0.8625 (m) REVERT: B 88 TYR cc_start: 0.7938 (m-10) cc_final: 0.7664 (m-10) REVERT: C 71 ASN cc_start: 0.8328 (m-40) cc_final: 0.8054 (t0) REVERT: C 88 LEU cc_start: 0.9065 (mt) cc_final: 0.8800 (tp) REVERT: D 34 LYS cc_start: 0.7817 (ptpt) cc_final: 0.7561 (mmtt) REVERT: E 39 HIS cc_start: 0.5127 (t-90) cc_final: 0.4015 (m-70) REVERT: E 77 ASP cc_start: 0.8455 (p0) cc_final: 0.8172 (p0) REVERT: F 82 THR cc_start: 0.9106 (m) cc_final: 0.8693 (m) REVERT: F 88 TYR cc_start: 0.8223 (m-10) cc_final: 0.7809 (m-10) REVERT: H 85 LYS cc_start: 0.8238 (mttp) cc_final: 0.7986 (mmtt) REVERT: H 90 THR cc_start: 0.8985 (m) cc_final: 0.8366 (p) REVERT: H 93 GLU cc_start: 0.9207 (mp0) cc_final: 0.8269 (mp0) REVERT: K 77 LEU cc_start: 0.7681 (mp) cc_final: 0.7340 (tt) REVERT: K 188 MET cc_start: 0.5127 (pmm) cc_final: 0.4902 (pmm) REVERT: K 195 PHE cc_start: 0.6932 (p90) cc_final: 0.6391 (p90) REVERT: K 358 LEU cc_start: 0.7388 (mt) cc_final: 0.6625 (tt) REVERT: L 72 MET cc_start: 0.3665 (pmm) cc_final: 0.3383 (ptp) REVERT: L 100 MET cc_start: 0.6833 (mmm) cc_final: 0.5921 (tpp) REVERT: L 181 HIS cc_start: 0.6086 (t70) cc_final: 0.5441 (t-90) REVERT: L 185 TYR cc_start: 0.5934 (m-10) cc_final: 0.5053 (m-10) REVERT: L 195 PHE cc_start: 0.8003 (p90) cc_final: 0.7751 (p90) REVERT: L 242 LEU cc_start: 0.7196 (mt) cc_final: 0.6990 (mt) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2775 time to fit residues: 124.2603 Evaluate side-chains 231 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 ASN ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.8925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17262 Z= 0.325 Angle : 0.719 13.887 24504 Z= 0.407 Chirality : 0.041 0.199 2736 Planarity : 0.005 0.064 2102 Dihedral : 29.016 175.854 4789 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.37 % Allowed : 2.04 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.22), residues: 1277 helix: 0.12 (0.19), residues: 703 sheet: -1.83 (0.61), residues: 58 loop : -1.99 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.005 TRP K 218 HIS 0.008 0.002 HIS B 75 PHE 0.030 0.002 PHE K 281 TYR 0.019 0.002 TYR D 40 ARG 0.004 0.001 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.405 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 86 SER cc_start: 0.9173 (m) cc_final: 0.8712 (t) REVERT: A 120 MET cc_start: 0.8445 (mtp) cc_final: 0.8107 (mtp) REVERT: B 88 TYR cc_start: 0.7920 (m-10) cc_final: 0.7564 (m-10) REVERT: C 88 LEU cc_start: 0.9239 (mt) cc_final: 0.8870 (tp) REVERT: D 34 LYS cc_start: 0.7869 (ptpt) cc_final: 0.7643 (mmtt) REVERT: D 51 ASP cc_start: 0.7683 (p0) cc_final: 0.7324 (p0) REVERT: E 39 HIS cc_start: 0.5356 (t-90) cc_final: 0.4250 (m-70) REVERT: E 73 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7665 (tm-30) REVERT: F 82 THR cc_start: 0.9084 (m) cc_final: 0.8616 (m) REVERT: F 88 TYR cc_start: 0.8213 (m-10) cc_final: 0.7772 (m-10) REVERT: H 85 LYS cc_start: 0.8244 (mttp) cc_final: 0.7937 (mmtt) REVERT: H 93 GLU cc_start: 0.9290 (mp0) cc_final: 0.8599 (mp0) REVERT: K 188 MET cc_start: 0.5078 (pmm) cc_final: 0.4590 (pmm) REVERT: K 358 LEU cc_start: 0.7379 (mt) cc_final: 0.6714 (tt) REVERT: L 72 MET cc_start: 0.3889 (pmm) cc_final: 0.3520 (ptp) REVERT: L 100 MET cc_start: 0.6797 (mmm) cc_final: 0.6021 (tpp) REVERT: L 183 PHE cc_start: 0.6818 (t80) cc_final: 0.6604 (t80) REVERT: L 195 PHE cc_start: 0.8180 (p90) cc_final: 0.7839 (p90) REVERT: L 242 LEU cc_start: 0.7280 (mt) cc_final: 0.7070 (mt) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2656 time to fit residues: 110.8459 Evaluate side-chains 212 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 ASN ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.9294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17262 Z= 0.270 Angle : 0.679 12.602 24504 Z= 0.388 Chirality : 0.040 0.187 2736 Planarity : 0.004 0.050 2102 Dihedral : 29.003 175.471 4789 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.37 % Allowed : 0.83 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.22), residues: 1277 helix: 0.26 (0.19), residues: 697 sheet: -2.03 (0.57), residues: 58 loop : -1.97 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 264 HIS 0.007 0.001 HIS B 75 PHE 0.018 0.002 PHE L 281 TYR 0.020 0.002 TYR L 185 ARG 0.006 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.411 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 50 GLU cc_start: 0.8155 (pt0) cc_final: 0.7889 (pt0) REVERT: A 86 SER cc_start: 0.9190 (m) cc_final: 0.8681 (t) REVERT: A 120 MET cc_start: 0.8375 (mtp) cc_final: 0.8101 (mtp) REVERT: A 128 ARG cc_start: 0.9045 (ttm-80) cc_final: 0.8834 (ttp80) REVERT: B 82 THR cc_start: 0.8843 (m) cc_final: 0.8642 (m) REVERT: B 88 TYR cc_start: 0.7827 (m-10) cc_final: 0.7501 (m-10) REVERT: C 88 LEU cc_start: 0.9220 (mt) cc_final: 0.8862 (tp) REVERT: D 51 ASP cc_start: 0.7660 (p0) cc_final: 0.7289 (p0) REVERT: E 39 HIS cc_start: 0.5233 (t-90) cc_final: 0.4378 (m-70) REVERT: E 50 GLU cc_start: 0.8562 (tt0) cc_final: 0.7853 (tt0) REVERT: E 73 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7610 (tm-30) REVERT: E 112 ILE cc_start: 0.9118 (tp) cc_final: 0.8917 (tp) REVERT: F 82 THR cc_start: 0.9093 (m) cc_final: 0.8767 (m) REVERT: F 88 TYR cc_start: 0.8189 (m-10) cc_final: 0.7755 (m-10) REVERT: H 85 LYS cc_start: 0.8179 (mttp) cc_final: 0.7951 (mmtt) REVERT: H 90 THR cc_start: 0.8979 (m) cc_final: 0.8014 (m) REVERT: H 93 GLU cc_start: 0.9333 (mp0) cc_final: 0.8521 (mp0) REVERT: K 188 MET cc_start: 0.5141 (pmm) cc_final: 0.4783 (pmm) REVERT: K 354 THR cc_start: 0.5698 (p) cc_final: 0.5411 (p) REVERT: K 358 LEU cc_start: 0.7287 (mt) cc_final: 0.6697 (tt) REVERT: L 72 MET cc_start: 0.4124 (pmm) cc_final: 0.3383 (ptp) REVERT: L 100 MET cc_start: 0.6711 (mmm) cc_final: 0.5961 (tpp) REVERT: L 145 LYS cc_start: 0.6604 (mttt) cc_final: 0.5867 (pttt) REVERT: L 195 PHE cc_start: 0.8106 (p90) cc_final: 0.7846 (p90) REVERT: L 242 LEU cc_start: 0.7113 (mt) cc_final: 0.6882 (mt) REVERT: L 352 ARG cc_start: 0.8718 (ttp-170) cc_final: 0.8212 (ppt170) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2646 time to fit residues: 111.4614 Evaluate side-chains 222 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 10.0000 chunk 140 optimal weight: 0.0980 chunk 144 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 0.0980 chunk 42 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS K 80 ASN K 181 HIS ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.9413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17262 Z= 0.183 Angle : 0.634 10.227 24504 Z= 0.361 Chirality : 0.038 0.179 2736 Planarity : 0.004 0.046 2102 Dihedral : 28.766 175.062 4789 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.37 % Allowed : 0.46 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1277 helix: 0.61 (0.20), residues: 705 sheet: -2.02 (0.55), residues: 62 loop : -2.02 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP K 218 HIS 0.004 0.001 HIS F 75 PHE 0.027 0.002 PHE A 67 TYR 0.017 0.001 TYR F 72 ARG 0.006 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8025 (pt0) cc_final: 0.7720 (pt0) REVERT: A 68 GLN cc_start: 0.8195 (mt0) cc_final: 0.7915 (mm-40) REVERT: A 86 SER cc_start: 0.8986 (m) cc_final: 0.8628 (t) REVERT: A 120 MET cc_start: 0.8360 (mtp) cc_final: 0.8027 (mtp) REVERT: B 82 THR cc_start: 0.8891 (m) cc_final: 0.8589 (m) REVERT: B 88 TYR cc_start: 0.7708 (m-10) cc_final: 0.7384 (m-10) REVERT: C 88 LEU cc_start: 0.9056 (mt) cc_final: 0.8851 (tp) REVERT: D 51 ASP cc_start: 0.7677 (p0) cc_final: 0.7377 (p0) REVERT: D 73 ILE cc_start: 0.9183 (tt) cc_final: 0.8983 (mt) REVERT: E 39 HIS cc_start: 0.5004 (t-90) cc_final: 0.4197 (m-70) REVERT: E 50 GLU cc_start: 0.8526 (tt0) cc_final: 0.7917 (tt0) REVERT: E 73 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7620 (tm-30) REVERT: E 87 SER cc_start: 0.8972 (p) cc_final: 0.8625 (t) REVERT: E 112 ILE cc_start: 0.8954 (tp) cc_final: 0.8751 (tp) REVERT: E 133 GLU cc_start: 0.7701 (mp0) cc_final: 0.6839 (tp30) REVERT: F 74 GLU cc_start: 0.8461 (tt0) cc_final: 0.8231 (tt0) REVERT: F 88 TYR cc_start: 0.7949 (m-10) cc_final: 0.7672 (m-80) REVERT: G 49 THR cc_start: 0.9377 (p) cc_final: 0.9108 (t) REVERT: G 121 LYS cc_start: 0.7054 (mptt) cc_final: 0.5702 (tptt) REVERT: H 68 ASP cc_start: 0.9027 (t70) cc_final: 0.8777 (t0) REVERT: H 85 LYS cc_start: 0.8064 (mttp) cc_final: 0.7835 (mmtt) REVERT: K 88 VAL cc_start: 0.7051 (p) cc_final: 0.6830 (t) REVERT: K 100 MET cc_start: 0.4794 (ptt) cc_final: 0.4343 (mtm) REVERT: K 195 PHE cc_start: 0.6777 (p90) cc_final: 0.6453 (p90) REVERT: K 254 TYR cc_start: 0.6072 (t80) cc_final: 0.5781 (t80) REVERT: K 358 LEU cc_start: 0.7255 (mt) cc_final: 0.6705 (tt) REVERT: L 72 MET cc_start: 0.4011 (pmm) cc_final: 0.3286 (ptp) REVERT: L 100 MET cc_start: 0.6699 (mmm) cc_final: 0.5675 (tpp) REVERT: L 145 LYS cc_start: 0.6251 (mttt) cc_final: 0.5852 (pttt) REVERT: L 195 PHE cc_start: 0.7926 (p90) cc_final: 0.7721 (p90) REVERT: L 241 MET cc_start: 0.5580 (ppp) cc_final: 0.5140 (ppp) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.2631 time to fit residues: 117.3143 Evaluate side-chains 225 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 30.0000 chunk 90 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.9588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17262 Z= 0.205 Angle : 0.644 11.514 24504 Z= 0.366 Chirality : 0.038 0.183 2736 Planarity : 0.004 0.041 2102 Dihedral : 28.753 177.167 4789 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.37 % Allowed : 0.28 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.23), residues: 1277 helix: 0.64 (0.20), residues: 706 sheet: -2.20 (0.50), residues: 76 loop : -2.07 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 218 HIS 0.010 0.001 HIS G 114 PHE 0.020 0.002 PHE G 27 TYR 0.021 0.002 TYR H 40 ARG 0.005 0.000 ARG E 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.9158 (m) cc_final: 0.8718 (t) REVERT: A 120 MET cc_start: 0.8312 (mtp) cc_final: 0.8047 (mtp) REVERT: B 82 THR cc_start: 0.8773 (m) cc_final: 0.8195 (m) REVERT: D 51 ASP cc_start: 0.7660 (p0) cc_final: 0.7362 (p0) REVERT: E 39 HIS cc_start: 0.5001 (t-90) cc_final: 0.4275 (m-70) REVERT: E 73 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7590 (tm-30) REVERT: E 87 SER cc_start: 0.9061 (p) cc_final: 0.8735 (t) REVERT: E 112 ILE cc_start: 0.8953 (tp) cc_final: 0.8751 (tp) REVERT: F 82 THR cc_start: 0.9132 (m) cc_final: 0.8838 (m) REVERT: F 88 TYR cc_start: 0.8064 (m-10) cc_final: 0.7764 (m-80) REVERT: G 49 THR cc_start: 0.9359 (p) cc_final: 0.9081 (t) REVERT: G 121 LYS cc_start: 0.7130 (mptt) cc_final: 0.5873 (tptt) REVERT: H 85 LYS cc_start: 0.8089 (mttp) cc_final: 0.7860 (mmtt) REVERT: K 88 VAL cc_start: 0.6995 (p) cc_final: 0.6778 (t) REVERT: K 100 MET cc_start: 0.4880 (ptt) cc_final: 0.4333 (mtm) REVERT: K 195 PHE cc_start: 0.6741 (p90) cc_final: 0.6470 (p90) REVERT: K 242 LEU cc_start: 0.6824 (mt) cc_final: 0.6620 (mt) REVERT: K 254 TYR cc_start: 0.6101 (t80) cc_final: 0.5879 (t80) REVERT: K 309 ASP cc_start: 0.5938 (m-30) cc_final: 0.5183 (t70) REVERT: K 358 LEU cc_start: 0.7266 (mt) cc_final: 0.6736 (tt) REVERT: L 72 MET cc_start: 0.4121 (pmm) cc_final: 0.3502 (ptp) REVERT: L 100 MET cc_start: 0.6848 (mmm) cc_final: 0.5753 (tpp) REVERT: L 145 LYS cc_start: 0.6376 (mttt) cc_final: 0.5917 (ptpt) REVERT: L 195 PHE cc_start: 0.8010 (p90) cc_final: 0.7805 (p90) REVERT: L 241 MET cc_start: 0.6052 (ppp) cc_final: 0.5370 (ppp) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2572 time to fit residues: 109.2797 Evaluate side-chains 217 residues out of total 1099 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 HIS ** K 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.136311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.101916 restraints weight = 65552.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103061 restraints weight = 52780.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.103795 restraints weight = 48485.123| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.9751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17262 Z= 0.212 Angle : 0.648 11.157 24504 Z= 0.366 Chirality : 0.038 0.184 2736 Planarity : 0.004 0.043 2102 Dihedral : 28.770 176.733 4789 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.37 % Allowed : 0.28 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1277 helix: 0.63 (0.20), residues: 707 sheet: -2.15 (0.51), residues: 74 loop : -2.08 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 218 HIS 0.010 0.001 HIS G 114 PHE 0.025 0.002 PHE G 27 TYR 0.018 0.002 TYR F 72 ARG 0.006 0.000 ARG K 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3077.22 seconds wall clock time: 56 minutes 42.26 seconds (3402.26 seconds total)