Starting phenix.real_space_refine on Tue Jul 29 05:56:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6puw_20483/07_2025/6puw_20483.cif Found real_map, /net/cci-nas-00/data/ceres_data/6puw_20483/07_2025/6puw_20483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6puw_20483/07_2025/6puw_20483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6puw_20483/07_2025/6puw_20483.map" model { file = "/net/cci-nas-00/data/ceres_data/6puw_20483/07_2025/6puw_20483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6puw_20483/07_2025/6puw_20483.cif" } resolution = 2.9 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= 0.024 sd= 0.693 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 72 5.49 5 Mg 4 5.21 5 S 34 5.16 5 C 6662 2.51 5 N 1914 2.21 5 O 2420 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11116 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1935 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "B" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 539 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "D" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} Chain: "E" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 371 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Conformer: "B" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} bond proxies already assigned to first conformer: 369 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 319 SG CYS A 40 26.812 44.982 52.090 1.00 27.12 S ATOM 342 SG CYS A 43 30.201 46.049 50.522 1.00 13.11 S ATOM 2241 SG CYS B 40 49.179 122.249 23.495 1.00 99.74 S ATOM 2264 SG CYS B 43 47.044 120.689 26.698 1.00107.94 S Restraints were copied for chains: K, J, G, L, H, I Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA F 21 " occ=0.60 ... (40 atoms not shown) pdb=" C4 B DA F 21 " occ=0.40 residue: pdb=" P A DA L 21 " occ=0.60 ... (40 atoms not shown) pdb=" C4 B DA L 21 " occ=0.40 Time building chain proxies: 8.10, per 1000 atoms: 0.73 Number of scatterers: 11116 At special positions: 0 Unit cell: (92.43, 133.51, 83.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 34 16.00 P 72 15.00 Mg 4 11.99 F 6 9.00 O 2420 8.00 N 1914 7.00 C 6662 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 303 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 40 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 40 " pdb=" ZN G 303 " pdb="ZN ZN G 303 " - pdb=" NE2 HIS G 12 " pdb="ZN ZN G 303 " - pdb=" ND1 HIS G 16 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 43 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 40 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 12 " pdb="ZN ZN H 301 " - pdb=" ND1 HIS H 16 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 43 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 40 " Number of angles added : 4 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 14 sheets defined 47.2% alpha, 19.3% beta 30 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 removed outlier: 3.920A pdb=" N LYS A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.598A pdb=" N TYR A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 166 Processing helix chain 'A' and resid 171 through 186 Processing helix chain 'A' and resid 195 through 221 removed outlier: 3.623A pdb=" N ILE A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 12 Processing helix chain 'B' and resid 18 through 27 removed outlier: 3.563A pdb=" N SER B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 39 Processing helix chain 'B' and resid 93 through 108 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 150 through 166 Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 171 through 186 Processing helix chain 'B' and resid 196 through 220 removed outlier: 3.602A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 222 Processing helix chain 'C' and resid 270 through 275 removed outlier: 3.735A pdb=" N GLN C 274 " --> pdb=" O TYR C 271 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET C 275 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 16 removed outlier: 3.920A pdb=" N LYS G 14 " --> pdb=" O GLU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 26 Processing helix chain 'G' and resid 29 through 39 Processing helix chain 'G' and resid 40 through 44 Processing helix chain 'G' and resid 93 through 108 removed outlier: 3.598A pdb=" N TYR G 99 " --> pdb=" O GLN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 123 Processing helix chain 'G' and resid 123 through 134 Processing helix chain 'G' and resid 144 through 147 Processing helix chain 'G' and resid 148 through 166 Processing helix chain 'G' and resid 171 through 186 Processing helix chain 'G' and resid 195 through 221 removed outlier: 3.623A pdb=" N ILE G 220 " --> pdb=" O GLN G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 12 Processing helix chain 'H' and resid 18 through 27 removed outlier: 3.563A pdb=" N SER H 24 " --> pdb=" O ARG H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 39 Processing helix chain 'H' and resid 93 through 108 Processing helix chain 'H' and resid 123 through 134 Processing helix chain 'H' and resid 150 through 166 Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing helix chain 'H' and resid 171 through 186 Processing helix chain 'H' and resid 196 through 220 removed outlier: 3.602A pdb=" N ILE H 220 " --> pdb=" O GLN H 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 222 Processing helix chain 'I' and resid 270 through 275 removed outlier: 3.735A pdb=" N GLN I 274 " --> pdb=" O TYR I 271 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET I 275 " --> pdb=" O GLY I 272 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.251A pdb=" N VAL A 72 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP A 61 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL A 113 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.623A pdb=" N TRP A 243 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 84 through 89 removed outlier: 4.086A pdb=" N VAL B 72 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL B 113 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 188 through 189 Processing sheet with id=5, first strand: chain 'B' and resid 240 through 244 removed outlier: 5.751A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP B 243 " --> pdb=" O VAL B 250 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 256 through 261 removed outlier: 7.091A pdb=" N ALA C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS C 244 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 250 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 256 through 261 removed outlier: 6.527A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL D 225 " --> pdb=" O PRO D 238 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D 224 " --> pdb=" O ILE D 268 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'G' and resid 87 through 89 removed outlier: 4.251A pdb=" N VAL G 72 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP G 61 " --> pdb=" O HIS G 114 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL G 113 " --> pdb=" O GLU G 138 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'G' and resid 224 through 225 removed outlier: 3.623A pdb=" N TRP G 243 " --> pdb=" O VAL G 250 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'H' and resid 84 through 89 removed outlier: 4.086A pdb=" N VAL H 72 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL H 113 " --> pdb=" O GLU H 138 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'H' and resid 188 through 189 Processing sheet with id=12, first strand: chain 'H' and resid 240 through 244 removed outlier: 5.751A pdb=" N LEU H 241 " --> pdb=" O GLN H 252 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN H 252 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP H 243 " --> pdb=" O VAL H 250 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'I' and resid 256 through 261 removed outlier: 7.091A pdb=" N ALA I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS I 244 " --> pdb=" O ALA I 248 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL I 250 " --> pdb=" O LEU I 242 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'J' and resid 256 through 261 removed outlier: 6.527A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL J 225 " --> pdb=" O PRO J 238 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG J 224 " --> pdb=" O ILE J 268 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1632 1.31 - 1.43: 3202 1.43 - 1.56: 6130 1.56 - 1.68: 146 1.68 - 1.81: 50 Bond restraints: 11160 Sorted by residual: bond pdb=" CAN KLQ A 304 " pdb=" CBB KLQ A 304 " ideal model delta sigma weight residual 1.520 1.276 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" CAN KLQ G 304 " pdb=" CBB KLQ G 304 " ideal model delta sigma weight residual 1.520 1.276 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" CBD KLQ G 304 " pdb=" OAQ KLQ G 304 " ideal model delta sigma weight residual 1.390 1.625 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" CBD KLQ A 304 " pdb=" OAQ KLQ A 304 " ideal model delta sigma weight residual 1.390 1.625 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" CAW KLQ G 304 " pdb=" CAZ KLQ G 304 " ideal model delta sigma weight residual 1.366 1.542 -0.176 2.00e-02 2.50e+03 7.77e+01 ... (remaining 11155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 15184 2.38 - 4.76: 160 4.76 - 7.14: 28 7.14 - 9.52: 0 9.52 - 11.90: 2 Bond angle restraints: 15374 Sorted by residual: angle pdb=" N SER G 123 " pdb=" CA SER G 123 " pdb=" C SER G 123 " ideal model delta sigma weight residual 110.41 117.17 -6.76 1.23e+00 6.61e-01 3.02e+01 angle pdb=" N SER A 123 " pdb=" CA SER A 123 " pdb=" C SER A 123 " ideal model delta sigma weight residual 110.41 117.17 -6.76 1.23e+00 6.61e-01 3.02e+01 angle pdb=" O LYS G 127 " pdb=" C LYS G 127 " pdb=" N ALA G 128 " ideal model delta sigma weight residual 122.15 116.92 5.23 1.14e+00 7.69e-01 2.10e+01 angle pdb=" O LYS A 127 " pdb=" C LYS A 127 " pdb=" N ALA A 128 " ideal model delta sigma weight residual 122.15 116.92 5.23 1.14e+00 7.69e-01 2.10e+01 angle pdb=" C LYS A 127 " pdb=" N ALA A 128 " pdb=" CA ALA A 128 " ideal model delta sigma weight residual 120.29 126.31 -6.02 1.42e+00 4.96e-01 1.80e+01 ... (remaining 15369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 5490 17.33 - 34.67: 594 34.67 - 52.00: 310 52.00 - 69.33: 152 69.33 - 86.66: 16 Dihedral angle restraints: 6562 sinusoidal: 3224 harmonic: 3338 Sorted by residual: dihedral pdb=" CA ARG D 228 " pdb=" C ARG D 228 " pdb=" N ASP D 229 " pdb=" CA ASP D 229 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ARG J 228 " pdb=" C ARG J 228 " pdb=" N ASP J 229 " pdb=" CA ASP J 229 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA TYR G 194 " pdb=" C TYR G 194 " pdb=" N SER G 195 " pdb=" CA SER G 195 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 6559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1510 0.067 - 0.134: 182 0.134 - 0.201: 10 0.201 - 0.268: 4 0.268 - 0.336: 2 Chirality restraints: 1708 Sorted by residual: chirality pdb=" CBC KLQ A 304 " pdb=" CAM KLQ A 304 " pdb=" CAN KLQ A 304 " pdb=" NBE KLQ A 304 " both_signs ideal model delta sigma weight residual False -2.86 -2.53 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CBC KLQ G 304 " pdb=" CAM KLQ G 304 " pdb=" CAN KLQ G 304 " pdb=" NBE KLQ G 304 " both_signs ideal model delta sigma weight residual False -2.86 -2.53 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CBD KLQ G 304 " pdb=" CAO KLQ G 304 " pdb=" NBE KLQ G 304 " pdb=" OAQ KLQ G 304 " both_signs ideal model delta sigma weight residual False 2.41 2.66 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1705 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 127 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C LYS G 127 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS G 127 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA G 128 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 127 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C LYS A 127 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 127 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 128 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 155 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C ASN G 155 " 0.022 2.00e-02 2.50e+03 pdb=" O ASN G 155 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS G 156 " -0.007 2.00e-02 2.50e+03 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 8 0.98 - 1.96: 8 1.96 - 2.94: 4699 2.94 - 3.92: 30716 3.92 - 4.90: 60476 Warning: very small nonbonded interaction distances. Nonbonded interactions: 95907 Sorted by model distance: nonbonded pdb=" O HOH A 464 " pdb=" O HOH G 438 " model vdw 0.000 3.040 nonbonded pdb=" O HOH A 459 " pdb=" O HOH L 109 " model vdw 0.000 3.040 nonbonded pdb=" O HOH A 488 " pdb=" O HOH K 105 " model vdw 0.000 3.040 nonbonded pdb=" O HOH E 105 " pdb=" O HOH G 488 " model vdw 0.000 3.040 nonbonded pdb=" O HOH F 109 " pdb=" O HOH G 459 " model vdw 0.000 3.040 ... (remaining 95902 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 33.590 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 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 : 0.009 0.244 11176 Z= 0.443 Angle : 0.663 13.487 15378 Z= 0.377 Chirality : 0.046 0.336 1708 Planarity : 0.003 0.026 1676 Dihedral : 19.820 86.664 4402 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.21), residues: 1130 helix: -1.14 (0.20), residues: 494 sheet: -1.04 (0.35), residues: 192 loop : -1.93 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 19 HIS 0.003 0.001 HIS B 183 PHE 0.008 0.001 PHE G 185 TYR 0.009 0.001 TYR A 194 ARG 0.002 0.000 ARG H 224 Details of bonding type rmsd hydrogen bonds : bond 0.14024 ( 576) hydrogen bonds : angle 6.65583 ( 1568) metal coordination : bond 0.08287 ( 16) metal coordination : angle 9.59377 ( 4) covalent geometry : bond 0.00863 (11160) covalent geometry : angle 0.64469 (15374) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 1.303 Fit side-chains TARDY: cannot create tardy model for: "GLU A 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8833 (ttm-80) cc_final: 0.8038 (ttp-170) REVERT: A 154 MET cc_start: 0.9280 (mmt) cc_final: 0.8885 (mmt) REVERT: B 35 GLU cc_start: 0.8053 (tp30) cc_final: 0.7266 (mp0) REVERT: B 251 ILE cc_start: 0.8842 (mm) cc_final: 0.8502 (pp) REVERT: G 20 ARG cc_start: 0.8832 (ttm-80) cc_final: 0.8039 (ttp-170) REVERT: G 154 MET cc_start: 0.9281 (mmt) cc_final: 0.8885 (mmt) REVERT: H 35 GLU cc_start: 0.8049 (tp30) cc_final: 0.7266 (mp0) REVERT: H 251 ILE cc_start: 0.8845 (mm) cc_final: 0.8503 (pp) outliers start: 2 outliers final: 2 residues processed: 220 average time/residue: 1.4841 time to fit residues: 348.3224 Evaluate side-chains 162 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain G residue 120 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.0170 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.0670 chunk 46 optimal weight: 0.0040 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 0.0000 chunk 105 optimal weight: 0.2980 overall best weight: 0.0772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN C 221 GLN ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 HIS G 214 GLN G 222 ASN H 164 GLN I 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.102097 restraints weight = 12780.367| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.61 r_work: 0.2955 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 11176 Z= 0.185 Angle : 0.822 13.592 15378 Z= 0.449 Chirality : 0.053 0.376 1708 Planarity : 0.009 0.134 1676 Dihedral : 22.056 61.032 2150 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.69 % Favored : 94.78 % Rotamer: Outliers : 3.07 % Allowed : 10.22 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.23), residues: 1130 helix: -0.98 (0.22), residues: 498 sheet: -1.16 (0.33), residues: 194 loop : -2.16 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.108 0.008 TRP G 61 HIS 0.042 0.004 HIS H 12 PHE 0.083 0.004 PHE G 26 TYR 0.116 0.006 TYR H 99 ARG 0.037 0.001 ARG I 269 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 576) hydrogen bonds : angle 5.53791 ( 1568) metal coordination : bond 0.01376 ( 16) metal coordination : angle 2.45181 ( 4) covalent geometry : bond 0.00404 (11160) covalent geometry : angle 0.82140 (15374) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 1.167 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8746 (ttm-80) cc_final: 0.7904 (ttp-170) REVERT: A 27 ASN cc_start: 0.8660 (p0) cc_final: 0.8322 (m110) REVERT: B 35 GLU cc_start: 0.8072 (tp30) cc_final: 0.6952 (mp0) REVERT: B 251 ILE cc_start: 0.8848 (mm) cc_final: 0.8523 (pp) REVERT: B 258 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7564 (ttmm) REVERT: G 10 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7797 (tm-30) REVERT: G 136 LYS cc_start: 0.8556 (tttm) cc_final: 0.8329 (tptp) REVERT: H 60 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8735 (mm) REVERT: H 251 ILE cc_start: 0.8856 (mm) cc_final: 0.8512 (pp) REVERT: H 258 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7514 (ttmm) REVERT: I 213 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8072 (tt) REVERT: I 262 ARG cc_start: 0.9131 (tpt90) cc_final: 0.8900 (tpt170) outliers start: 30 outliers final: 6 residues processed: 194 average time/residue: 1.2418 time to fit residues: 260.1187 Evaluate side-chains 157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 260 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS A 148 GLN A 155 ASN A 168 GLN B 117 ASN ** G 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 ASN G 168 GLN H 164 GLN H 221 GLN I 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.097439 restraints weight = 14259.846| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.73 r_work: 0.2873 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11176 Z= 0.182 Angle : 0.512 10.619 15378 Z= 0.287 Chirality : 0.042 0.149 1708 Planarity : 0.004 0.050 1676 Dihedral : 21.851 61.129 2148 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.17 % Allowed : 12.78 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.02 (0.23), residues: 1130 helix: 0.32 (0.22), residues: 500 sheet: -0.67 (0.33), residues: 194 loop : -1.80 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 19 HIS 0.006 0.001 HIS G 171 PHE 0.016 0.001 PHE G 121 TYR 0.012 0.001 TYR A 194 ARG 0.002 0.000 ARG J 224 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 576) hydrogen bonds : angle 4.71603 ( 1568) metal coordination : bond 0.00867 ( 16) metal coordination : angle 1.56855 ( 4) covalent geometry : bond 0.00418 (11160) covalent geometry : angle 0.51178 (15374) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.169 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 85 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8754 (ttm-80) cc_final: 0.7877 (ttp-170) REVERT: A 95 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: B 35 GLU cc_start: 0.8058 (tp30) cc_final: 0.6869 (mp0) REVERT: B 154 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7507 (mmt) REVERT: B 258 LYS cc_start: 0.8015 (ttmm) cc_final: 0.7668 (mtmt) REVERT: G 20 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8093 (ttm110) REVERT: G 136 LYS cc_start: 0.8567 (tttm) cc_final: 0.8307 (tptp) REVERT: H 35 GLU cc_start: 0.8002 (tp30) cc_final: 0.7688 (tp30) REVERT: H 252 GLN cc_start: 0.8264 (tt0) cc_final: 0.7963 (tt0) REVERT: H 258 LYS cc_start: 0.7999 (ttmm) cc_final: 0.7669 (mtmt) outliers start: 31 outliers final: 12 residues processed: 173 average time/residue: 1.2846 time to fit residues: 239.3301 Evaluate side-chains 167 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain J residue 257 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 117 ASN G 155 ASN H 117 ASN H 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.093916 restraints weight = 14018.285| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.70 r_work: 0.2887 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11176 Z= 0.227 Angle : 0.514 5.170 15378 Z= 0.293 Chirality : 0.044 0.147 1708 Planarity : 0.004 0.038 1676 Dihedral : 21.922 61.858 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.07 % Allowed : 14.52 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.37 (0.24), residues: 1130 helix: 0.91 (0.22), residues: 498 sheet: -0.45 (0.33), residues: 194 loop : -1.47 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 19 HIS 0.004 0.001 HIS G 171 PHE 0.018 0.002 PHE G 121 TYR 0.013 0.001 TYR A 194 ARG 0.004 0.000 ARG G 199 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 576) hydrogen bonds : angle 4.62063 ( 1568) metal coordination : bond 0.01002 ( 16) metal coordination : angle 1.59969 ( 4) covalent geometry : bond 0.00526 (11160) covalent geometry : angle 0.51369 (15374) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 1.130 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8860 (ttm-80) cc_final: 0.8102 (ttp-170) REVERT: A 95 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: B 35 GLU cc_start: 0.7993 (tp30) cc_final: 0.6905 (mp0) REVERT: G 20 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8281 (ttm110) REVERT: H 35 GLU cc_start: 0.8028 (tp30) cc_final: 0.7703 (tp30) REVERT: H 252 GLN cc_start: 0.8441 (tt0) cc_final: 0.8030 (tt0) REVERT: I 257 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8661 (mm) outliers start: 30 outliers final: 14 residues processed: 164 average time/residue: 1.3223 time to fit residues: 233.4745 Evaluate side-chains 157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 117 ASN Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain I residue 257 ILE Chi-restraints excluded: chain J residue 251 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 60 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 HIS A 148 GLN A 155 ASN B 117 ASN C 221 GLN G 155 ASN H 117 ASN H 221 GLN I 221 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.098882 restraints weight = 13755.935| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.67 r_work: 0.2904 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11176 Z= 0.126 Angle : 0.461 6.780 15378 Z= 0.265 Chirality : 0.040 0.145 1708 Planarity : 0.003 0.040 1676 Dihedral : 21.705 62.207 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.15 % Allowed : 16.36 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.15 (0.24), residues: 1130 helix: 1.38 (0.22), residues: 500 sheet: -0.21 (0.34), residues: 194 loop : -1.25 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 19 HIS 0.004 0.001 HIS H 171 PHE 0.010 0.001 PHE B 26 TYR 0.010 0.001 TYR B 83 ARG 0.003 0.000 ARG C 262 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 576) hydrogen bonds : angle 4.39211 ( 1568) metal coordination : bond 0.00308 ( 16) metal coordination : angle 0.75088 ( 4) covalent geometry : bond 0.00279 (11160) covalent geometry : angle 0.46133 (15374) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.036 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 20 ARG cc_start: 0.8760 (ttm-80) cc_final: 0.7931 (ttp-170) REVERT: A 136 LYS cc_start: 0.8640 (tttm) cc_final: 0.8383 (tptp) REVERT: B 35 GLU cc_start: 0.7930 (tp30) cc_final: 0.6762 (mp0) REVERT: G 20 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8062 (ttm110) REVERT: G 154 MET cc_start: 0.9322 (mmt) cc_final: 0.9100 (mmt) REVERT: H 35 GLU cc_start: 0.7974 (tp30) cc_final: 0.7605 (tp30) REVERT: H 252 GLN cc_start: 0.8240 (tt0) cc_final: 0.7819 (tt0) outliers start: 21 outliers final: 9 residues processed: 155 average time/residue: 1.2144 time to fit residues: 203.7317 Evaluate side-chains 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain I residue 260 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 117 ASN G 114 HIS G 148 GLN G 155 ASN G 214 GLN H 117 ASN H 221 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.095172 restraints weight = 19171.432| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.98 r_work: 0.2803 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11176 Z= 0.215 Angle : 0.503 7.451 15378 Z= 0.285 Chirality : 0.043 0.142 1708 Planarity : 0.003 0.041 1676 Dihedral : 21.838 62.570 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.66 % Allowed : 16.36 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.20 (0.24), residues: 1130 helix: 1.38 (0.22), residues: 498 sheet: -0.19 (0.34), residues: 194 loop : -1.15 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 131 HIS 0.002 0.001 HIS B 171 PHE 0.011 0.001 PHE G 121 TYR 0.012 0.001 TYR A 194 ARG 0.003 0.000 ARG G 199 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 576) hydrogen bonds : angle 4.48012 ( 1568) metal coordination : bond 0.00830 ( 16) metal coordination : angle 1.33327 ( 4) covalent geometry : bond 0.00494 (11160) covalent geometry : angle 0.50251 (15374) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.097 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8839 (ttm-80) cc_final: 0.7964 (ttp-170) REVERT: B 35 GLU cc_start: 0.7994 (tp30) cc_final: 0.6800 (mp0) REVERT: G 20 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8157 (ttm110) REVERT: G 170 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8366 (tm-30) REVERT: H 35 GLU cc_start: 0.8049 (tp30) cc_final: 0.6962 (mp0) outliers start: 26 outliers final: 11 residues processed: 156 average time/residue: 1.2956 time to fit residues: 217.5221 Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain I residue 260 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 88 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 148 GLN A 155 ASN B 117 ASN C 221 GLN G 155 ASN H 117 ASN H 221 GLN I 221 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.132175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096537 restraints weight = 15312.941| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.76 r_work: 0.2872 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11176 Z= 0.153 Angle : 0.467 5.499 15378 Z= 0.268 Chirality : 0.041 0.146 1708 Planarity : 0.003 0.039 1676 Dihedral : 21.728 62.755 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.94 % Allowed : 17.08 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.41 (0.24), residues: 1130 helix: 1.58 (0.22), residues: 500 sheet: -0.07 (0.34), residues: 194 loop : -1.09 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 131 HIS 0.002 0.001 HIS B 183 PHE 0.007 0.001 PHE G 100 TYR 0.010 0.001 TYR A 194 ARG 0.003 0.000 ARG C 262 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 576) hydrogen bonds : angle 4.36734 ( 1568) metal coordination : bond 0.00379 ( 16) metal coordination : angle 0.55948 ( 4) covalent geometry : bond 0.00347 (11160) covalent geometry : angle 0.46746 (15374) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.123 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8787 (ttm-80) cc_final: 0.7912 (ttp-170) REVERT: A 136 LYS cc_start: 0.8639 (tttm) cc_final: 0.8349 (tptp) REVERT: B 35 GLU cc_start: 0.7917 (tp30) cc_final: 0.6733 (mp0) REVERT: G 20 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8086 (ttm110) REVERT: G 170 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8337 (tm-30) REVERT: H 35 GLU cc_start: 0.7983 (tp30) cc_final: 0.6800 (mp0) outliers start: 19 outliers final: 10 residues processed: 150 average time/residue: 1.2318 time to fit residues: 200.0298 Evaluate side-chains 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain I residue 260 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 78 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 117 ASN C 221 GLN G 155 ASN H 117 ASN H 221 GLN I 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.135594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101490 restraints weight = 11871.943| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.53 r_work: 0.2950 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11176 Z= 0.133 Angle : 0.464 9.575 15378 Z= 0.263 Chirality : 0.041 0.145 1708 Planarity : 0.003 0.038 1676 Dihedral : 21.609 62.875 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.15 % Allowed : 17.08 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.61 (0.25), residues: 1130 helix: 1.74 (0.23), residues: 500 sheet: 0.06 (0.34), residues: 194 loop : -1.00 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 131 HIS 0.002 0.001 HIS H 183 PHE 0.014 0.001 PHE H 26 TYR 0.009 0.001 TYR B 83 ARG 0.003 0.000 ARG C 262 Details of bonding type rmsd hydrogen bonds : bond 0.03068 ( 576) hydrogen bonds : angle 4.26741 ( 1568) metal coordination : bond 0.00356 ( 16) metal coordination : angle 0.55925 ( 4) covalent geometry : bond 0.00299 (11160) covalent geometry : angle 0.46400 (15374) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.215 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8805 (ttm-80) cc_final: 0.8070 (ttp-170) REVERT: A 136 LYS cc_start: 0.8660 (tttm) cc_final: 0.8425 (tptp) REVERT: B 35 GLU cc_start: 0.7835 (tp30) cc_final: 0.6761 (mp0) REVERT: G 20 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8274 (ttp-170) REVERT: G 154 MET cc_start: 0.9314 (mmt) cc_final: 0.9090 (mmt) REVERT: H 35 GLU cc_start: 0.7832 (tp30) cc_final: 0.6848 (mp0) outliers start: 21 outliers final: 10 residues processed: 153 average time/residue: 1.2185 time to fit residues: 201.7006 Evaluate side-chains 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain I residue 260 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 148 GLN A 155 ASN B 117 ASN G 114 HIS G 148 GLN G 155 ASN H 117 ASN H 221 GLN I 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100801 restraints weight = 15112.892| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.76 r_work: 0.2922 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11176 Z= 0.143 Angle : 0.468 5.834 15378 Z= 0.267 Chirality : 0.041 0.144 1708 Planarity : 0.003 0.037 1676 Dihedral : 21.633 62.793 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.94 % Allowed : 17.18 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.67 (0.25), residues: 1130 helix: 1.77 (0.23), residues: 500 sheet: 0.12 (0.34), residues: 194 loop : -0.96 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 131 HIS 0.002 0.001 HIS G 171 PHE 0.015 0.001 PHE B 26 TYR 0.010 0.001 TYR B 83 ARG 0.002 0.000 ARG C 262 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 576) hydrogen bonds : angle 4.26339 ( 1568) metal coordination : bond 0.00333 ( 16) metal coordination : angle 0.35230 ( 4) covalent geometry : bond 0.00325 (11160) covalent geometry : angle 0.46774 (15374) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.188 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8830 (ttm-80) cc_final: 0.8062 (ttp-170) REVERT: A 136 LYS cc_start: 0.8683 (tttm) cc_final: 0.8438 (tptp) REVERT: B 35 GLU cc_start: 0.7878 (tp30) cc_final: 0.6771 (mp0) REVERT: G 20 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8302 (ttp-170) REVERT: H 35 GLU cc_start: 0.7831 (tp30) cc_final: 0.6801 (mp0) outliers start: 19 outliers final: 12 residues processed: 147 average time/residue: 1.2345 time to fit residues: 196.6973 Evaluate side-chains 154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 117 ASN Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain I residue 260 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 117 ASN C 221 GLN G 155 ASN H 117 ASN H 221 GLN I 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.098843 restraints weight = 14880.683| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.72 r_work: 0.2919 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11176 Z= 0.158 Angle : 0.481 6.877 15378 Z= 0.274 Chirality : 0.041 0.144 1708 Planarity : 0.003 0.037 1676 Dihedral : 21.652 62.576 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.84 % Allowed : 18.00 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.68 (0.25), residues: 1130 helix: 1.77 (0.23), residues: 500 sheet: 0.15 (0.34), residues: 194 loop : -0.95 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 131 HIS 0.006 0.001 HIS A 171 PHE 0.007 0.001 PHE A 185 TYR 0.010 0.001 TYR B 83 ARG 0.002 0.000 ARG C 262 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 576) hydrogen bonds : angle 4.27501 ( 1568) metal coordination : bond 0.00443 ( 16) metal coordination : angle 0.50456 ( 4) covalent geometry : bond 0.00363 (11160) covalent geometry : angle 0.48052 (15374) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 1.147 Fit side-chains TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8846 (ttm-80) cc_final: 0.8167 (ttp-170) REVERT: A 136 LYS cc_start: 0.8676 (tttm) cc_final: 0.8433 (tptp) REVERT: B 35 GLU cc_start: 0.7897 (tp30) cc_final: 0.6812 (mp0) REVERT: G 20 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8310 (ttp-170) REVERT: H 35 GLU cc_start: 0.7814 (tp30) cc_final: 0.6804 (mp0) outliers start: 18 outliers final: 13 residues processed: 147 average time/residue: 1.2691 time to fit residues: 202.0017 Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 258 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain I residue 260 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 42 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN C 221 GLN G 155 ASN H 117 ASN H 221 GLN I 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.099981 restraints weight = 11757.006| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.51 r_work: 0.2937 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11176 Z= 0.181 Angle : 0.786 59.199 15378 Z= 0.485 Chirality : 0.042 0.413 1708 Planarity : 0.003 0.037 1676 Dihedral : 21.662 62.576 2146 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % Rotamer: Outliers : 1.74 % Allowed : 18.30 % Favored : 79.96 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.26 % 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: 0.69 (0.25), residues: 1130 helix: 1.77 (0.23), residues: 500 sheet: 0.15 (0.34), residues: 194 loop : -0.94 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 131 HIS 0.006 0.001 HIS A 171 PHE 0.007 0.001 PHE G 100 TYR 0.010 0.001 TYR B 83 ARG 0.002 0.000 ARG C 262 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 576) hydrogen bonds : angle 4.27387 ( 1568) metal coordination : bond 0.00437 ( 16) metal coordination : angle 0.50200 ( 4) covalent geometry : bond 0.00385 (11160) covalent geometry : angle 0.78558 (15374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9464.43 seconds wall clock time: 165 minutes 11.13 seconds (9911.13 seconds total)