Starting phenix.real_space_refine on Tue Aug 26 23:49:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b6g_15866/08_2025/8b6g_15866_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b6g_15866/08_2025/8b6g_15866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b6g_15866/08_2025/8b6g_15866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b6g_15866/08_2025/8b6g_15866.map" model { file = "/net/cci-nas-00/data/ceres_data/8b6g_15866/08_2025/8b6g_15866_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b6g_15866/08_2025/8b6g_15866_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.004 sd= 0.109 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 Ca 2 9.91 5 Fe 10 7.16 5 P 20 5.49 5 S 91 5.16 5 C 13349 2.51 5 N 3358 2.21 5 O 3772 1.98 5 H 19247 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39849 Number of models: 1 Model: "" Number of chains: 25 Chain: "CH" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1700 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "CM" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1232 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "CL" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1522 Classifications: {'peptide': 88} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "CA" Number of atoms: 9198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 9198 Classifications: {'peptide': 599} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 576} Chain: "CI" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1805 Classifications: {'peptide': 114} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 113} Chain: "CB" Number of atoms: 4561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4561 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 19, 'TRANS': 265} Chain: "CF" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3598 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain: "CG" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3247 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "CK" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1577 Classifications: {'peptide': 93} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "CE" Number of atoms: 5115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 5115 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 310} Chain: "CJ" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1663 Classifications: {'peptide': 103} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "CN" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1029 Classifications: {'peptide': 62} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "CC" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 976 Classifications: {'peptide': 59} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 58} Chain: "CO" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 742 Classifications: {'peptide': 43} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "CD" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 807 Classifications: {'peptide': 44} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 43} Chain: "CM" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "CA" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' CA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "CB" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Unusual residues: {' CA': 1, 'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "CG" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 200 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "CK" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 151 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "CE" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "CJ" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "CC" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 158 Unusual residues: {'3PE': 1, 'PC1': 1, 'UQ8': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "CO" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "CD" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 151 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17107 SG CYSCB 130 58.047 61.250 36.579 1.00 98.27 S ATOM 17266 SG CYSCB 142 55.322 63.714 37.025 1.00 90.96 S ATOM 17004 SG CYSCB 122 50.606 62.551 38.423 1.00118.37 S ATOM 17079 SG CYSCB 127 52.727 58.411 39.139 1.00 92.21 S ATOM 18465 SG CYSCB 215 56.445 59.856 50.808 1.00 94.69 S ATOM 18540 SG CYSCB 221 63.374 60.714 50.191 1.00 86.87 S ATOM 19518 SG CYSCB 282 59.990 66.584 48.721 1.00 80.22 S ATOM 18510 SG CYSCB 218 60.197 60.730 44.994 1.00 89.77 S ATOM 19376 SG CYSCB 272 69.852 61.475 59.587 1.00111.34 S ATOM 19463 SG CYSCB 278 66.389 64.627 53.942 1.00 97.90 S ATOM 18586 SG CYSCB 225 70.594 58.377 53.283 1.00 89.06 S Time building chain proxies: 6.96, per 1000 atoms: 0.17 Number of scatterers: 39849 At special positions: 0 Unit cell: (180, 98.75, 142.5, 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) Fe 10 26.01 Ca 2 19.99 S 91 16.00 P 20 15.00 O 3772 8.00 N 3358 7.00 C 13349 6.00 H 19247 1.00 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.80 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.7 microseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3SCB1002 " pdb="FE3 F3SCB1002 " - pdb=" SG CYSCB 278 " pdb="FE1 F3SCB1002 " - pdb=" SG CYSCB 272 " pdb="FE4 F3SCB1002 " - pdb=" SG CYSCB 225 " pdb=" FESCB1000 " pdb="FE1 FESCB1000 " - pdb=" SG CYSCB 130 " pdb="FE1 FESCB1000 " - pdb=" SG CYSCB 142 " pdb="FE2 FESCB1000 " - pdb=" SG CYSCB 127 " pdb=" SF4CB1001 " pdb="FE4 SF4CB1001 " - pdb=" SG CYSCB 218 " pdb="FE2 SF4CB1001 " - pdb=" SG CYSCB 221 " pdb="FE1 SF4CB1001 " - pdb=" SG CYSCB 215 " pdb="FE3 SF4CB1001 " - pdb=" SG CYSCB 282 " Number of angles added : 26 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4564 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 18 sheets defined 60.4% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'CH' and resid 95 through 113 removed outlier: 3.723A pdb=" N LYSCH 111 " --> pdb=" O ILECH 107 " (cutoff:3.500A) Processing helix chain 'CH' and resid 113 through 124 Processing helix chain 'CH' and resid 126 through 131 Processing helix chain 'CH' and resid 134 through 153 removed outlier: 3.619A pdb=" N LEUCH 138 " --> pdb=" O PROCH 134 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASPCH 139 " --> pdb=" O GLUCH 135 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LYSCH 140 " --> pdb=" O LYSCH 136 " (cutoff:3.500A) Processing helix chain 'CH' and resid 156 through 176 Processing helix chain 'CH' and resid 184 through 193 Processing helix chain 'CM' and resid 11 through 15 Processing helix chain 'CM' and resid 25 through 49 removed outlier: 3.635A pdb=" N TRPCM 49 " --> pdb=" O CYSCM 45 " (cutoff:3.500A) Processing helix chain 'CM' and resid 55 through 59 Processing helix chain 'CL' and resid 2 through 7 Processing helix chain 'CL' and resid 7 through 12 Processing helix chain 'CL' and resid 22 through 35 Processing helix chain 'CL' and resid 39 through 52 removed outlier: 4.446A pdb=" N ILECL 45 " --> pdb=" O ALACL 41 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARGCL 49 " --> pdb=" O ILECL 45 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYSCL 50 " --> pdb=" O ARGCL 46 " (cutoff:3.500A) Processing helix chain 'CL' and resid 57 through 83 Processing helix chain 'CL' and resid 84 through 88 Processing helix chain 'CA' and resid 57 through 71 Processing helix chain 'CA' and resid 81 through 90 removed outlier: 7.034A pdb=" N HISCA 86 " --> pdb=" O THRCA 83 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THRCA 87 " --> pdb=" O ARGCA 84 " (cutoff:3.500A) Processing helix chain 'CA' and resid 105 through 118 Processing helix chain 'CA' and resid 122 through 144 Proline residue: CA 134 - end of helix Processing helix chain 'CA' and resid 182 through 198 Processing helix chain 'CA' and resid 247 through 251 Processing helix chain 'CA' and resid 262 through 271 removed outlier: 3.676A pdb=" N ALACA 268 " --> pdb=" O GLYCA 264 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THRCA 269 " --> pdb=" O METCA 265 " (cutoff:3.500A) Processing helix chain 'CA' and resid 296 through 303 removed outlier: 4.193A pdb=" N ARGCA 300 " --> pdb=" O THRCA 296 " (cutoff:3.500A) Processing helix chain 'CA' and resid 314 through 319 removed outlier: 3.867A pdb=" N TYRCA 318 " --> pdb=" O PHECA 314 " (cutoff:3.500A) Processing helix chain 'CA' and resid 327 through 341 Processing helix chain 'CA' and resid 346 through 350 removed outlier: 3.841A pdb=" N ASPCA 350 " --> pdb=" O PROCA 347 " (cutoff:3.500A) Processing helix chain 'CA' and resid 360 through 368 Processing helix chain 'CA' and resid 368 through 380 Processing helix chain 'CA' and resid 382 through 386 removed outlier: 3.596A pdb=" N GLUCA 386 " --> pdb=" O VALCA 383 " (cutoff:3.500A) Processing helix chain 'CA' and resid 427 through 429 No H-bonds generated for 'chain 'CA' and resid 427 through 429' Processing helix chain 'CA' and resid 444 through 464 Processing helix chain 'CA' and resid 478 through 490 Processing helix chain 'CA' and resid 497 through 512 Processing helix chain 'CA' and resid 517 through 536 removed outlier: 3.535A pdb=" N LYSCA 536 " --> pdb=" O TYRCA 532 " (cutoff:3.500A) Processing helix chain 'CA' and resid 548 through 574 Processing helix chain 'CI' and resid 3 through 50 Processing helix chain 'CI' and resid 65 through 68 Processing helix chain 'CI' and resid 69 through 85 Processing helix chain 'CI' and resid 95 through 114 Processing helix chain 'CB' and resid 31 through 49 Processing helix chain 'CB' and resid 63 through 68 Processing helix chain 'CB' and resid 93 through 97 removed outlier: 4.139A pdb=" N PHECB 97 " --> pdb=" O ILECB 94 " (cutoff:3.500A) Processing helix chain 'CB' and resid 100 through 112 Processing helix chain 'CB' and resid 142 through 144 No H-bonds generated for 'chain 'CB' and resid 142 through 144' Processing helix chain 'CB' and resid 172 through 181 removed outlier: 3.505A pdb=" N METCB 181 " --> pdb=" O ALACB 177 " (cutoff:3.500A) Processing helix chain 'CB' and resid 202 through 208 Processing helix chain 'CB' and resid 221 through 224 Processing helix chain 'CB' and resid 225 through 231 Processing helix chain 'CB' and resid 237 through 250 Processing helix chain 'CB' and resid 255 through 264 Processing helix chain 'CB' and resid 276 through 282 Processing helix chain 'CB' and resid 287 through 309 removed outlier: 3.931A pdb=" N ILECB 307 " --> pdb=" O ARGCB 303 " (cutoff:3.500A) Processing helix chain 'CF' and resid 92 through 125 removed outlier: 4.465A pdb=" N GLUCF 107 " --> pdb=" O ARGCF 103 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLUCF 108 " --> pdb=" O GLNCF 104 " (cutoff:3.500A) Processing helix chain 'CF' and resid 127 through 133 removed outlier: 5.937A pdb=" N GLUCF 132 " --> pdb=" O VALCF 129 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TRPCF 133 " --> pdb=" O PHECF 130 " (cutoff:3.500A) Processing helix chain 'CF' and resid 134 through 139 removed outlier: 3.663A pdb=" N TYRCF 138 " --> pdb=" O METCF 134 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHECF 139 " --> pdb=" O TYRCF 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'CF' and resid 134 through 139' Processing helix chain 'CF' and resid 139 through 156 removed outlier: 3.657A pdb=" N ILECF 143 " --> pdb=" O PHECF 139 " (cutoff:3.500A) Processing helix chain 'CF' and resid 159 through 167 removed outlier: 3.523A pdb=" N VALCF 163 " --> pdb=" O TYRCF 159 " (cutoff:3.500A) Processing helix chain 'CF' and resid 172 through 178 Processing helix chain 'CF' and resid 188 through 206 Processing helix chain 'CF' and resid 208 through 228 Proline residue: CF 219 - end of helix Processing helix chain 'CF' and resid 231 through 257 Processing helix chain 'CF' and resid 261 through 270 removed outlier: 3.767A pdb=" N LYSCF 270 " --> pdb=" O ALACF 266 " (cutoff:3.500A) Processing helix chain 'CF' and resid 277 through 293 Processing helix chain 'CG' and resid 3 through 33 removed outlier: 4.021A pdb=" N GLNCG 22 " --> pdb=" O GLYCG 18 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLNCG 24 " --> pdb=" O SERCG 20 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARGCG 25 " --> pdb=" O PHECG 21 " (cutoff:3.500A) Processing helix chain 'CG' and resid 39 through 45 Processing helix chain 'CG' and resid 49 through 63 removed outlier: 4.329A pdb=" N ARGCG 58 " --> pdb=" O VALCG 54 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEUCG 59 " --> pdb=" O PHECG 55 " (cutoff:3.500A) Processing helix chain 'CG' and resid 66 through 70 Processing helix chain 'CG' and resid 71 through 117 Processing helix chain 'CG' and resid 129 through 150 Processing helix chain 'CG' and resid 153 through 175 removed outlier: 4.148A pdb=" N TYRCG 166 " --> pdb=" O GLUCG 162 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYRCG 167 " --> pdb=" O GLUCG 163 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALACG 168 " --> pdb=" O ILECG 164 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VALCG 175 " --> pdb=" O ILECG 171 " (cutoff:3.500A) Processing helix chain 'CG' and resid 180 through 185 Processing helix chain 'CG' and resid 185 through 190 removed outlier: 3.766A pdb=" N LYSCG 190 " --> pdb=" O LYSCG 186 " (cutoff:3.500A) Processing helix chain 'CG' and resid 191 through 196 Processing helix chain 'CK' and resid 4 through 13 Processing helix chain 'CK' and resid 23 through 40 Processing helix chain 'CK' and resid 41 through 57 removed outlier: 3.868A pdb=" N PHECK 45 " --> pdb=" O VALCK 41 " (cutoff:3.500A) Proline residue: CK 53 - end of helix Processing helix chain 'CE' and resid 10 through 22 Processing helix chain 'CE' and resid 37 through 49 removed outlier: 3.719A pdb=" N LEUCE 41 " --> pdb=" O LYSCE 37 " (cutoff:3.500A) Processing helix chain 'CE' and resid 65 through 75 Processing helix chain 'CE' and resid 94 through 107 Processing helix chain 'CE' and resid 117 through 121 Processing helix chain 'CE' and resid 127 through 143 Processing helix chain 'CE' and resid 160 through 172 Processing helix chain 'CE' and resid 189 through 203 removed outlier: 4.157A pdb=" N ASNCE 203 " --> pdb=" O ILECE 199 " (cutoff:3.500A) Processing helix chain 'CE' and resid 219 through 232 Processing helix chain 'CE' and resid 240 through 247 Processing helix chain 'CE' and resid 252 through 259 Processing helix chain 'CE' and resid 260 through 273 Processing helix chain 'CE' and resid 285 through 288 Processing helix chain 'CE' and resid 294 through 299 Processing helix chain 'CE' and resid 305 through 310 removed outlier: 3.821A pdb=" N GLNCE 310 " --> pdb=" O GLNCE 307 " (cutoff:3.500A) Processing helix chain 'CE' and resid 314 through 321 Processing helix chain 'CJ' and resid 2 through 26 Processing helix chain 'CJ' and resid 26 through 46 removed outlier: 3.574A pdb=" N TYRCJ 38 " --> pdb=" O HISCJ 34 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 57 through 61 removed outlier: 3.670A pdb=" N THRCJ 61 " --> pdb=" O PROCJ 58 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 63 through 102 removed outlier: 6.397A pdb=" N VALCJ 69 " --> pdb=" O ASNCJ 65 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYRCJ 70 " --> pdb=" O LYSCJ 66 " (cutoff:3.500A) Processing helix chain 'CN' and resid 14 through 26 Proline residue: CN 22 - end of helix removed outlier: 3.630A pdb=" N LEUCN 26 " --> pdb=" O PROCN 22 " (cutoff:3.500A) Processing helix chain 'CN' and resid 26 through 45 Proline residue: CN 35 - end of helix removed outlier: 4.264A pdb=" N ASNCN 44 " --> pdb=" O ILECN 40 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SERCN 45 " --> pdb=" O VALCN 41 " (cutoff:3.500A) Processing helix chain 'CC' and resid 8 through 12 Processing helix chain 'CC' and resid 16 through 49 removed outlier: 3.603A pdb=" N ILECC 25 " --> pdb=" O HISCC 21 " (cutoff:3.500A) Processing helix chain 'CO' and resid 7 through 28 Processing helix chain 'CO' and resid 37 through 41 Processing helix chain 'CD' and resid 2 through 13 Processing helix chain 'CD' and resid 14 through 19 Processing helix chain 'CD' and resid 20 through 43 removed outlier: 3.877A pdb=" N PHECD 43 " --> pdb=" O LEUCD 39 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'CM' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'CM' and resid 60 through 61 Processing sheet with id=AA3, first strand: chain 'CA' and resid 202 through 204 removed outlier: 7.967A pdb=" N PHECA 203 " --> pdb=" O THRCA 74 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYSCA 76 " --> pdb=" O PHECA 203 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALACA 75 " --> pdb=" O TYRCA 49 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALACA 51 " --> pdb=" O ALACA 75 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILECA 77 " --> pdb=" O ALACA 51 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VALCA 53 " --> pdb=" O ILECA 77 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N VALCA 44 " --> pdb=" O HISCA 233 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N ILECA 235 " --> pdb=" O VALCA 44 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N ASPCA 46 " --> pdb=" O ILECA 235 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N ALACA 237 " --> pdb=" O ASPCA 46 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N THRCA 48 " --> pdb=" O ALACA 237 " (cutoff:3.500A) removed outlier: 10.594A pdb=" N TYRCA 239 " --> pdb=" O THRCA 48 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASPCA 50 " --> pdb=" O TYRCA 239 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N VALCA 241 " --> pdb=" O ASPCA 50 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILECA 52 " --> pdb=" O VALCA 241 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ARGCA 220 " --> pdb=" O ALACA 237 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N CYSCA 219 " --> pdb=" O METCA 213 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N METCA 213 " --> pdb=" O CYSCA 219 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLYCA 221 " --> pdb=" O LEUCA 211 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEUCA 211 " --> pdb=" O GLYCA 221 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILECA 223 " --> pdb=" O ILECA 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'CA' and resid 94 through 95 Processing sheet with id=AA5, first strand: chain 'CA' and resid 275 through 276 removed outlier: 4.077A pdb=" N LYSCA 603 " --> pdb=" O LYSCA 609 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYSCA 609 " --> pdb=" O LYSCA 603 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'CA' and resid 281 through 284 removed outlier: 6.598A pdb=" N GLNCA 282 " --> pdb=" O HISCA 395 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'CA' and resid 305 through 307 Processing sheet with id=AA8, first strand: chain 'CA' and resid 401 through 402 removed outlier: 5.945A pdb=" N VALCA 401 " --> pdb=" O CYSCA 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'CA' and resid 410 through 412 Processing sheet with id=AB1, first strand: chain 'CA' and resid 495 through 496 removed outlier: 6.351A pdb=" N TYRCA 495 " --> pdb=" O LYSCA 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'CA' and resid 515 through 516 Processing sheet with id=AB3, first strand: chain 'CI' and resid 53 through 56 Processing sheet with id=AB4, first strand: chain 'CB' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'CB' and resid 164 through 166 removed outlier: 6.927A pdb=" N VALCB 169 " --> pdb=" O LEUCB 165 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'CE' and resid 57 through 62 removed outlier: 6.394A pdb=" N LEUCE 4 " --> pdb=" O VALCE 80 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VALCE 82 " --> pdb=" O LEUCE 4 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VALCE 6 " --> pdb=" O VALCE 82 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VALCE 79 " --> pdb=" O VALCE 113 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VALCE 115 " --> pdb=" O VALCE 79 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYRCE 81 " --> pdb=" O VALCE 115 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEUCE 112 " --> pdb=" O VALCE 147 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEUCE 149 " --> pdb=" O LEUCE 112 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASNCE 114 " --> pdb=" O LEUCE 149 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THRCE 151 " --> pdb=" O ASNCE 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'CE' and resid 154 through 155 Processing sheet with id=AB8, first strand: chain 'CJ' and resid 52 through 53 removed outlier: 3.628A pdb=" N TYRCJ 52 " --> pdb=" O ARGCO 6 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'CN' and resid 50 through 51 1082 hydrogen bonds defined for protein. 3069 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.97 Time building geometry restraints manager: 6.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.53: 39656 1.53 - 2.20: 646 2.20 - 2.88: 13 2.88 - 3.55: 0 3.55 - 4.22: 3 Bond restraints: 40318 Sorted by residual: bond pdb=" S4 F3SCB1002 " pdb="FE1 F3SCB1002 " ideal model delta sigma weight residual 2.233 4.216 -1.983 2.00e-02 2.50e+03 9.83e+03 bond pdb=" S1 F3SCB1002 " pdb="FE4 F3SCB1002 " ideal model delta sigma weight residual 2.258 4.220 -1.962 2.00e-02 2.50e+03 9.63e+03 bond pdb=" S2 F3SCB1002 " pdb="FE3 F3SCB1002 " ideal model delta sigma weight residual 2.300 4.194 -1.894 2.00e-02 2.50e+03 8.97e+03 bond pdb=" NE1 TRPCB 230 " pdb=" HE1 TRPCB 230 " ideal model delta sigma weight residual 0.860 1.083 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRPCG 103 " pdb=" HE1 TRPCG 103 " ideal model delta sigma weight residual 0.860 1.083 -0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 40313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.85: 71917 14.85 - 29.69: 12 29.69 - 44.54: 2 44.54 - 59.38: 0 59.38 - 74.23: 2 Bond angle restraints: 71933 Sorted by residual: angle pdb=" S1 F3SCB1002 " pdb="FE4 F3SCB1002 " pdb=" S3 F3SCB1002 " ideal model delta sigma weight residual 114.75 40.52 74.23 3.00e+00 1.11e-01 6.12e+02 angle pdb=" S3 F3SCB1002 " pdb="FE1 F3SCB1002 " pdb=" S4 F3SCB1002 " ideal model delta sigma weight residual 112.59 41.17 71.42 3.00e+00 1.11e-01 5.67e+02 angle pdb=" S1 F3SCB1002 " pdb="FE3 F3SCB1002 " pdb=" S4 F3SCB1002 " ideal model delta sigma weight residual 112.54 147.48 -34.94 3.00e+00 1.11e-01 1.36e+02 angle pdb="FE1 F3SCB1002 " pdb=" S4 F3SCB1002 " pdb="FE3 F3SCB1002 " ideal model delta sigma weight residual 74.86 43.90 30.96 3.00e+00 1.11e-01 1.06e+02 angle pdb="FE3 F3SCB1002 " pdb=" S1 F3SCB1002 " pdb="FE4 F3SCB1002 " ideal model delta sigma weight residual 73.06 43.82 29.24 3.00e+00 1.11e-01 9.50e+01 ... (remaining 71928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.59: 18640 28.59 - 57.19: 735 57.19 - 85.78: 83 85.78 - 114.38: 9 114.38 - 142.97: 4 Dihedral angle restraints: 19471 sinusoidal: 10783 harmonic: 8688 Sorted by residual: dihedral pdb=" CA PHECF 130 " pdb=" C PHECF 130 " pdb=" N GLYCF 131 " pdb=" CA GLYCF 131 " ideal model delta harmonic sigma weight residual -180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" C28 UQ8CC 303 " pdb=" C29 UQ8CC 303 " pdb=" C31 UQ8CC 303 " pdb=" C32 UQ8CC 303 " ideal model delta sinusoidal sigma weight residual 104.70 -112.33 -142.97 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" CA5 CDLCO 101 " pdb=" CA4 CDLCO 101 " pdb=" OA6 CDLCO 101 " pdb=" CA6 CDLCO 101 " ideal model delta sinusoidal sigma weight residual 168.24 -50.77 -140.99 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 19468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.640: 2943 1.640 - 3.280: 1 3.280 - 4.919: 0 4.919 - 6.559: 0 6.559 - 8.199: 1 Chirality restraints: 2945 Sorted by residual: chirality pdb=" S2 F3SCB1002 " pdb="FE1 F3SCB1002 " pdb="FE3 F3SCB1002 " pdb="FE4 F3SCB1002 " both_signs ideal model delta sigma weight residual False 10.77 2.57 8.20 2.00e-01 2.50e+01 1.68e+03 chirality pdb=" CG LEUCF 83 " pdb=" CB LEUCF 83 " pdb=" CD1 LEUCF 83 " pdb=" CD2 LEUCF 83 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.72 2.00e-01 2.50e+01 7.44e+01 chirality pdb=" CA METCF 134 " pdb=" N METCF 134 " pdb=" C METCF 134 " pdb=" CB METCF 134 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 2942 not shown) Planarity restraints: 5832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ8CC 303 " -0.014 2.00e-02 2.50e+03 7.65e-02 1.76e+02 pdb=" C1M UQ8CC 303 " -0.034 2.00e-02 2.50e+03 pdb=" C2 UQ8CC 303 " -0.014 2.00e-02 2.50e+03 pdb=" C3 UQ8CC 303 " 0.019 2.00e-02 2.50e+03 pdb=" C4 UQ8CC 303 " 0.027 2.00e-02 2.50e+03 pdb=" C5 UQ8CC 303 " -0.044 2.00e-02 2.50e+03 pdb=" C6 UQ8CC 303 " 0.039 2.00e-02 2.50e+03 pdb=" C7 UQ8CC 303 " 0.142 2.00e-02 2.50e+03 pdb=" O2 UQ8CC 303 " -0.041 2.00e-02 2.50e+03 pdb=" O3 UQ8CC 303 " 0.013 2.00e-02 2.50e+03 pdb=" O4 UQ8CC 303 " 0.091 2.00e-02 2.50e+03 pdb=" O5 UQ8CC 303 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HECCE 401 " 0.016 2.00e-02 2.50e+03 4.32e-02 4.19e+01 pdb=" C2C HECCE 401 " -0.118 2.00e-02 2.50e+03 pdb=" C3C HECCE 401 " 0.017 2.00e-02 2.50e+03 pdb=" C4C HECCE 401 " 0.007 2.00e-02 2.50e+03 pdb=" CAC HECCE 401 " 0.021 2.00e-02 2.50e+03 pdb=" CHC HECCE 401 " 0.019 2.00e-02 2.50e+03 pdb=" CHD HECCE 401 " -0.004 2.00e-02 2.50e+03 pdb=" CMC HECCE 401 " 0.037 2.00e-02 2.50e+03 pdb=" NC HECCE 401 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEUCE 3 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C LEUCE 3 " 0.046 2.00e-02 2.50e+03 pdb=" O LEUCE 3 " -0.017 2.00e-02 2.50e+03 pdb=" N LEUCE 4 " -0.016 2.00e-02 2.50e+03 ... (remaining 5829 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.85: 237 1.85 - 2.54: 32633 2.54 - 3.23: 124108 3.23 - 3.91: 157478 3.91 - 4.60: 252436 Nonbonded interactions: 566892 Sorted by model distance: nonbonded pdb=" HH TYRCN 37 " pdb=" HH TYRCO 37 " model vdw 1.163 2.100 nonbonded pdb="HE22 GLNCG 22 " pdb=" HG1 THRCE 64 " model vdw 1.178 2.100 nonbonded pdb=" HH TYRCF 109 " pdb=" HZ2 LYSCF 152 " model vdw 1.271 2.100 nonbonded pdb=" HG1 THRCA 269 " pdb="HE22 GLNCA 566 " model vdw 1.286 2.100 nonbonded pdb=" O GLNCL 35 " pdb=" HZ1 LYSCL 69 " model vdw 1.306 2.450 ... (remaining 566887 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 13.500 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: 0.290 Extract box with map and model: 0.550 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 44.000 Find NCS groups from input model: 0.120 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:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 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 : 0.029 1.983 21086 Z= 1.537 Angle : 1.270 74.229 28347 Z= 0.395 Chirality : 0.159 8.199 2945 Planarity : 0.003 0.077 3521 Dihedral : 15.248 142.973 8280 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.28 % Favored : 96.51 % Rotamer: Outliers : 0.67 % Allowed : 2.48 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.18), residues: 2379 helix: 2.02 (0.14), residues: 1290 sheet: -0.73 (0.39), residues: 166 loop : -0.85 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGCH 117 TYR 0.013 0.001 TYRCF 268 PHE 0.022 0.001 PHECA 65 TRP 0.012 0.001 TRPCK 32 HIS 0.006 0.001 HISCG 99 Details of bonding type rmsd covalent geometry : bond 0.02370 (21071) covalent geometry : angle 0.98636 (28321) hydrogen bonds : bond 0.13515 ( 1080) hydrogen bonds : angle 5.69881 ( 3069) metal coordination : bond 0.63699 ( 10) metal coordination : angle 26.44346 ( 26) Misc. bond : bond 0.56085 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 628 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 116 GLU cc_start: 0.7101 (mp0) cc_final: 0.6563 (mp0) REVERT: CH 184 CYS cc_start: 0.4325 (m) cc_final: 0.3913 (m) REVERT: CL 2 LYS cc_start: 0.7601 (mttp) cc_final: 0.6939 (mppt) REVERT: CL 21 LEU cc_start: 0.6339 (mt) cc_final: 0.5878 (mt) REVERT: CL 82 LYS cc_start: 0.8482 (tttt) cc_final: 0.7935 (tppt) REVERT: CL 83 PHE cc_start: 0.6719 (m-80) cc_final: 0.6471 (m-80) REVERT: CA 226 SER cc_start: 0.6971 (t) cc_final: 0.6710 (p) REVERT: CA 324 ASP cc_start: 0.6498 (m-30) cc_final: 0.6125 (m-30) REVERT: CA 384 THR cc_start: 0.8218 (m) cc_final: 0.7919 (p) REVERT: CA 633 LYS cc_start: 0.7292 (pttt) cc_final: 0.7059 (tmtt) REVERT: CI 31 GLU cc_start: 0.7034 (tt0) cc_final: 0.6771 (tt0) REVERT: CI 32 ASN cc_start: 0.7074 (m-40) cc_final: 0.6782 (m-40) REVERT: CI 64 ARG cc_start: 0.8150 (mmt180) cc_final: 0.6372 (ptm160) REVERT: CI 108 LYS cc_start: 0.7423 (mtmt) cc_final: 0.7196 (ptmt) REVERT: CB 62 SER cc_start: 0.7846 (p) cc_final: 0.7526 (p) REVERT: CB 66 LYS cc_start: 0.7752 (mttt) cc_final: 0.7301 (mptp) REVERT: CB 157 THR cc_start: 0.4255 (p) cc_final: 0.3922 (p) REVERT: CB 171 ASP cc_start: 0.6729 (t0) cc_final: 0.6458 (t0) REVERT: CB 225 CYS cc_start: 0.6082 (OUTLIER) cc_final: 0.5672 (t) REVERT: CB 231 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.6488 (t-170) REVERT: CB 298 MET cc_start: 0.5518 (mtm) cc_final: 0.4999 (mtm) REVERT: CF 263 GLU cc_start: 0.7274 (tt0) cc_final: 0.6951 (pm20) REVERT: CF 264 LYS cc_start: 0.7746 (mmtt) cc_final: 0.7045 (ttmm) REVERT: CG 22 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7379 (mm-40) REVERT: CG 56 TYR cc_start: 0.8106 (m-80) cc_final: 0.7524 (m-80) REVERT: CK 89 THR cc_start: 0.6622 (p) cc_final: 0.6264 (p) REVERT: CE 87 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6983 (m-80) REVERT: CE 219 ASP cc_start: 0.6360 (m-30) cc_final: 0.6155 (m-30) REVERT: CE 221 ASN cc_start: 0.7043 (t0) cc_final: 0.6645 (m110) REVERT: CJ 66 LYS cc_start: 0.7414 (mtmt) cc_final: 0.6980 (tmtt) REVERT: CD 12 TYR cc_start: 0.6530 (m-80) cc_final: 0.6218 (m-80) outliers start: 14 outliers final: 4 residues processed: 639 average time/residue: 1.0415 time to fit residues: 768.7502 Evaluate side-chains 339 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 332 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 345 VAL Chi-restraints excluded: chain CB residue 215 CYS Chi-restraints excluded: chain CB residue 225 CYS Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CE residue 3 LEU Chi-restraints excluded: chain CE residue 47 PHE Chi-restraints excluded: chain CE residue 87 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 201 ASN CA 284 HIS CA 476 ASN CG 157 GLN CK 88 ASN CE 197 GLN CE 206 GLN CE 302 ASN CJ 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.121269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.109555 restraints weight = 89401.157| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.66 r_work: 0.3378 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 21086 Z= 0.177 Angle : 1.140 76.399 28347 Z= 0.350 Chirality : 0.052 1.863 2945 Planarity : 0.004 0.067 3521 Dihedral : 16.969 143.761 3604 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.83 % Favored : 96.05 % Rotamer: Outliers : 2.05 % Allowed : 14.52 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.17), residues: 2379 helix: 2.04 (0.14), residues: 1282 sheet: -0.88 (0.39), residues: 160 loop : -0.78 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGCJ 49 TYR 0.016 0.001 TYRCB 235 PHE 0.022 0.001 PHECA 65 TRP 0.011 0.001 TRPCK 32 HIS 0.007 0.001 HISCF 260 Details of bonding type rmsd covalent geometry : bond 0.00373 (21071) covalent geometry : angle 0.77869 (28321) hydrogen bonds : bond 0.05273 ( 1080) hydrogen bonds : angle 4.78524 ( 3069) metal coordination : bond 0.02450 ( 10) metal coordination : angle 27.48761 ( 26) Misc. bond : bond 0.00572 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 352 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 97 GLU cc_start: 0.7524 (tt0) cc_final: 0.7322 (tt0) REVERT: CH 116 GLU cc_start: 0.7585 (mp0) cc_final: 0.7094 (mp0) REVERT: CL 21 LEU cc_start: 0.6662 (mt) cc_final: 0.6418 (mt) REVERT: CL 82 LYS cc_start: 0.8473 (tttt) cc_final: 0.8038 (tppt) REVERT: CA 324 ASP cc_start: 0.6584 (m-30) cc_final: 0.6308 (m-30) REVERT: CA 502 THR cc_start: 0.7856 (m) cc_final: 0.7618 (t) REVERT: CI 31 GLU cc_start: 0.7499 (tt0) cc_final: 0.7213 (tt0) REVERT: CI 32 ASN cc_start: 0.7389 (m-40) cc_final: 0.7057 (m-40) REVERT: CI 38 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7599 (mm-30) REVERT: CI 64 ARG cc_start: 0.8180 (mmt180) cc_final: 0.6576 (ptm160) REVERT: CB 62 SER cc_start: 0.7908 (p) cc_final: 0.7696 (p) REVERT: CB 66 LYS cc_start: 0.7877 (mttt) cc_final: 0.7612 (mptp) REVERT: CB 190 THR cc_start: 0.8509 (m) cc_final: 0.8299 (m) REVERT: CB 231 HIS cc_start: 0.7855 (OUTLIER) cc_final: 0.7297 (t-170) REVERT: CB 296 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7625 (mtt) REVERT: CF 137 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7266 (tmm-80) REVERT: CF 241 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7475 (mmm) REVERT: CF 263 GLU cc_start: 0.7473 (tt0) cc_final: 0.7071 (pm20) REVERT: CF 264 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7110 (ttmm) REVERT: CF 270 LYS cc_start: 0.7467 (tppp) cc_final: 0.7122 (mtpt) REVERT: CG 56 TYR cc_start: 0.8616 (m-80) cc_final: 0.8083 (m-80) REVERT: CG 166 TYR cc_start: 0.7305 (t80) cc_final: 0.6073 (t80) REVERT: CK 71 GLN cc_start: 0.7146 (mt0) cc_final: 0.6870 (mt0) REVERT: CK 89 THR cc_start: 0.7219 (p) cc_final: 0.6796 (p) REVERT: CE 160 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7369 (p) REVERT: CJ 100 LYS cc_start: 0.6916 (pttt) cc_final: 0.6658 (ptmm) REVERT: CC 1 MET cc_start: 0.6248 (mtt) cc_final: 0.6018 (mtt) REVERT: CD 12 TYR cc_start: 0.7052 (m-80) cc_final: 0.6723 (m-80) outliers start: 43 outliers final: 15 residues processed: 386 average time/residue: 1.0071 time to fit residues: 457.9449 Evaluate side-chains 304 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 284 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CM residue 17 GLN Chi-restraints excluded: chain CM residue 58 SER Chi-restraints excluded: chain CL residue 4 ASP Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 345 VAL Chi-restraints excluded: chain CB residue 164 ILE Chi-restraints excluded: chain CB residue 208 LEU Chi-restraints excluded: chain CB residue 227 SER Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CB residue 296 MET Chi-restraints excluded: chain CB residue 306 ARG Chi-restraints excluded: chain CF residue 137 ARG Chi-restraints excluded: chain CF residue 241 MET Chi-restraints excluded: chain CG residue 79 ASN Chi-restraints excluded: chain CG residue 99 HIS Chi-restraints excluded: chain CE residue 3 LEU Chi-restraints excluded: chain CE residue 47 PHE Chi-restraints excluded: chain CE residue 146 LEU Chi-restraints excluded: chain CE residue 160 THR Chi-restraints excluded: chain CE residue 194 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 182 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CM 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 498 HIS CA 548 ASN CI 30 GLN CI 104 ASN CF 257 ASN CG 189 ASN CK 21 GLN CE 197 GLN CE 203 ASN CE 290 ASN CE 302 ASN CN 24 ASN ** CD 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108356 restraints weight = 94436.443| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.63 r_work: 0.3392 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.6737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.294 21086 Z= 0.282 Angle : 1.129 85.429 28347 Z= 0.459 Chirality : 0.051 1.121 2945 Planarity : 0.006 0.096 3521 Dihedral : 15.793 138.417 3600 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.05 % Favored : 93.74 % Rotamer: Outliers : 3.76 % Allowed : 14.66 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.16), residues: 2379 helix: 1.08 (0.14), residues: 1285 sheet: -1.42 (0.39), residues: 152 loop : -1.34 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGCE 111 TYR 0.028 0.002 TYRCK 7 PHE 0.067 0.003 PHECA 353 TRP 0.024 0.003 TRPCB 229 HIS 0.010 0.002 HISCJ 82 Details of bonding type rmsd covalent geometry : bond 0.00621 (21071) covalent geometry : angle 0.97643 (28321) hydrogen bonds : bond 0.05717 ( 1080) hydrogen bonds : angle 4.96425 ( 3069) metal coordination : bond 0.03507 ( 10) metal coordination : angle 18.76077 ( 26) Misc. bond : bond 0.13141 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 310 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 97 GLU cc_start: 0.8397 (tt0) cc_final: 0.8187 (tt0) REVERT: CH 107 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6848 (mt) REVERT: CH 118 LYS cc_start: 0.8376 (mttt) cc_final: 0.8089 (mtmt) REVERT: CM 17 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8742 (mt0) REVERT: CM 58 SER cc_start: 0.7900 (OUTLIER) cc_final: 0.7520 (p) REVERT: CL 60 GLN cc_start: 0.7935 (mt0) cc_final: 0.7735 (mt0) REVERT: CA 104 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7145 (m-30) REVERT: CA 324 ASP cc_start: 0.7621 (m-30) cc_final: 0.7385 (m-30) REVERT: CA 486 ASP cc_start: 0.8156 (t70) cc_final: 0.7751 (t0) REVERT: CA 578 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8057 (ttm170) REVERT: CA 633 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7697 (tmtm) REVERT: CI 64 ARG cc_start: 0.8300 (mmt180) cc_final: 0.7071 (ptm160) REVERT: CB 233 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8366 (p0) REVERT: CB 277 MET cc_start: 0.8069 (tpt) cc_final: 0.7612 (tpt) REVERT: CF 89 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8114 (tm-30) REVERT: CF 127 ILE cc_start: 0.9007 (pp) cc_final: 0.8640 (mt) REVERT: CF 201 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.6169 (m-80) REVERT: CG 30 MET cc_start: 0.8849 (ttp) cc_final: 0.8251 (ttp) REVERT: CG 169 HIS cc_start: 0.8815 (OUTLIER) cc_final: 0.8479 (t-170) REVERT: CK 41 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8656 (t) REVERT: CK 54 LYS cc_start: 0.9048 (mttm) cc_final: 0.8786 (mtmt) REVERT: CK 91 LYS cc_start: 0.7849 (pmtt) cc_final: 0.7649 (pmtt) REVERT: CE 25 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7980 (mtpp) REVERT: CJ 1 MET cc_start: 0.7325 (ptm) cc_final: 0.7040 (ptp) REVERT: CJ 89 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7322 (ttpp) REVERT: CJ 100 LYS cc_start: 0.7474 (pttt) cc_final: 0.7192 (ptmm) outliers start: 79 outliers final: 25 residues processed: 372 average time/residue: 1.2230 time to fit residues: 524.8153 Evaluate side-chains 258 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 107 ILE Chi-restraints excluded: chain CH residue 127 VAL Chi-restraints excluded: chain CH residue 179 SER Chi-restraints excluded: chain CM residue 17 GLN Chi-restraints excluded: chain CM residue 20 SER Chi-restraints excluded: chain CM residue 58 SER Chi-restraints excluded: chain CL residue 73 THR Chi-restraints excluded: chain CA residue 65 PHE Chi-restraints excluded: chain CA residue 104 ASP Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 434 SER Chi-restraints excluded: chain CA residue 578 ARG Chi-restraints excluded: chain CA residue 620 HIS Chi-restraints excluded: chain CB residue 112 LEU Chi-restraints excluded: chain CB residue 161 HIS Chi-restraints excluded: chain CB residue 164 ILE Chi-restraints excluded: chain CB residue 208 LEU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CB residue 233 ASP Chi-restraints excluded: chain CF residue 201 PHE Chi-restraints excluded: chain CG residue 99 HIS Chi-restraints excluded: chain CG residue 146 LEU Chi-restraints excluded: chain CG residue 169 HIS Chi-restraints excluded: chain CG residue 174 SER Chi-restraints excluded: chain CG residue 186 LYS Chi-restraints excluded: chain CK residue 22 LEU Chi-restraints excluded: chain CK residue 41 VAL Chi-restraints excluded: chain CE residue 11 LYS Chi-restraints excluded: chain CE residue 25 LYS Chi-restraints excluded: chain CE residue 47 PHE Chi-restraints excluded: chain CE residue 104 SER Chi-restraints excluded: chain CE residue 221 ASN Chi-restraints excluded: chain CE residue 231 ILE Chi-restraints excluded: chain CJ residue 103 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 113 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CM 64 ASN CA 358 HIS CA 397 ASN CA 593 ASN CI 104 ASN CB 133 ASN CB 196 ASN CE 53 GLN CE 120 ASN CE 197 GLN CJ 6 GLN ** CD 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.117957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.106331 restraints weight = 95054.139| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.68 r_work: 0.3392 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.7899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 21086 Z= 0.224 Angle : 0.948 75.963 28347 Z= 0.365 Chirality : 0.052 1.800 2945 Planarity : 0.004 0.052 3521 Dihedral : 14.919 140.036 3597 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.67 % Favored : 95.17 % Rotamer: Outliers : 2.95 % Allowed : 17.75 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.17), residues: 2379 helix: 1.53 (0.14), residues: 1278 sheet: -1.21 (0.39), residues: 162 loop : -1.37 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGCE 111 TYR 0.018 0.002 TYRCK 7 PHE 0.028 0.002 PHECA 353 TRP 0.013 0.001 TRPCA 119 HIS 0.008 0.001 HISCE 78 Details of bonding type rmsd covalent geometry : bond 0.00506 (21071) covalent geometry : angle 0.79935 (28321) hydrogen bonds : bond 0.05031 ( 1080) hydrogen bonds : angle 4.65248 ( 3069) metal coordination : bond 0.02628 ( 10) metal coordination : angle 16.83810 ( 26) Misc. bond : bond 0.01536 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 241 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 101 GLU cc_start: 0.7702 (pp20) cc_final: 0.7162 (mt-10) REVERT: CH 118 LYS cc_start: 0.8574 (mttt) cc_final: 0.8201 (mtmt) REVERT: CM 4 LEU cc_start: 0.9151 (mm) cc_final: 0.8916 (mp) REVERT: CM 17 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.9027 (mt0) REVERT: CM 58 SER cc_start: 0.8114 (OUTLIER) cc_final: 0.7892 (p) REVERT: CL 21 LEU cc_start: 0.8830 (mt) cc_final: 0.8585 (mp) REVERT: CL 38 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8156 (mt-10) REVERT: CL 40 ASP cc_start: 0.8309 (m-30) cc_final: 0.8020 (m-30) REVERT: CL 82 LYS cc_start: 0.8718 (tttt) cc_final: 0.8365 (tppt) REVERT: CA 104 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: CA 227 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7289 (mpp) REVERT: CA 324 ASP cc_start: 0.8069 (m-30) cc_final: 0.7858 (m-30) REVERT: CA 401 VAL cc_start: 0.8180 (t) cc_final: 0.7942 (m) REVERT: CA 446 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8631 (mp) REVERT: CA 486 ASP cc_start: 0.8339 (t70) cc_final: 0.8107 (t70) REVERT: CA 633 LYS cc_start: 0.8140 (tmtt) cc_final: 0.7817 (tmtm) REVERT: CI 7 MET cc_start: 0.8724 (mmt) cc_final: 0.8388 (mmt) REVERT: CI 31 GLU cc_start: 0.8065 (tt0) cc_final: 0.7671 (mm-30) REVERT: CI 32 ASN cc_start: 0.8366 (m-40) cc_final: 0.8156 (m-40) REVERT: CI 64 ARG cc_start: 0.8528 (mmt180) cc_final: 0.7112 (ptm160) REVERT: CB 257 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7521 (mm-40) REVERT: CB 277 MET cc_start: 0.8193 (tpt) cc_final: 0.7758 (tpt) REVERT: CF 89 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8154 (tm-30) REVERT: CF 127 ILE cc_start: 0.8954 (pp) cc_final: 0.8711 (mt) REVERT: CF 192 MET cc_start: 0.8594 (mtp) cc_final: 0.8367 (mtp) REVERT: CF 201 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.6413 (m-80) REVERT: CF 242 ASP cc_start: 0.8302 (t70) cc_final: 0.8078 (t0) REVERT: CG 180 ASN cc_start: 0.8493 (m110) cc_final: 0.8128 (m110) REVERT: CK 54 LYS cc_start: 0.8943 (mttm) cc_final: 0.8712 (mtmt) REVERT: CE 25 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8230 (mtpp) REVERT: CE 130 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8046 (mm) REVERT: CE 160 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7927 (p) REVERT: CJ 10 GLU cc_start: 0.7023 (tp30) cc_final: 0.6779 (tp30) REVERT: CJ 89 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7494 (ttpp) REVERT: CJ 100 LYS cc_start: 0.7715 (pttt) cc_final: 0.7449 (ptmm) outliers start: 62 outliers final: 19 residues processed: 286 average time/residue: 1.2435 time to fit residues: 411.2379 Evaluate side-chains 234 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 179 SER Chi-restraints excluded: chain CM residue 17 GLN Chi-restraints excluded: chain CM residue 58 SER Chi-restraints excluded: chain CM residue 60 SER Chi-restraints excluded: chain CL residue 4 ASP Chi-restraints excluded: chain CL residue 73 THR Chi-restraints excluded: chain CA residue 104 ASP Chi-restraints excluded: chain CA residue 227 MET Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 446 LEU Chi-restraints excluded: chain CA residue 611 GLU Chi-restraints excluded: chain CA residue 620 HIS Chi-restraints excluded: chain CB residue 157 THR Chi-restraints excluded: chain CB residue 161 HIS Chi-restraints excluded: chain CB residue 208 LEU Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CF residue 201 PHE Chi-restraints excluded: chain CG residue 174 SER Chi-restraints excluded: chain CK residue 1 MET Chi-restraints excluded: chain CK residue 4 ASP Chi-restraints excluded: chain CK residue 22 LEU Chi-restraints excluded: chain CK residue 64 THR Chi-restraints excluded: chain CE residue 7 SER Chi-restraints excluded: chain CE residue 25 LYS Chi-restraints excluded: chain CE residue 130 LEU Chi-restraints excluded: chain CE residue 146 LEU Chi-restraints excluded: chain CE residue 160 THR Chi-restraints excluded: chain CE residue 231 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 51 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CM 64 ASN CL 70 GLN CA 397 ASN ** CK 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 197 GLN ** CD 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.118442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.106911 restraints weight = 94768.430| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.67 r_work: 0.3402 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.8298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 21086 Z= 0.152 Angle : 0.886 80.237 28347 Z= 0.329 Chirality : 0.047 1.562 2945 Planarity : 0.004 0.053 3521 Dihedral : 14.076 143.734 3595 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 1.95 % Allowed : 19.47 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.17), residues: 2379 helix: 1.85 (0.14), residues: 1279 sheet: -1.25 (0.39), residues: 164 loop : -1.24 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGCL 49 TYR 0.016 0.001 TYRCG 109 PHE 0.032 0.001 PHECB 280 TRP 0.012 0.001 TRPCK 32 HIS 0.005 0.001 HISCH 105 Details of bonding type rmsd covalent geometry : bond 0.00330 (21071) covalent geometry : angle 0.74771 (28321) hydrogen bonds : bond 0.04570 ( 1080) hydrogen bonds : angle 4.43748 ( 3069) metal coordination : bond 0.01493 ( 10) metal coordination : angle 15.68477 ( 26) Misc. bond : bond 0.04329 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 118 LYS cc_start: 0.8576 (mttt) cc_final: 0.8183 (mtmt) REVERT: CM 4 LEU cc_start: 0.9222 (mm) cc_final: 0.8988 (mp) REVERT: CM 17 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8732 (mt0) REVERT: CL 21 LEU cc_start: 0.8872 (mt) cc_final: 0.8602 (mp) REVERT: CL 38 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7969 (mt-10) REVERT: CL 40 ASP cc_start: 0.8500 (m-30) cc_final: 0.8249 (m-30) REVERT: CL 60 GLN cc_start: 0.8210 (mt0) cc_final: 0.8004 (mt0) REVERT: CL 82 LYS cc_start: 0.8756 (tttt) cc_final: 0.8378 (tppt) REVERT: CA 104 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: CA 227 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7197 (mpp) REVERT: CA 324 ASP cc_start: 0.8082 (m-30) cc_final: 0.7860 (m-30) REVERT: CA 325 LEU cc_start: 0.7513 (tp) cc_final: 0.7310 (tp) REVERT: CA 620 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6800 (p-80) REVERT: CA 633 LYS cc_start: 0.8190 (tmtt) cc_final: 0.7903 (tmtm) REVERT: CI 7 MET cc_start: 0.8739 (mmt) cc_final: 0.8429 (mmt) REVERT: CI 31 GLU cc_start: 0.8060 (tt0) cc_final: 0.7653 (mp0) REVERT: CI 32 ASN cc_start: 0.8404 (m-40) cc_final: 0.8147 (m-40) REVERT: CI 64 ARG cc_start: 0.8542 (mmt180) cc_final: 0.7118 (ptm160) REVERT: CI 84 LYS cc_start: 0.7082 (tttt) cc_final: 0.6847 (mttt) REVERT: CB 38 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8074 (mm-30) REVERT: CB 257 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7533 (mm-40) REVERT: CB 277 MET cc_start: 0.8196 (tpt) cc_final: 0.7827 (tpt) REVERT: CF 89 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8183 (tm-30) REVERT: CF 192 MET cc_start: 0.8581 (mtp) cc_final: 0.8318 (mtp) REVERT: CF 242 ASP cc_start: 0.8267 (t70) cc_final: 0.8047 (t0) REVERT: CF 292 GLN cc_start: 0.7821 (mm110) cc_final: 0.7601 (mm-40) REVERT: CG 36 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7116 (tt0) REVERT: CG 111 GLU cc_start: 0.8347 (tt0) cc_final: 0.8024 (tt0) REVERT: CG 180 ASN cc_start: 0.8595 (m110) cc_final: 0.8276 (m110) REVERT: CK 47 TYR cc_start: 0.8809 (t80) cc_final: 0.8512 (t80) REVERT: CK 54 LYS cc_start: 0.8941 (mttm) cc_final: 0.8703 (mtmt) REVERT: CJ 10 GLU cc_start: 0.7135 (tp30) cc_final: 0.6902 (tp30) REVERT: CJ 100 LYS cc_start: 0.7770 (pttt) cc_final: 0.7507 (ptmm) outliers start: 41 outliers final: 20 residues processed: 243 average time/residue: 1.3201 time to fit residues: 367.8664 Evaluate side-chains 219 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 179 SER Chi-restraints excluded: chain CM residue 17 GLN Chi-restraints excluded: chain CL residue 88 THR Chi-restraints excluded: chain CA residue 104 ASP Chi-restraints excluded: chain CA residue 195 SER Chi-restraints excluded: chain CA residue 227 MET Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 434 SER Chi-restraints excluded: chain CA residue 602 ILE Chi-restraints excluded: chain CA residue 611 GLU Chi-restraints excluded: chain CA residue 620 HIS Chi-restraints excluded: chain CB residue 157 THR Chi-restraints excluded: chain CB residue 161 HIS Chi-restraints excluded: chain CB residue 171 ASP Chi-restraints excluded: chain CB residue 208 LEU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CF residue 185 LEU Chi-restraints excluded: chain CG residue 36 GLU Chi-restraints excluded: chain CG residue 174 SER Chi-restraints excluded: chain CG residue 186 LYS Chi-restraints excluded: chain CK residue 4 ASP Chi-restraints excluded: chain CK residue 22 LEU Chi-restraints excluded: chain CK residue 64 THR Chi-restraints excluded: chain CE residue 231 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 183 optimal weight: 3.9990 chunk 151 optimal weight: 0.3980 chunk 208 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 188 optimal weight: 0.0770 chunk 213 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CB 196 ASN CG 145 GLN CE 197 GLN ** CD 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.118934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.107426 restraints weight = 94444.672| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.67 r_work: 0.3411 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.8564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 21086 Z= 0.134 Angle : 0.865 80.182 28347 Z= 0.316 Chirality : 0.047 1.589 2945 Planarity : 0.003 0.053 3521 Dihedral : 13.358 147.512 3595 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.37 % Favored : 95.46 % Rotamer: Outliers : 1.67 % Allowed : 19.51 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.17), residues: 2379 helix: 2.03 (0.14), residues: 1286 sheet: -1.12 (0.40), residues: 164 loop : -1.15 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGCG 25 TYR 0.016 0.001 TYRCG 109 PHE 0.021 0.001 PHECA 65 TRP 0.011 0.001 TRPCK 32 HIS 0.005 0.001 HISCH 105 Details of bonding type rmsd covalent geometry : bond 0.00289 (21071) covalent geometry : angle 0.73022 (28321) hydrogen bonds : bond 0.04272 ( 1080) hydrogen bonds : angle 4.30148 ( 3069) metal coordination : bond 0.01222 ( 10) metal coordination : angle 15.35667 ( 26) Misc. bond : bond 0.03698 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 118 LYS cc_start: 0.8685 (mttt) cc_final: 0.8205 (mtmt) REVERT: CM 17 GLN cc_start: 0.9377 (OUTLIER) cc_final: 0.8794 (mt0) REVERT: CL 18 ASP cc_start: 0.8600 (t70) cc_final: 0.8333 (t70) REVERT: CL 21 LEU cc_start: 0.8849 (mt) cc_final: 0.8563 (mp) REVERT: CL 38 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7992 (mt-10) REVERT: CL 82 LYS cc_start: 0.8752 (tttt) cc_final: 0.8351 (tppt) REVERT: CA 104 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7225 (m-30) REVERT: CA 227 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7184 (mpp) REVERT: CA 324 ASP cc_start: 0.8157 (m-30) cc_final: 0.7943 (m-30) REVERT: CA 325 LEU cc_start: 0.7485 (tp) cc_final: 0.7285 (tp) REVERT: CA 446 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8632 (mp) REVERT: CA 620 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.6734 (p90) REVERT: CA 624 SER cc_start: 0.8537 (m) cc_final: 0.8153 (p) REVERT: CA 633 LYS cc_start: 0.8142 (tmtt) cc_final: 0.7871 (tmtm) REVERT: CI 7 MET cc_start: 0.8763 (mmt) cc_final: 0.8474 (mmt) REVERT: CI 31 GLU cc_start: 0.8058 (tt0) cc_final: 0.7840 (mp0) REVERT: CI 64 ARG cc_start: 0.8540 (mmt180) cc_final: 0.7132 (ptm160) REVERT: CI 84 LYS cc_start: 0.7317 (tttt) cc_final: 0.6779 (mttt) REVERT: CB 38 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8102 (mm-30) REVERT: CB 257 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7512 (mm-40) REVERT: CB 277 MET cc_start: 0.8205 (tpt) cc_final: 0.7896 (tpt) REVERT: CF 89 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8215 (tm-30) REVERT: CF 192 MET cc_start: 0.8552 (mtp) cc_final: 0.8330 (mtp) REVERT: CG 111 GLU cc_start: 0.8426 (tt0) cc_final: 0.8033 (tt0) REVERT: CG 180 ASN cc_start: 0.8638 (m110) cc_final: 0.8346 (m110) REVERT: CK 47 TYR cc_start: 0.8829 (t80) cc_final: 0.8499 (t80) REVERT: CK 54 LYS cc_start: 0.8852 (mttm) cc_final: 0.8592 (mtmt) REVERT: CE 130 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8032 (mm) REVERT: CJ 10 GLU cc_start: 0.7185 (tp30) cc_final: 0.6946 (tp30) REVERT: CJ 100 LYS cc_start: 0.7852 (pttt) cc_final: 0.7539 (ptmm) outliers start: 35 outliers final: 16 residues processed: 239 average time/residue: 1.3139 time to fit residues: 363.1068 Evaluate side-chains 214 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 179 SER Chi-restraints excluded: chain CM residue 17 GLN Chi-restraints excluded: chain CL residue 88 THR Chi-restraints excluded: chain CA residue 104 ASP Chi-restraints excluded: chain CA residue 227 MET Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 279 GLU Chi-restraints excluded: chain CA residue 371 ILE Chi-restraints excluded: chain CA residue 434 SER Chi-restraints excluded: chain CA residue 446 LEU Chi-restraints excluded: chain CA residue 602 ILE Chi-restraints excluded: chain CA residue 620 HIS Chi-restraints excluded: chain CB residue 161 HIS Chi-restraints excluded: chain CB residue 208 LEU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CG residue 160 VAL Chi-restraints excluded: chain CG residue 169 HIS Chi-restraints excluded: chain CK residue 22 LEU Chi-restraints excluded: chain CE residue 130 LEU Chi-restraints excluded: chain CE residue 146 LEU Chi-restraints excluded: chain CE residue 231 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 156 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 160 GLN CM 64 ASN CE 197 GLN ** CD 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.118876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.107164 restraints weight = 94666.816| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.69 r_work: 0.3396 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.8859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 21086 Z= 0.145 Angle : 0.869 80.698 28347 Z= 0.319 Chirality : 0.047 1.567 2945 Planarity : 0.003 0.053 3521 Dihedral : 13.110 157.861 3595 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 1.67 % Allowed : 19.51 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.17), residues: 2379 helix: 2.09 (0.14), residues: 1286 sheet: -1.18 (0.39), residues: 166 loop : -1.13 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGCL 16 TYR 0.017 0.001 TYRCG 109 PHE 0.020 0.001 PHECA 65 TRP 0.011 0.001 TRPCK 32 HIS 0.006 0.001 HISCE 21 Details of bonding type rmsd covalent geometry : bond 0.00320 (21071) covalent geometry : angle 0.73530 (28321) hydrogen bonds : bond 0.04291 ( 1080) hydrogen bonds : angle 4.27506 ( 3069) metal coordination : bond 0.01238 ( 10) metal coordination : angle 15.33660 ( 26) Misc. bond : bond 0.04188 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 118 LYS cc_start: 0.8731 (mttt) cc_final: 0.8239 (mtmt) REVERT: CM 17 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.8817 (mt0) REVERT: CL 18 ASP cc_start: 0.8620 (t0) cc_final: 0.8358 (t70) REVERT: CL 21 LEU cc_start: 0.8903 (mt) cc_final: 0.8634 (mp) REVERT: CL 38 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7994 (mt-10) REVERT: CL 82 LYS cc_start: 0.8794 (tttt) cc_final: 0.8335 (tppt) REVERT: CA 227 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7160 (mpp) REVERT: CA 324 ASP cc_start: 0.8264 (m-30) cc_final: 0.8058 (m-30) REVERT: CA 325 LEU cc_start: 0.7553 (tp) cc_final: 0.7336 (tp) REVERT: CA 446 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8675 (mp) REVERT: CA 620 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.6748 (p90) REVERT: CA 624 SER cc_start: 0.8580 (m) cc_final: 0.8213 (p) REVERT: CA 633 LYS cc_start: 0.8164 (tmtt) cc_final: 0.7897 (tmtm) REVERT: CI 7 MET cc_start: 0.8822 (mmt) cc_final: 0.8542 (mmt) REVERT: CI 64 ARG cc_start: 0.8569 (mmt180) cc_final: 0.7179 (ptm160) REVERT: CI 84 LYS cc_start: 0.7353 (tttt) cc_final: 0.6768 (mttt) REVERT: CI 111 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7741 (mp0) REVERT: CB 257 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7548 (mm-40) REVERT: CB 277 MET cc_start: 0.8214 (tpt) cc_final: 0.7933 (tpt) REVERT: CF 89 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8250 (tm-30) REVERT: CG 180 ASN cc_start: 0.8683 (m110) cc_final: 0.8416 (m110) REVERT: CK 9 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7330 (mt0) REVERT: CK 47 TYR cc_start: 0.8890 (t80) cc_final: 0.8583 (t80) REVERT: CK 54 LYS cc_start: 0.8885 (mttm) cc_final: 0.8591 (mtmt) REVERT: CE 130 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8036 (mm) REVERT: CJ 10 GLU cc_start: 0.7470 (tp30) cc_final: 0.7232 (tp30) REVERT: CJ 100 LYS cc_start: 0.7847 (pttt) cc_final: 0.7619 (ptmm) outliers start: 35 outliers final: 22 residues processed: 234 average time/residue: 1.3286 time to fit residues: 358.8086 Evaluate side-chains 220 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 179 SER Chi-restraints excluded: chain CM residue 17 GLN Chi-restraints excluded: chain CL residue 88 THR Chi-restraints excluded: chain CA residue 160 PHE Chi-restraints excluded: chain CA residue 227 MET Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 279 GLU Chi-restraints excluded: chain CA residue 371 ILE Chi-restraints excluded: chain CA residue 434 SER Chi-restraints excluded: chain CA residue 446 LEU Chi-restraints excluded: chain CA residue 602 ILE Chi-restraints excluded: chain CA residue 620 HIS Chi-restraints excluded: chain CB residue 157 THR Chi-restraints excluded: chain CB residue 161 HIS Chi-restraints excluded: chain CB residue 171 ASP Chi-restraints excluded: chain CB residue 208 LEU Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CF residue 185 LEU Chi-restraints excluded: chain CG residue 160 VAL Chi-restraints excluded: chain CG residue 169 HIS Chi-restraints excluded: chain CG residue 186 LYS Chi-restraints excluded: chain CK residue 4 ASP Chi-restraints excluded: chain CK residue 22 LEU Chi-restraints excluded: chain CE residue 130 LEU Chi-restraints excluded: chain CE residue 231 ILE Chi-restraints excluded: chain CE residue 253 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 212 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 105 HIS CM 64 ASN CB 196 ASN CF 182 ASN CG 145 GLN CE 197 GLN CD 23 ASN ** CD 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.116045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104518 restraints weight = 94940.443| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.66 r_work: 0.3369 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.9288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 21086 Z= 0.183 Angle : 0.893 81.103 28347 Z= 0.333 Chirality : 0.048 1.531 2945 Planarity : 0.004 0.053 3521 Dihedral : 13.405 165.165 3595 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.83 % Favored : 95.00 % Rotamer: Outliers : 1.76 % Allowed : 19.70 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.17), residues: 2379 helix: 1.98 (0.14), residues: 1280 sheet: -1.17 (0.39), residues: 166 loop : -1.16 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGCA 440 TYR 0.015 0.001 TYRCG 109 PHE 0.023 0.001 PHECA 65 TRP 0.012 0.001 TRPCK 32 HIS 0.007 0.001 HISCG 99 Details of bonding type rmsd covalent geometry : bond 0.00411 (21071) covalent geometry : angle 0.75726 (28321) hydrogen bonds : bond 0.04507 ( 1080) hydrogen bonds : angle 4.35512 ( 3069) metal coordination : bond 0.01688 ( 10) metal coordination : angle 15.62006 ( 26) Misc. bond : bond 0.05225 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 107 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7636 (mt) REVERT: CH 118 LYS cc_start: 0.8770 (mttt) cc_final: 0.8279 (mtmt) REVERT: CM 17 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.8893 (mt0) REVERT: CL 18 ASP cc_start: 0.8647 (t0) cc_final: 0.8439 (t70) REVERT: CL 38 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8219 (mt-10) REVERT: CL 82 LYS cc_start: 0.8808 (tttt) cc_final: 0.8272 (tppt) REVERT: CA 227 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7232 (mpp) REVERT: CA 325 LEU cc_start: 0.7663 (tp) cc_final: 0.7452 (tp) REVERT: CA 446 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8726 (mp) REVERT: CA 508 MET cc_start: 0.9041 (mmm) cc_final: 0.8753 (mmm) REVERT: CA 620 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.6888 (p90) REVERT: CA 624 SER cc_start: 0.8674 (m) cc_final: 0.8339 (p) REVERT: CI 7 MET cc_start: 0.8830 (mmt) cc_final: 0.8500 (mmt) REVERT: CI 64 ARG cc_start: 0.8610 (mmt180) cc_final: 0.7260 (ptm160) REVERT: CI 84 LYS cc_start: 0.7456 (tttt) cc_final: 0.6756 (mttt) REVERT: CB 152 LYS cc_start: 0.8720 (mtpm) cc_final: 0.8345 (mttt) REVERT: CB 257 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7745 (mm-40) REVERT: CB 277 MET cc_start: 0.8230 (tpt) cc_final: 0.7916 (tpt) REVERT: CF 89 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8264 (tm-30) REVERT: CF 204 LEU cc_start: 0.8314 (tp) cc_final: 0.7898 (mp) REVERT: CG 162 GLU cc_start: 0.8392 (tt0) cc_final: 0.8167 (pt0) REVERT: CG 180 ASN cc_start: 0.8691 (m110) cc_final: 0.8452 (m110) REVERT: CK 9 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7455 (mt0) REVERT: CK 47 TYR cc_start: 0.8944 (t80) cc_final: 0.8637 (t80) REVERT: CK 54 LYS cc_start: 0.8833 (mttm) cc_final: 0.8501 (mtmt) REVERT: CE 25 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8404 (mtpp) REVERT: CE 130 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8229 (mm) REVERT: CJ 10 GLU cc_start: 0.7534 (tp30) cc_final: 0.7245 (tp30) REVERT: CC 58 ARG cc_start: 0.6665 (mpt180) cc_final: 0.6445 (mtp85) outliers start: 37 outliers final: 21 residues processed: 232 average time/residue: 1.3712 time to fit residues: 363.2642 Evaluate side-chains 217 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 107 ILE Chi-restraints excluded: chain CH residue 179 SER Chi-restraints excluded: chain CM residue 17 GLN Chi-restraints excluded: chain CM residue 60 SER Chi-restraints excluded: chain CL residue 88 THR Chi-restraints excluded: chain CA residue 160 PHE Chi-restraints excluded: chain CA residue 227 MET Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 279 GLU Chi-restraints excluded: chain CA residue 434 SER Chi-restraints excluded: chain CA residue 446 LEU Chi-restraints excluded: chain CA residue 602 ILE Chi-restraints excluded: chain CA residue 620 HIS Chi-restraints excluded: chain CI residue 113 ASP Chi-restraints excluded: chain CB residue 157 THR Chi-restraints excluded: chain CB residue 161 HIS Chi-restraints excluded: chain CB residue 171 ASP Chi-restraints excluded: chain CB residue 208 LEU Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CG residue 160 VAL Chi-restraints excluded: chain CG residue 174 SER Chi-restraints excluded: chain CG residue 186 LYS Chi-restraints excluded: chain CK residue 4 ASP Chi-restraints excluded: chain CK residue 20 VAL Chi-restraints excluded: chain CK residue 22 LEU Chi-restraints excluded: chain CE residue 25 LYS Chi-restraints excluded: chain CE residue 130 LEU Chi-restraints excluded: chain CE residue 231 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 99 optimal weight: 0.0020 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 160 GLN CA 358 HIS CE 197 GLN ** CD 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.117043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.105475 restraints weight = 95009.671| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.67 r_work: 0.3377 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.9508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 21086 Z= 0.151 Angle : 0.874 80.829 28347 Z= 0.323 Chirality : 0.047 1.542 2945 Planarity : 0.003 0.053 3521 Dihedral : 13.161 164.903 3595 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.75 % Favored : 95.08 % Rotamer: Outliers : 1.24 % Allowed : 20.66 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.17), residues: 2379 helix: 2.06 (0.14), residues: 1280 sheet: -1.16 (0.39), residues: 166 loop : -1.10 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGCJ 49 TYR 0.016 0.001 TYRCG 109 PHE 0.020 0.001 PHECA 65 TRP 0.012 0.001 TRPCK 32 HIS 0.006 0.001 HISCE 21 Details of bonding type rmsd covalent geometry : bond 0.00335 (21071) covalent geometry : angle 0.74244 (28321) hydrogen bonds : bond 0.04318 ( 1080) hydrogen bonds : angle 4.28500 ( 3069) metal coordination : bond 0.01165 ( 10) metal coordination : angle 15.26463 ( 26) Misc. bond : bond 0.04209 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 118 LYS cc_start: 0.8749 (mttt) cc_final: 0.8240 (mtmt) REVERT: CM 17 GLN cc_start: 0.9431 (OUTLIER) cc_final: 0.8893 (mt0) REVERT: CM 60 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8280 (m) REVERT: CL 18 ASP cc_start: 0.8632 (t0) cc_final: 0.8430 (t70) REVERT: CL 52 LYS cc_start: 0.8759 (mtpp) cc_final: 0.7657 (mmpt) REVERT: CL 82 LYS cc_start: 0.8820 (tttt) cc_final: 0.8278 (tppt) REVERT: CA 227 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7185 (mpp) REVERT: CA 325 LEU cc_start: 0.7654 (tp) cc_final: 0.7441 (tp) REVERT: CA 446 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8659 (mp) REVERT: CA 620 HIS cc_start: 0.7571 (OUTLIER) cc_final: 0.7069 (p-80) REVERT: CA 624 SER cc_start: 0.8679 (m) cc_final: 0.8337 (p) REVERT: CI 4 ASP cc_start: 0.8614 (m-30) cc_final: 0.8393 (m-30) REVERT: CI 7 MET cc_start: 0.8805 (mmt) cc_final: 0.8490 (mmt) REVERT: CI 64 ARG cc_start: 0.8600 (mmt180) cc_final: 0.7267 (ptm160) REVERT: CI 84 LYS cc_start: 0.7476 (tttt) cc_final: 0.6738 (mttt) REVERT: CB 152 LYS cc_start: 0.8713 (mtpm) cc_final: 0.8316 (mttt) REVERT: CB 257 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7785 (mm-40) REVERT: CB 277 MET cc_start: 0.8240 (tpt) cc_final: 0.7935 (tpt) REVERT: CF 89 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8229 (tm-30) REVERT: CF 201 PHE cc_start: 0.7591 (t80) cc_final: 0.7354 (t80) REVERT: CF 204 LEU cc_start: 0.8272 (tp) cc_final: 0.7863 (mp) REVERT: CG 180 ASN cc_start: 0.8703 (m110) cc_final: 0.8477 (m110) REVERT: CK 9 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7552 (mt0) REVERT: CK 47 TYR cc_start: 0.8932 (t80) cc_final: 0.8617 (t80) REVERT: CK 54 LYS cc_start: 0.8846 (mttm) cc_final: 0.8467 (mtmt) REVERT: CE 130 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8232 (mm) outliers start: 26 outliers final: 17 residues processed: 225 average time/residue: 1.1797 time to fit residues: 305.3194 Evaluate side-chains 212 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CM residue 17 GLN Chi-restraints excluded: chain CM residue 60 SER Chi-restraints excluded: chain CL residue 88 THR Chi-restraints excluded: chain CA residue 160 PHE Chi-restraints excluded: chain CA residue 195 SER Chi-restraints excluded: chain CA residue 227 MET Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 279 GLU Chi-restraints excluded: chain CA residue 434 SER Chi-restraints excluded: chain CA residue 446 LEU Chi-restraints excluded: chain CA residue 602 ILE Chi-restraints excluded: chain CA residue 620 HIS Chi-restraints excluded: chain CI residue 113 ASP Chi-restraints excluded: chain CB residue 157 THR Chi-restraints excluded: chain CB residue 161 HIS Chi-restraints excluded: chain CB residue 171 ASP Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CG residue 160 VAL Chi-restraints excluded: chain CG residue 174 SER Chi-restraints excluded: chain CG residue 186 LYS Chi-restraints excluded: chain CK residue 22 LEU Chi-restraints excluded: chain CE residue 130 LEU Chi-restraints excluded: chain CE residue 231 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 178 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 99 optimal weight: 0.0970 chunk 142 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 358 HIS ** CD 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.118042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106492 restraints weight = 94146.785| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.66 r_work: 0.3394 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.9645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 21086 Z= 0.128 Angle : 0.867 80.798 28347 Z= 0.318 Chirality : 0.047 1.547 2945 Planarity : 0.004 0.110 3521 Dihedral : 12.841 167.526 3595 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.38 % Rotamer: Outliers : 1.09 % Allowed : 21.23 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.17), residues: 2379 helix: 2.17 (0.14), residues: 1275 sheet: -1.13 (0.39), residues: 168 loop : -1.01 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGCB 123 TYR 0.015 0.001 TYRCG 109 PHE 0.019 0.001 PHECA 65 TRP 0.011 0.001 TRPCK 32 HIS 0.005 0.001 HISCE 21 Details of bonding type rmsd covalent geometry : bond 0.00281 (21071) covalent geometry : angle 0.73617 (28321) hydrogen bonds : bond 0.04124 ( 1080) hydrogen bonds : angle 4.20159 ( 3069) metal coordination : bond 0.00938 ( 10) metal coordination : angle 15.15390 ( 26) Misc. bond : bond 0.03885 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 107 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7579 (mt) REVERT: CH 118 LYS cc_start: 0.8796 (mttt) cc_final: 0.8229 (mtmt) REVERT: CM 60 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8346 (m) REVERT: CL 82 LYS cc_start: 0.8826 (tttt) cc_final: 0.8287 (tppt) REVERT: CA 325 LEU cc_start: 0.7622 (tp) cc_final: 0.7405 (tp) REVERT: CA 446 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8646 (mp) REVERT: CA 620 HIS cc_start: 0.7550 (OUTLIER) cc_final: 0.6898 (p90) REVERT: CA 624 SER cc_start: 0.8718 (m) cc_final: 0.8379 (p) REVERT: CI 7 MET cc_start: 0.8810 (mmt) cc_final: 0.8499 (mmt) REVERT: CI 64 ARG cc_start: 0.8600 (mmt180) cc_final: 0.7258 (ptm160) REVERT: CI 84 LYS cc_start: 0.7465 (tttt) cc_final: 0.6708 (mttt) REVERT: CI 111 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7996 (mt-10) REVERT: CB 139 THR cc_start: 0.8857 (t) cc_final: 0.8606 (p) REVERT: CB 152 LYS cc_start: 0.8707 (mtpm) cc_final: 0.8307 (mttt) REVERT: CB 257 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7684 (mm-40) REVERT: CB 277 MET cc_start: 0.8215 (tpt) cc_final: 0.7919 (tpt) REVERT: CF 89 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8232 (tm-30) REVERT: CF 201 PHE cc_start: 0.7509 (t80) cc_final: 0.7287 (t80) REVERT: CF 204 LEU cc_start: 0.8257 (tp) cc_final: 0.7847 (mp) REVERT: CG 180 ASN cc_start: 0.8712 (m110) cc_final: 0.8496 (m110) REVERT: CK 9 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7578 (mt0) REVERT: CK 47 TYR cc_start: 0.8925 (t80) cc_final: 0.8631 (t80) REVERT: CK 54 LYS cc_start: 0.8836 (mttm) cc_final: 0.8452 (mtmt) REVERT: CE 54 ASN cc_start: 0.7264 (m-40) cc_final: 0.6784 (m-40) REVERT: CE 130 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8217 (mm) outliers start: 23 outliers final: 16 residues processed: 225 average time/residue: 1.1127 time to fit residues: 288.4997 Evaluate side-chains 217 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 107 ILE Chi-restraints excluded: chain CM residue 60 SER Chi-restraints excluded: chain CA residue 160 PHE Chi-restraints excluded: chain CA residue 195 SER Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 279 GLU Chi-restraints excluded: chain CA residue 446 LEU Chi-restraints excluded: chain CA residue 602 ILE Chi-restraints excluded: chain CA residue 620 HIS Chi-restraints excluded: chain CI residue 113 ASP Chi-restraints excluded: chain CB residue 161 HIS Chi-restraints excluded: chain CB residue 171 ASP Chi-restraints excluded: chain CB residue 208 LEU Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CG residue 160 VAL Chi-restraints excluded: chain CG residue 174 SER Chi-restraints excluded: chain CG residue 186 LYS Chi-restraints excluded: chain CK residue 22 LEU Chi-restraints excluded: chain CE residue 130 LEU Chi-restraints excluded: chain CE residue 231 ILE Chi-restraints excluded: chain CJ residue 10 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 358 HIS CG 145 GLN ** CD 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.117789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.106194 restraints weight = 94639.491| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.67 r_work: 0.3383 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.9641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 21086 Z= 0.180 Angle : 0.986 80.802 28347 Z= 0.379 Chirality : 0.048 1.562 2945 Planarity : 0.004 0.106 3521 Dihedral : 12.843 167.636 3595 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.50 % Favored : 95.33 % Rotamer: Outliers : 1.14 % Allowed : 21.09 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.17), residues: 2379 helix: 2.16 (0.14), residues: 1275 sheet: -1.13 (0.39), residues: 168 loop : -1.01 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGCB 123 TYR 0.014 0.001 TYRCG 109 PHE 0.019 0.001 PHECA 65 TRP 0.011 0.001 TRPCK 32 HIS 0.005 0.001 HISCG 99 Details of bonding type rmsd covalent geometry : bond 0.00379 (21071) covalent geometry : angle 0.87367 (28321) hydrogen bonds : bond 0.04194 ( 1080) hydrogen bonds : angle 4.20225 ( 3069) metal coordination : bond 0.00983 ( 10) metal coordination : angle 15.14456 ( 26) Misc. bond : bond 0.03843 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11408.86 seconds wall clock time: 194 minutes 23.97 seconds (11663.97 seconds total)