Starting phenix.real_space_refine on Sat Feb 24 04:29:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6g_15866/02_2024/8b6g_15866_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6g_15866/02_2024/8b6g_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6g_15866/02_2024/8b6g_15866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6g_15866/02_2024/8b6g_15866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6g_15866/02_2024/8b6g_15866_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6g_15866/02_2024/8b6g_15866_trim_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 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 Residue "CH TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "CM PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "CM TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "CL PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "CA PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "CA PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "CA TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "CF ASP 101": "OD1" <-> "OD2" Residue "CF TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "CE TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "CJ TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "CJ TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "CO PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "CD PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "CD TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 17.28, per 1000 atoms: 0.43 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 43.82 Conformation dependent library (CDL) restraints added in 5.5 seconds 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... running ksdssp... Secondary structure from input PDB file: 102 helices and 11 sheets defined 52.7% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.92 Creating SS restraints... Processing helix chain 'CH' and resid 96 through 112 removed outlier: 3.723A pdb=" N LYSCH 111 " --> pdb=" O ILECH 107 " (cutoff:3.500A) Processing helix chain 'CH' and resid 114 through 123 Processing helix chain 'CH' and resid 127 through 130 No H-bonds generated for 'chain 'CH' and resid 127 through 130' Processing helix chain 'CH' and resid 134 through 152 removed outlier: 4.826A pdb=" N ASPCH 139 " --> pdb=" O LYSCH 136 " (cutoff:3.500A) Processing helix chain 'CH' and resid 157 through 175 Processing helix chain 'CH' and resid 185 through 192 Processing helix chain 'CM' and resid 12 through 14 No H-bonds generated for 'chain 'CM' and resid 12 through 14' Processing helix chain 'CM' and resid 26 through 48 Processing helix chain 'CM' and resid 56 through 58 No H-bonds generated for 'chain 'CM' and resid 56 through 58' Processing helix chain 'CL' and resid 3 through 11 removed outlier: 4.322A pdb=" N SERCL 8 " --> pdb=" O ASPCL 4 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYRCL 9 " --> pdb=" O GLNCL 5 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYRCL 10 " --> pdb=" O ILECL 6 " (cutoff:3.500A) Processing helix chain 'CL' and resid 23 through 34 Processing helix chain 'CL' and resid 38 through 53 removed outlier: 4.901A pdb=" N ASNCL 44 " --> pdb=" O ALACL 41 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N HISCL 48 " --> pdb=" O ILECL 45 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARGCL 49 " --> pdb=" O ARGCL 46 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYSCL 52 " --> pdb=" O ARGCL 49 " (cutoff:3.500A) Processing helix chain 'CL' and resid 58 through 82 Processing helix chain 'CL' and resid 84 through 87 Processing helix chain 'CA' and resid 58 through 70 Processing helix chain 'CA' and resid 82 through 84 No H-bonds generated for 'chain 'CA' and resid 82 through 84' Processing helix chain 'CA' and resid 86 through 89 Processing helix chain 'CA' and resid 106 through 116 Processing helix chain 'CA' and resid 123 through 143 Proline residue: CA 134 - end of helix Processing helix chain 'CA' and resid 183 through 197 Processing helix chain 'CA' and resid 248 through 250 No H-bonds generated for 'chain 'CA' and resid 248 through 250' Processing helix chain 'CA' and resid 263 through 270 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 297 through 302 Processing helix chain 'CA' and resid 315 through 318 No H-bonds generated for 'chain 'CA' and resid 315 through 318' Processing helix chain 'CA' and resid 328 through 340 Processing helix chain 'CA' and resid 347 through 349 No H-bonds generated for 'chain 'CA' and resid 347 through 349' Processing helix chain 'CA' and resid 361 through 367 Processing helix chain 'CA' and resid 369 through 379 Processing helix chain 'CA' and resid 428 through 430 No H-bonds generated for 'chain 'CA' and resid 428 through 430' Processing helix chain 'CA' and resid 445 through 463 Processing helix chain 'CA' and resid 479 through 489 Processing helix chain 'CA' and resid 497 through 511 Processing helix chain 'CA' and resid 518 through 537 removed outlier: 3.535A pdb=" N LYSCA 536 " --> pdb=" O TYRCA 532 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SERCA 537 " --> pdb=" O GLUCA 533 " (cutoff:3.500A) Processing helix chain 'CA' and resid 549 through 573 Processing helix chain 'CI' and resid 4 through 49 Processing helix chain 'CI' and resid 66 through 68 No H-bonds generated for 'chain 'CI' and resid 66 through 68' Processing helix chain 'CI' and resid 70 through 84 Processing helix chain 'CI' and resid 96 through 113 Processing helix chain 'CB' and resid 32 through 48 Processing helix chain 'CB' and resid 64 through 67 Processing helix chain 'CB' and resid 101 through 111 Processing helix chain 'CB' and resid 141 through 143 No H-bonds generated for 'chain 'CB' and resid 141 through 143' Processing helix chain 'CB' and resid 173 through 182 removed outlier: 3.505A pdb=" N METCB 181 " --> pdb=" O ALACB 177 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILECB 182 " --> pdb=" O GLNCB 178 " (cutoff:3.500A) Processing helix chain 'CB' and resid 203 through 209 removed outlier: 4.486A pdb=" N LEUCB 209 " --> pdb=" O GLNCB 205 " (cutoff:3.500A) Processing helix chain 'CB' and resid 222 through 224 No H-bonds generated for 'chain 'CB' and resid 222 through 224' Processing helix chain 'CB' and resid 226 through 230 Processing helix chain 'CB' and resid 238 through 249 Processing helix chain 'CB' and resid 256 through 264 Processing helix chain 'CB' and resid 277 through 281 Processing helix chain 'CB' and resid 288 through 308 removed outlier: 3.931A pdb=" N ILECB 307 " --> pdb=" O ARGCB 303 " (cutoff:3.500A) Processing helix chain 'CF' and resid 93 through 124 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 128 through 130 No H-bonds generated for 'chain 'CF' and resid 128 through 130' Processing helix chain 'CF' and resid 132 through 138 Proline residue: CF 136 - end of helix Processing helix chain 'CF' and resid 140 through 155 Processing helix chain 'CF' and resid 160 through 168 removed outlier: 4.469A pdb=" N GLNCF 168 " --> pdb=" O SERCF 164 " (cutoff:3.500A) Processing helix chain 'CF' and resid 173 through 177 Processing helix chain 'CF' and resid 189 through 205 Processing helix chain 'CF' and resid 209 through 227 Proline residue: CF 219 - end of helix Processing helix chain 'CF' and resid 232 through 256 Processing helix chain 'CF' and resid 262 through 269 Processing helix chain 'CF' and resid 278 through 292 Processing helix chain 'CG' and resid 3 through 32 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 40 through 44 Processing helix chain 'CG' and resid 50 through 62 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 67 through 69 No H-bonds generated for 'chain 'CG' and resid 67 through 69' Processing helix chain 'CG' and resid 72 through 116 Processing helix chain 'CG' and resid 130 through 150 Processing helix chain 'CG' and resid 154 through 174 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) Processing helix chain 'CG' and resid 181 through 184 No H-bonds generated for 'chain 'CG' and resid 181 through 184' Processing helix chain 'CG' and resid 192 through 195 No H-bonds generated for 'chain 'CG' and resid 192 through 195' Processing helix chain 'CK' and resid 5 through 12 Processing helix chain 'CK' and resid 24 through 39 Processing helix chain 'CK' and resid 42 through 56 Proline residue: CK 53 - end of helix Processing helix chain 'CK' and resid 74 through 76 No H-bonds generated for 'chain 'CK' and resid 74 through 76' Processing helix chain 'CE' and resid 11 through 23 removed outlier: 3.735A pdb=" N SERCE 23 " --> pdb=" O GLYCE 19 " (cutoff:3.500A) Processing helix chain 'CE' and resid 38 through 48 Processing helix chain 'CE' and resid 66 through 75 Processing helix chain 'CE' and resid 95 through 106 Processing helix chain 'CE' and resid 118 through 120 No H-bonds generated for 'chain 'CE' and resid 118 through 120' Processing helix chain 'CE' and resid 128 through 142 Processing helix chain 'CE' and resid 161 through 171 Processing helix chain 'CE' and resid 189 through 202 Processing helix chain 'CE' and resid 220 through 231 Processing helix chain 'CE' and resid 241 through 246 Processing helix chain 'CE' and resid 253 through 258 Processing helix chain 'CE' and resid 261 through 272 Processing helix chain 'CE' and resid 284 through 287 Processing helix chain 'CE' and resid 295 through 298 No H-bonds generated for 'chain 'CE' and resid 295 through 298' Processing helix chain 'CE' and resid 306 through 309 Processing helix chain 'CE' and resid 315 through 320 Processing helix chain 'CJ' and resid 3 through 25 Processing helix chain 'CJ' and resid 27 through 45 removed outlier: 3.574A pdb=" N TYRCJ 38 " --> pdb=" O HISCJ 34 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 58 through 60 No H-bonds generated for 'chain 'CJ' and resid 58 through 60' Processing helix chain 'CJ' and resid 64 through 101 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 15 through 43 Proline residue: CN 22 - end of helix removed outlier: 3.630A pdb=" N LEUCN 26 " --> pdb=" O PROCN 22 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VALCN 27 " --> pdb=" O LYSCN 23 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYRCN 28 " --> pdb=" O ASNCN 24 " (cutoff:3.500A) Proline residue: CN 29 - end of helix Proline residue: CN 35 - end of helix Processing helix chain 'CC' and resid 9 through 11 No H-bonds generated for 'chain 'CC' and resid 9 through 11' Processing helix chain 'CC' and resid 17 through 47 removed outlier: 3.603A pdb=" N ILECC 25 " --> pdb=" O HISCC 21 " (cutoff:3.500A) Processing helix chain 'CO' and resid 8 through 27 Processing helix chain 'CO' and resid 38 through 40 No H-bonds generated for 'chain 'CO' and resid 38 through 40' Processing helix chain 'CD' and resid 2 through 12 Processing helix chain 'CD' and resid 15 through 18 Processing helix chain 'CD' and resid 21 through 43 removed outlier: 3.877A pdb=" N PHECD 43 " --> pdb=" O LEUCD 39 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'CA' and resid 44 through 48 removed outlier: 6.539A pdb=" N ILECA 232 " --> pdb=" O ILECA 45 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HISCA 47 " --> pdb=" O ILECA 232 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARGCA 234 " --> pdb=" O HISCA 47 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N METCA 225 " --> pdb=" O VALCA 208 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VALCA 208 " --> pdb=" O METCA 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'CA' and resid 239 through 242 Processing sheet with id= C, first strand: chain 'CA' and resid 305 through 307 Processing sheet with id= D, first strand: chain 'CA' and resid 410 through 412 Processing sheet with id= E, first strand: chain 'CA' and resid 596 through 602 Processing sheet with id= F, first strand: chain 'CA' and resid 281 through 284 removed outlier: 5.559A pdb=" N HISCA 284 " --> pdb=" O VALCA 394 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VALCA 394 " --> pdb=" O HISCA 284 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'CI' and resid 53 through 56 Processing sheet with id= H, first strand: chain 'CB' and resid 53 through 55 removed outlier: 6.579A pdb=" N TYRCB 87 " --> pdb=" O VALCB 54 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THRCB 154 " --> pdb=" O LEUCB 72 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N TYRCB 74 " --> pdb=" O THRCB 154 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILECB 156 " --> pdb=" O TYRCB 74 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'CB' and resid 131 through 133 Processing sheet with id= J, first strand: chain 'CK' and resid 64 through 73 Processing sheet with id= K, first strand: chain 'CE' and resid 209 through 212 removed outlier: 5.965A pdb=" N GLUCE 148 " --> pdb=" O TYRCE 210 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ALACE 212 " --> pdb=" O GLUCE 148 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYSCE 150 " --> pdb=" O ALACE 212 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LYSCE 57 " --> pdb=" O ILECE 29 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VALCE 31 " --> pdb=" O LYSCE 57 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLUCE 59 " --> pdb=" O VALCE 31 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASPCE 33 " --> pdb=" O GLUCE 59 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VALCE 61 " --> pdb=" O ASPCE 33 " (cutoff:3.500A) 904 hydrogen bonds defined for protein. 2571 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: 14.94 Time building geometry restraints manager: 43.97 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: 40.52 - 67.79: 6 67.79 - 95.07: 27 95.07 - 122.34: 66593 122.34 - 149.61: 5305 149.61 - 176.88: 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: 248 1.85 - 2.54: 32786 2.54 - 3.23: 124250 3.23 - 3.91: 157714 3.91 - 4.60: 252778 Nonbonded interactions: 567776 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 1.850 ... (remaining 567771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 7.050 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: 0.570 Extract box with map and model: 24.980 Check model and map are aligned: 0.620 Set scattering table: 0.340 Process input model: 151.750 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 198.030 ------------------------------------------------------------------------------- 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 : 0.024 1.983 21071 Z= 1.139 Angle : 0.986 74.229 28321 Z= 0.388 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 : 3.96 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (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 TRP 0.012 0.001 TRPCK 32 HIS 0.006 0.001 HISCG 99 PHE 0.022 0.001 PHECA 65 TYR 0.013 0.001 TYRCF 268 ARG 0.002 0.000 ARGCH 117 *********************** 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 fitting. rotamer outliers: 14 poor density : 628 time to evaluate : 3.115 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: CH 116 GLU cc_start: 0.7101 (mp0) cc_final: 0.6564 (mp0) REVERT: CH 184 CYS cc_start: 0.4325 (m) cc_final: 0.3914 (m) REVERT: CL 2 LYS cc_start: 0.7601 (mttp) cc_final: 0.6938 (mppt) REVERT: CL 21 LEU cc_start: 0.6339 (mt) cc_final: 0.5878 (mt) REVERT: CL 83 PHE cc_start: 0.6719 (m-80) cc_final: 0.6515 (m-80) REVERT: CA 226 SER cc_start: 0.6971 (t) cc_final: 0.6701 (p) REVERT: CA 324 ASP cc_start: 0.6498 (m-30) cc_final: 0.6126 (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: 0.7058 (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: 0.5671 (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: 0.5000 (mtm) REVERT: CF 263 GLU cc_start: 0.7274 (tt0) cc_final: 0.6950 (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: 0.7522 (m-80) REVERT: CK 89 THR cc_start: 0.6622 (p) cc_final: 0.6302 (p) REVERT: CE 87 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6969 (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: 0.6979 (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: 2.3472 time to fit residues: 1741.2807 Evaluate side-chains 338 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 331 time to evaluate : 2.991 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 212 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 201 ASN CA 476 ASN CG 157 GLN CE 197 GLN CE 206 GLN CE 302 ASN CJ 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 21071 Z= 0.239 Angle : 0.709 66.284 28321 Z= 0.308 Chirality : 0.055 2.185 2945 Planarity : 0.004 0.072 3521 Dihedral : 17.130 145.445 3604 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.74 % Favored : 96.13 % Rotamer: Outliers : 2.05 % Allowed : 14.80 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2379 helix: 2.09 (0.14), residues: 1272 sheet: -0.78 (0.38), residues: 166 loop : -0.73 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPCK 32 HIS 0.006 0.001 HISCF 260 PHE 0.022 0.001 PHECA 65 TYR 0.014 0.001 TYRCO 24 ARG 0.008 0.001 ARGCO 6 *********************** 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 383 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 340 time to evaluate : 3.238 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: CH 97 GLU cc_start: 0.7703 (tt0) cc_final: 0.7192 (tt0) REVERT: CH 116 GLU cc_start: 0.7131 (mp0) cc_final: 0.6572 (mp0) REVERT: CL 21 LEU cc_start: 0.6418 (mt) cc_final: 0.6183 (mt) REVERT: CA 226 SER cc_start: 0.7252 (t) cc_final: 0.6778 (p) REVERT: CA 295 MET cc_start: 0.7772 (mmm) cc_final: 0.7500 (mmm) REVERT: CA 324 ASP cc_start: 0.6676 (m-30) cc_final: 0.6360 (m-30) REVERT: CA 633 LYS cc_start: 0.7364 (pttt) cc_final: 0.7079 (tmtt) REVERT: CI 31 GLU cc_start: 0.7242 (tt0) cc_final: 0.6951 (tt0) REVERT: CI 32 ASN cc_start: 0.7162 (m-40) cc_final: 0.6929 (m-40) REVERT: CI 64 ARG cc_start: 0.8251 (mmt180) cc_final: 0.6488 (ptm160) REVERT: CB 62 SER cc_start: 0.7953 (p) cc_final: 0.7560 (p) REVERT: CB 66 LYS cc_start: 0.7845 (mttt) cc_final: 0.7391 (mptp) REVERT: CB 171 ASP cc_start: 0.7208 (t0) cc_final: 0.6909 (t70) REVERT: CB 231 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.6860 (t-170) REVERT: CB 233 ASP cc_start: 0.5655 (OUTLIER) cc_final: 0.5368 (p0) REVERT: CB 296 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7282 (mtp) REVERT: CF 137 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7280 (tmm-80) REVERT: CF 263 GLU cc_start: 0.7388 (tt0) cc_final: 0.6983 (pm20) REVERT: CF 264 LYS cc_start: 0.7784 (mmtt) cc_final: 0.7153 (tppp) REVERT: CF 270 LYS cc_start: 0.7465 (tppp) cc_final: 0.7103 (mtpt) REVERT: CG 22 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7394 (mm-40) REVERT: CG 36 GLU cc_start: 0.5677 (tt0) cc_final: 0.5401 (tt0) REVERT: CG 56 TYR cc_start: 0.8284 (m-80) cc_final: 0.7688 (m-80) REVERT: CG 166 TYR cc_start: 0.7117 (t80) cc_final: 0.5806 (t80) REVERT: CK 2 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6894 (tp) REVERT: CK 89 THR cc_start: 0.7135 (p) cc_final: 0.6760 (p) REVERT: CE 87 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7515 (m-80) REVERT: CE 221 ASN cc_start: 0.7198 (t0) cc_final: 0.6801 (m110) REVERT: CD 12 TYR cc_start: 0.7080 (m-80) cc_final: 0.6535 (m-80) outliers start: 43 outliers final: 18 residues processed: 371 average time/residue: 2.0682 time to fit residues: 910.2874 Evaluate side-chains 304 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 280 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CM residue 58 SER Chi-restraints excluded: chain CL residue 18 ASP Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 345 VAL 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 227 SER Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CB residue 233 ASP 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 CG residue 79 ASN Chi-restraints excluded: chain CG residue 99 HIS Chi-restraints excluded: chain CG residue 139 SER Chi-restraints excluded: chain CK residue 2 LEU Chi-restraints excluded: chain CK residue 8 ILE Chi-restraints excluded: chain CE residue 3 LEU Chi-restraints excluded: chain CE residue 47 PHE Chi-restraints excluded: chain CE residue 87 TYR Chi-restraints excluded: chain CE residue 104 SER Chi-restraints excluded: chain CE residue 146 LEU 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 118 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 212 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 170 optimal weight: 0.4980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 498 HIS CA 505 GLN CA 548 ASN CI 30 GLN CB 231 HIS CF 257 ASN CG 157 GLN ** CG 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 21 GLN ** CE 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 302 ASN CN 24 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.191 21071 Z= 0.302 Angle : 0.899 85.096 28321 Z= 0.405 Chirality : 0.050 1.295 2945 Planarity : 0.005 0.060 3521 Dihedral : 15.335 142.605 3602 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.76 % Favored : 94.03 % Rotamer: Outliers : 3.66 % Allowed : 14.18 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2379 helix: 1.22 (0.14), residues: 1279 sheet: -0.78 (0.40), residues: 159 loop : -1.09 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPCB 229 HIS 0.009 0.002 HISCE 188 PHE 0.032 0.002 PHECG 185 TYR 0.040 0.002 TYRCF 247 ARG 0.009 0.001 ARGCA 333 *********************** 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 399 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 322 time to evaluate : 3.147 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: CH 104 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.6940 (mm) REVERT: CH 116 GLU cc_start: 0.7473 (mp0) cc_final: 0.6957 (mp0) REVERT: CH 118 LYS cc_start: 0.7330 (mttt) cc_final: 0.6917 (mmtm) REVERT: CH 161 SER cc_start: 0.7970 (t) cc_final: 0.7649 (p) REVERT: CH 171 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7098 (mmmm) REVERT: CM 58 SER cc_start: 0.7601 (OUTLIER) cc_final: 0.7252 (t) REVERT: CL 38 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7805 (mt-10) REVERT: CA 295 MET cc_start: 0.8268 (mmm) cc_final: 0.8003 (mmm) REVERT: CA 324 ASP cc_start: 0.7412 (m-30) cc_final: 0.7132 (m-30) REVERT: CA 486 ASP cc_start: 0.7844 (t70) cc_final: 0.7230 (t0) REVERT: CA 633 LYS cc_start: 0.7518 (pttt) cc_final: 0.7301 (ttpp) REVERT: CI 31 GLU cc_start: 0.7761 (tt0) cc_final: 0.6816 (mm-30) REVERT: CI 64 ARG cc_start: 0.8676 (mmt180) cc_final: 0.6806 (ptm160) REVERT: CI 112 GLN cc_start: 0.7295 (mt0) cc_final: 0.7018 (tm-30) REVERT: CB 38 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7758 (mm-30) REVERT: CB 48 GLN cc_start: 0.7422 (tt0) cc_final: 0.6975 (tp40) REVERT: CB 62 SER cc_start: 0.7962 (p) cc_final: 0.7627 (p) REVERT: CB 66 LYS cc_start: 0.7998 (mttt) cc_final: 0.7656 (mptp) REVERT: CB 126 ILE cc_start: 0.8316 (mt) cc_final: 0.8114 (tp) REVERT: CB 162 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7624 (tpt) REVERT: CB 233 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7566 (p0) REVERT: CB 296 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7509 (tpp) REVERT: CF 89 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8002 (tm-30) REVERT: CF 201 PHE cc_start: 0.5313 (OUTLIER) cc_final: 0.5045 (t80) REVERT: CF 263 GLU cc_start: 0.7814 (tt0) cc_final: 0.7294 (pm20) REVERT: CF 270 LYS cc_start: 0.7972 (tppp) cc_final: 0.7751 (mtpt) REVERT: CG 22 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7654 (mm-40) REVERT: CG 26 VAL cc_start: 0.8355 (t) cc_final: 0.8123 (t) REVERT: CG 36 GLU cc_start: 0.7093 (tt0) cc_final: 0.6800 (tt0) REVERT: CG 87 ASP cc_start: 0.7518 (m-30) cc_final: 0.7272 (m-30) REVERT: CG 169 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.8082 (t-170) REVERT: CK 54 LYS cc_start: 0.8380 (mttm) cc_final: 0.8024 (mtmt) REVERT: CK 91 LYS cc_start: 0.7380 (pmtt) cc_final: 0.7058 (pmtt) REVERT: CE 194 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: CE 234 ASN cc_start: 0.7540 (m-40) cc_final: 0.6912 (p0) REVERT: CE 259 HIS cc_start: 0.7731 (m90) cc_final: 0.7203 (m-70) REVERT: CJ 1 MET cc_start: 0.6208 (ptm) cc_final: 0.5654 (ptp) REVERT: CJ 66 LYS cc_start: 0.7694 (mtmt) cc_final: 0.7256 (tmtt) REVERT: CJ 89 LYS cc_start: 0.7306 (mmtt) cc_final: 0.6612 (ttpp) REVERT: CJ 100 LYS cc_start: 0.7532 (pttt) cc_final: 0.6979 (ptmm) outliers start: 77 outliers final: 20 residues processed: 383 average time/residue: 2.2798 time to fit residues: 1021.3228 Evaluate side-chains 264 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 235 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 104 ILE Chi-restraints excluded: chain CH residue 171 LYS Chi-restraints excluded: chain CH residue 179 SER 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 253 SER Chi-restraints excluded: chain CA residue 345 VAL Chi-restraints excluded: chain CA residue 434 SER Chi-restraints excluded: chain CA residue 620 HIS Chi-restraints excluded: chain CB residue 161 HIS Chi-restraints excluded: chain CB residue 162 MET Chi-restraints excluded: chain CB residue 164 ILE Chi-restraints excluded: chain CB residue 227 SER Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CB residue 233 ASP Chi-restraints excluded: chain CB residue 296 MET Chi-restraints excluded: chain CF residue 134 MET Chi-restraints excluded: chain CF residue 201 PHE Chi-restraints excluded: chain CG residue 99 HIS Chi-restraints excluded: chain CG residue 139 SER 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 CK residue 22 LEU Chi-restraints excluded: chain CE residue 11 LYS Chi-restraints excluded: chain CE residue 104 SER Chi-restraints excluded: chain CE residue 194 GLU Chi-restraints excluded: chain CE residue 231 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 101 optimal weight: 0.0980 chunk 142 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 226 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CL 32 GLN CA 358 HIS ** CB 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 257 ASN CG 189 ASN CE 53 GLN CE 197 GLN CE 203 ASN CE 302 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 21071 Z= 0.215 Angle : 0.751 79.911 28321 Z= 0.325 Chirality : 0.048 1.565 2945 Planarity : 0.003 0.041 3521 Dihedral : 14.495 144.129 3596 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.20 % Favored : 95.63 % Rotamer: Outliers : 2.67 % Allowed : 17.75 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2379 helix: 1.65 (0.14), residues: 1279 sheet: -0.78 (0.39), residues: 174 loop : -0.95 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPCK 32 HIS 0.014 0.001 HISCE 282 PHE 0.019 0.001 PHECA 65 TYR 0.016 0.001 TYRCG 109 ARG 0.003 0.000 ARGCE 111 *********************** 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 307 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 251 time to evaluate : 3.174 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: CH 116 GLU cc_start: 0.7509 (mp0) cc_final: 0.7010 (mp0) REVERT: CH 118 LYS cc_start: 0.7391 (mttt) cc_final: 0.6902 (mmtm) REVERT: CH 161 SER cc_start: 0.8044 (t) cc_final: 0.7731 (p) REVERT: CH 171 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7138 (mmtt) REVERT: CM 58 SER cc_start: 0.7753 (OUTLIER) cc_final: 0.7372 (p) REVERT: CL 78 MET cc_start: 0.7768 (mtp) cc_final: 0.7535 (mtm) REVERT: CA 324 ASP cc_start: 0.7552 (m-30) cc_final: 0.7289 (m-30) REVERT: CA 486 ASP cc_start: 0.7997 (t70) cc_final: 0.7448 (t0) REVERT: CA 625 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7200 (mm-30) REVERT: CA 633 LYS cc_start: 0.7509 (pttt) cc_final: 0.7306 (ttpp) REVERT: CI 31 GLU cc_start: 0.7837 (tt0) cc_final: 0.6960 (mm-30) REVERT: CI 64 ARG cc_start: 0.8693 (mmt180) cc_final: 0.6818 (ptm160) REVERT: CI 112 GLN cc_start: 0.7414 (mt0) cc_final: 0.7122 (tm-30) REVERT: CB 48 GLN cc_start: 0.7589 (tt0) cc_final: 0.7279 (tp40) REVERT: CB 66 LYS cc_start: 0.8002 (mttt) cc_final: 0.7645 (mptp) REVERT: CB 126 ILE cc_start: 0.8387 (mt) cc_final: 0.8106 (tp) REVERT: CF 89 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7981 (tm-30) REVERT: CF 114 ASP cc_start: 0.8733 (m-30) cc_final: 0.8305 (m-30) REVERT: CF 127 ILE cc_start: 0.8659 (pp) cc_final: 0.8381 (mt) REVERT: CF 201 PHE cc_start: 0.5550 (OUTLIER) cc_final: 0.5256 (t80) REVERT: CG 22 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7816 (mm-40) REVERT: CG 26 VAL cc_start: 0.8397 (t) cc_final: 0.8164 (t) REVERT: CG 36 GLU cc_start: 0.7366 (tt0) cc_final: 0.7036 (tt0) REVERT: CG 87 ASP cc_start: 0.7643 (m-30) cc_final: 0.7383 (m-30) REVERT: CG 180 ASN cc_start: 0.8267 (m110) cc_final: 0.7794 (m110) REVERT: CK 54 LYS cc_start: 0.8366 (mttm) cc_final: 0.7896 (mtmt) REVERT: CE 234 ASN cc_start: 0.7549 (m-40) cc_final: 0.6893 (p0) REVERT: CJ 1 MET cc_start: 0.6509 (ptm) cc_final: 0.6054 (ptp) REVERT: CJ 66 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7527 (tmtt) REVERT: CJ 89 LYS cc_start: 0.7092 (mmtt) cc_final: 0.6586 (ttpp) REVERT: CJ 100 LYS cc_start: 0.7587 (pttt) cc_final: 0.7053 (ptmm) REVERT: CN 59 VAL cc_start: 0.7403 (OUTLIER) cc_final: 0.7173 (m) outliers start: 56 outliers final: 22 residues processed: 291 average time/residue: 2.2339 time to fit residues: 765.0091 Evaluate side-chains 242 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 216 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 171 LYS Chi-restraints excluded: chain CH residue 179 SER Chi-restraints excluded: chain CM residue 58 SER Chi-restraints excluded: chain CM residue 60 SER Chi-restraints excluded: chain CL residue 88 THR Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 345 VAL Chi-restraints excluded: chain CA residue 398 MET 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 209 LEU Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CF residue 201 PHE Chi-restraints excluded: chain CF residue 290 SER Chi-restraints excluded: chain CG residue 177 HIS Chi-restraints excluded: chain CG residue 186 LYS Chi-restraints excluded: chain CK residue 1 MET Chi-restraints excluded: chain CK residue 22 LEU Chi-restraints excluded: chain CK residue 64 THR Chi-restraints excluded: chain CE residue 197 GLN Chi-restraints excluded: chain CE residue 231 ILE Chi-restraints excluded: chain CJ residue 103 ASP Chi-restraints excluded: chain CN residue 59 VAL Chi-restraints excluded: chain CD residue 15 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 203 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 397 ASN CF 257 ASN CK 87 GLN CE 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.7856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 21071 Z= 0.281 Angle : 0.781 81.101 28321 Z= 0.346 Chirality : 0.048 1.503 2945 Planarity : 0.004 0.049 3521 Dihedral : 14.264 143.359 3596 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.72 % Favored : 94.12 % Rotamer: Outliers : 2.48 % Allowed : 18.18 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2379 helix: 1.49 (0.14), residues: 1285 sheet: -0.75 (0.39), residues: 171 loop : -1.08 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPCK 32 HIS 0.009 0.001 HISCE 78 PHE 0.021 0.002 PHECA 65 TYR 0.019 0.002 TYRCK 7 ARG 0.005 0.001 ARGCG 114 *********************** 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 289 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 237 time to evaluate : 3.575 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: CH 107 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6342 (mt) REVERT: CH 118 LYS cc_start: 0.7725 (mttt) cc_final: 0.7319 (mtmt) REVERT: CM 58 SER cc_start: 0.7847 (OUTLIER) cc_final: 0.7454 (p) REVERT: CL 11 ILE cc_start: 0.8975 (mt) cc_final: 0.8758 (mt) REVERT: CA 227 MET cc_start: 0.6580 (OUTLIER) cc_final: 0.6000 (mpp) REVERT: CA 277 ASP cc_start: 0.8742 (m-30) cc_final: 0.8120 (m-30) REVERT: CA 324 ASP cc_start: 0.8090 (m-30) cc_final: 0.7858 (m-30) REVERT: CA 486 ASP cc_start: 0.8146 (t70) cc_final: 0.7643 (t0) REVERT: CA 625 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7301 (mm-30) REVERT: CA 633 LYS cc_start: 0.7642 (pttt) cc_final: 0.7410 (ttpp) REVERT: CI 7 MET cc_start: 0.8527 (mmt) cc_final: 0.8266 (mmt) REVERT: CI 31 GLU cc_start: 0.8075 (tt0) cc_final: 0.7258 (mm-30) REVERT: CI 64 ARG cc_start: 0.8657 (mmt180) cc_final: 0.6945 (ptm160) REVERT: CI 112 GLN cc_start: 0.7500 (mt0) cc_final: 0.7298 (tm-30) REVERT: CB 38 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7600 (mm-30) REVERT: CB 48 GLN cc_start: 0.7492 (tt0) cc_final: 0.7267 (tp40) REVERT: CB 66 LYS cc_start: 0.8041 (mttt) cc_final: 0.7670 (mptp) REVERT: CB 126 ILE cc_start: 0.8425 (mt) cc_final: 0.8092 (tp) REVERT: CB 197 LYS cc_start: 0.7109 (mttt) cc_final: 0.6693 (mmtp) REVERT: CF 89 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7905 (tm-30) REVERT: CF 127 ILE cc_start: 0.8753 (pp) cc_final: 0.8516 (mt) REVERT: CF 201 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.5908 (t80) REVERT: CF 242 ASP cc_start: 0.8421 (t70) cc_final: 0.8044 (t0) REVERT: CG 22 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7944 (mm-40) REVERT: CG 26 VAL cc_start: 0.8378 (t) cc_final: 0.8163 (t) REVERT: CG 87 ASP cc_start: 0.7657 (m-30) cc_final: 0.7344 (m-30) REVERT: CG 111 GLU cc_start: 0.8146 (tt0) cc_final: 0.7816 (tt0) REVERT: CG 180 ASN cc_start: 0.8301 (m110) cc_final: 0.7920 (m110) REVERT: CK 54 LYS cc_start: 0.8283 (mttm) cc_final: 0.7820 (mtmt) REVERT: CE 130 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7254 (mm) REVERT: CE 207 ASN cc_start: 0.6592 (OUTLIER) cc_final: 0.6109 (m-40) REVERT: CJ 10 GLU cc_start: 0.7004 (tp30) cc_final: 0.6736 (tp30) REVERT: CJ 66 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7772 (tmtt) REVERT: CJ 89 LYS cc_start: 0.7554 (mmtt) cc_final: 0.6815 (ttpp) REVERT: CJ 100 LYS cc_start: 0.7862 (pttt) cc_final: 0.7323 (ptmm) REVERT: CN 23 LYS cc_start: 0.8482 (pttt) cc_final: 0.8194 (pttp) outliers start: 52 outliers final: 25 residues processed: 273 average time/residue: 2.3277 time to fit residues: 744.6644 Evaluate side-chains 241 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 210 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 107 ILE Chi-restraints excluded: chain CH residue 179 SER Chi-restraints excluded: chain CH residue 184 CYS Chi-restraints excluded: chain CM residue 58 SER Chi-restraints excluded: chain CM residue 60 SER Chi-restraints excluded: chain CL residue 88 THR Chi-restraints excluded: chain CA residue 227 MET Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 345 VAL Chi-restraints excluded: chain CA residue 397 ASN Chi-restraints excluded: chain CA residue 398 MET Chi-restraints excluded: chain CA residue 611 GLU Chi-restraints excluded: chain CA residue 620 HIS Chi-restraints excluded: chain CB residue 62 SER Chi-restraints excluded: chain CB residue 157 THR Chi-restraints excluded: chain CB residue 161 HIS Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CB residue 279 SER Chi-restraints excluded: chain CB residue 296 MET Chi-restraints excluded: chain CF residue 185 LEU Chi-restraints excluded: chain CF residue 201 PHE Chi-restraints excluded: chain CF residue 250 SER Chi-restraints excluded: chain CF residue 290 SER Chi-restraints excluded: chain CG residue 139 SER Chi-restraints excluded: chain CG residue 144 ILE 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 207 ASN 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 76 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CL 70 GLN CA 238 HIS CA 284 HIS ** CB 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 257 ASN CK 87 GLN CE 197 GLN CE 302 ASN CD 23 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.8585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 21071 Z= 0.364 Angle : 0.795 80.270 28321 Z= 0.356 Chirality : 0.050 1.551 2945 Planarity : 0.004 0.044 3521 Dihedral : 14.459 148.431 3596 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.25 % Favored : 94.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2379 helix: 1.36 (0.14), residues: 1279 sheet: -0.81 (0.39), residues: 167 loop : -1.27 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPCK 32 HIS 0.021 0.002 HISCE 282 PHE 0.024 0.002 PHECA 65 TYR 0.022 0.002 TYRCA 247 ARG 0.006 0.001 ARGCK 34 *********************** 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 279 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 217 time to evaluate : 3.220 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 118 LYS cc_start: 0.7931 (mttt) cc_final: 0.7479 (mtmt) REVERT: CM 58 SER cc_start: 0.7840 (OUTLIER) cc_final: 0.7450 (p) REVERT: CM 73 LYS cc_start: 0.8346 (mtmt) cc_final: 0.7884 (mttt) REVERT: CA 227 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6104 (mpp) REVERT: CA 295 MET cc_start: 0.8126 (mmm) cc_final: 0.7855 (mmm) REVERT: CA 486 ASP cc_start: 0.8169 (t70) cc_final: 0.7772 (t0) REVERT: CA 625 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7583 (mm-30) REVERT: CA 633 LYS cc_start: 0.7758 (pttt) cc_final: 0.7451 (ttpp) REVERT: CI 64 ARG cc_start: 0.8716 (mmt180) cc_final: 0.7027 (ptm160) REVERT: CI 84 LYS cc_start: 0.6546 (tttt) cc_final: 0.5936 (mttt) REVERT: CI 105 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6946 (mm-30) REVERT: CI 112 GLN cc_start: 0.7652 (mt0) cc_final: 0.7426 (tm-30) REVERT: CB 38 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7767 (mm-30) REVERT: CB 66 LYS cc_start: 0.8411 (mttt) cc_final: 0.7942 (mptp) REVERT: CB 126 ILE cc_start: 0.8466 (mt) cc_final: 0.8137 (tp) REVERT: CB 296 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7786 (mtt) REVERT: CF 89 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7973 (tm-30) REVERT: CF 127 ILE cc_start: 0.8773 (pp) cc_final: 0.8491 (mt) REVERT: CF 242 ASP cc_start: 0.8459 (t70) cc_final: 0.8109 (t0) REVERT: CG 87 ASP cc_start: 0.7739 (m-30) cc_final: 0.7411 (m-30) REVERT: CG 111 GLU cc_start: 0.8234 (tt0) cc_final: 0.7854 (tt0) REVERT: CG 180 ASN cc_start: 0.8389 (m110) cc_final: 0.8030 (m110) REVERT: CK 54 LYS cc_start: 0.8326 (mttm) cc_final: 0.7812 (mtmt) REVERT: CE 27 GLU cc_start: 0.7249 (tm-30) cc_final: 0.7011 (tm-30) REVERT: CE 130 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7307 (mm) REVERT: CJ 10 GLU cc_start: 0.7306 (tp30) cc_final: 0.7066 (tp30) REVERT: CJ 66 LYS cc_start: 0.8336 (mtmt) cc_final: 0.7837 (tmtt) REVERT: CN 23 LYS cc_start: 0.8622 (pttt) cc_final: 0.8308 (pttp) REVERT: CD 15 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8395 (p) outliers start: 62 outliers final: 30 residues processed: 261 average time/residue: 2.5256 time to fit residues: 761.2051 Evaluate side-chains 226 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 191 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 179 SER Chi-restraints excluded: chain CM residue 58 SER Chi-restraints excluded: chain CM residue 60 SER Chi-restraints excluded: chain CL residue 88 THR Chi-restraints excluded: chain CA residue 65 PHE 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 345 VAL Chi-restraints excluded: chain CA residue 564 SER Chi-restraints excluded: chain CA residue 602 ILE Chi-restraints excluded: chain CA residue 620 HIS Chi-restraints excluded: chain CB residue 62 SER 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 209 LEU Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CB residue 296 MET Chi-restraints excluded: chain CF residue 185 LEU Chi-restraints excluded: chain CF residue 290 SER Chi-restraints excluded: chain CG residue 139 SER Chi-restraints excluded: chain CG residue 144 ILE Chi-restraints excluded: chain CG residue 160 VAL Chi-restraints excluded: chain CG residue 162 GLU Chi-restraints excluded: chain CG residue 174 SER Chi-restraints excluded: chain CG residue 186 LYS Chi-restraints excluded: chain CK residue 20 VAL Chi-restraints excluded: chain CK residue 22 LEU Chi-restraints excluded: chain CK residue 64 THR Chi-restraints excluded: chain CE residue 10 ASN Chi-restraints excluded: chain CE residue 130 LEU Chi-restraints excluded: chain CE residue 231 ILE Chi-restraints excluded: chain CN residue 1 MET Chi-restraints excluded: chain CD residue 15 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 165 optimal weight: 0.0970 chunk 190 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CB 70 GLN CF 257 ASN CG 145 GLN CK 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.8945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 21071 Z= 0.225 Angle : 0.746 80.854 28321 Z= 0.321 Chirality : 0.047 1.523 2945 Planarity : 0.003 0.046 3521 Dihedral : 13.943 151.819 3596 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.41 % Favored : 95.38 % Rotamer: Outliers : 2.28 % Allowed : 19.23 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.17), residues: 2379 helix: 1.51 (0.14), residues: 1292 sheet: -0.66 (0.39), residues: 170 loop : -1.10 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPCK 32 HIS 0.005 0.001 HISCE 21 PHE 0.019 0.001 PHECA 353 TYR 0.014 0.001 TYRCG 109 ARG 0.005 0.000 ARGCL 16 *********************** 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 256 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 208 time to evaluate : 3.509 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 118 LYS cc_start: 0.7951 (mttt) cc_final: 0.7425 (mtmt) REVERT: CH 139 ASP cc_start: 0.7740 (t70) cc_final: 0.7540 (t0) REVERT: CM 58 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7692 (p) REVERT: CM 73 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7883 (mttt) REVERT: CL 38 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8143 (mt-10) REVERT: CL 82 LYS cc_start: 0.8714 (tttt) cc_final: 0.8054 (tppt) REVERT: CA 227 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.5999 (mpp) REVERT: CA 295 MET cc_start: 0.8057 (mmm) cc_final: 0.7816 (mmm) REVERT: CA 486 ASP cc_start: 0.8174 (t70) cc_final: 0.7812 (t0) REVERT: CA 625 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7614 (mm-30) REVERT: CA 633 LYS cc_start: 0.7819 (pttt) cc_final: 0.7504 (ttpp) REVERT: CI 4 ASP cc_start: 0.8409 (m-30) cc_final: 0.8201 (m-30) REVERT: CI 31 GLU cc_start: 0.8156 (tt0) cc_final: 0.7444 (mp0) REVERT: CI 64 ARG cc_start: 0.8729 (mmt180) cc_final: 0.7063 (ptm160) REVERT: CI 84 LYS cc_start: 0.6480 (tttt) cc_final: 0.5872 (mttt) REVERT: CB 38 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7739 (mm-30) REVERT: CB 66 LYS cc_start: 0.8414 (mttt) cc_final: 0.7939 (mptp) REVERT: CB 126 ILE cc_start: 0.8482 (mt) cc_final: 0.8139 (tp) REVERT: CF 89 GLN cc_start: 0.8463 (tm-30) cc_final: 0.7984 (tm-30) REVERT: CF 127 ILE cc_start: 0.8720 (pp) cc_final: 0.8431 (mt) REVERT: CF 242 ASP cc_start: 0.8424 (t70) cc_final: 0.8102 (t0) REVERT: CG 87 ASP cc_start: 0.7780 (m-30) cc_final: 0.7470 (m-30) REVERT: CG 111 GLU cc_start: 0.8279 (tt0) cc_final: 0.7873 (tt0) REVERT: CG 180 ASN cc_start: 0.8415 (m110) cc_final: 0.8088 (m110) REVERT: CK 9 GLN cc_start: 0.7256 (tm-30) cc_final: 0.6496 (mt0) REVERT: CK 54 LYS cc_start: 0.8319 (mttm) cc_final: 0.7765 (mtmt) REVERT: CE 27 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6978 (tm-30) REVERT: CE 130 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7269 (mm) REVERT: CE 205 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7259 (mp) REVERT: CE 275 GLU cc_start: 0.6634 (tt0) cc_final: 0.5468 (mt-10) REVERT: CJ 10 GLU cc_start: 0.7482 (tp30) cc_final: 0.7097 (tp30) REVERT: CJ 66 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7878 (tmtt) REVERT: CN 23 LYS cc_start: 0.8599 (pttt) cc_final: 0.8379 (pttp) REVERT: CC 58 ARG cc_start: 0.6257 (mpt180) cc_final: 0.5883 (mtp85) REVERT: CD 15 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8308 (p) outliers start: 48 outliers final: 26 residues processed: 240 average time/residue: 2.6136 time to fit residues: 726.8732 Evaluate side-chains 220 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 179 SER Chi-restraints excluded: chain CM residue 58 SER Chi-restraints excluded: chain CL residue 88 THR Chi-restraints excluded: chain CA residue 129 MET Chi-restraints excluded: chain CA residue 227 MET Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 345 VAL Chi-restraints excluded: chain CA residue 348 LYS Chi-restraints excluded: chain CA residue 564 SER Chi-restraints excluded: chain CA residue 620 HIS Chi-restraints excluded: chain CB residue 62 SER Chi-restraints excluded: chain CB residue 157 THR Chi-restraints excluded: chain CB residue 161 HIS Chi-restraints excluded: chain CB residue 209 LEU Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CB residue 296 MET Chi-restraints excluded: chain CF residue 290 SER Chi-restraints excluded: chain CG residue 144 ILE Chi-restraints excluded: chain CG residue 160 VAL Chi-restraints excluded: chain CG residue 162 GLU Chi-restraints excluded: chain CG residue 169 HIS Chi-restraints excluded: chain CG residue 174 SER Chi-restraints excluded: chain CK residue 20 VAL Chi-restraints excluded: chain CK residue 22 LEU Chi-restraints excluded: chain CK residue 64 THR Chi-restraints excluded: chain CE residue 11 LYS Chi-restraints excluded: chain CE residue 130 LEU Chi-restraints excluded: chain CE residue 205 LEU Chi-restraints excluded: chain CE residue 231 ILE Chi-restraints excluded: chain CE residue 321 CYS Chi-restraints excluded: chain CD residue 15 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 3.9990 chunk 134 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 111 optimal weight: 0.0370 chunk 21 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 160 GLN ** CB 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 257 ASN CK 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.9114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 21071 Z= 0.187 Angle : 0.728 80.619 28321 Z= 0.309 Chirality : 0.047 1.551 2945 Planarity : 0.003 0.036 3521 Dihedral : 13.580 157.501 3596 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.08 % Favored : 95.71 % Rotamer: Outliers : 1.90 % Allowed : 19.66 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.17), residues: 2379 helix: 1.69 (0.15), residues: 1296 sheet: -0.56 (0.39), residues: 171 loop : -1.01 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPCK 32 HIS 0.005 0.001 HISCG 99 PHE 0.022 0.001 PHECA 65 TYR 0.018 0.001 TYRCG 109 ARG 0.003 0.000 ARGCL 16 *********************** 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 246 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 206 time to evaluate : 3.169 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: CH 118 LYS cc_start: 0.7956 (mttt) cc_final: 0.7443 (mtmt) REVERT: CM 58 SER cc_start: 0.8088 (OUTLIER) cc_final: 0.7831 (p) REVERT: CM 73 LYS cc_start: 0.8336 (mtmt) cc_final: 0.7881 (mttt) REVERT: CL 38 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8345 (mt-10) REVERT: CL 82 LYS cc_start: 0.8734 (tttt) cc_final: 0.8041 (tppt) REVERT: CA 295 MET cc_start: 0.8013 (mmm) cc_final: 0.7775 (mmm) REVERT: CA 486 ASP cc_start: 0.7952 (t70) cc_final: 0.7586 (t0) REVERT: CA 625 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7628 (mm-30) REVERT: CA 633 LYS cc_start: 0.7821 (pttt) cc_final: 0.7515 (ttpp) REVERT: CI 31 GLU cc_start: 0.8206 (tt0) cc_final: 0.7540 (mp0) REVERT: CI 33 GLN cc_start: 0.7258 (tm-30) cc_final: 0.6999 (tt0) REVERT: CI 64 ARG cc_start: 0.8760 (mmt180) cc_final: 0.7106 (ptm160) REVERT: CI 84 LYS cc_start: 0.6525 (tttt) cc_final: 0.5835 (mttt) REVERT: CB 38 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7756 (mm-30) REVERT: CB 66 LYS cc_start: 0.8367 (mttt) cc_final: 0.7916 (mptp) REVERT: CB 139 THR cc_start: 0.8365 (t) cc_final: 0.8011 (p) REVERT: CF 89 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8011 (tm-30) REVERT: CF 127 ILE cc_start: 0.8722 (pp) cc_final: 0.8418 (mt) REVERT: CF 242 ASP cc_start: 0.8450 (t70) cc_final: 0.8113 (t0) REVERT: CG 87 ASP cc_start: 0.7782 (m-30) cc_final: 0.7464 (m-30) REVERT: CG 180 ASN cc_start: 0.8450 (m110) cc_final: 0.8151 (m110) REVERT: CG 191 VAL cc_start: 0.8473 (t) cc_final: 0.8229 (p) REVERT: CK 4 ASP cc_start: 0.6872 (p0) cc_final: 0.6599 (p0) REVERT: CK 9 GLN cc_start: 0.6904 (tm-30) cc_final: 0.6437 (mt0) REVERT: CK 54 LYS cc_start: 0.8208 (mttm) cc_final: 0.7641 (mtmt) REVERT: CE 27 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6887 (tm-30) REVERT: CE 130 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7354 (mm) REVERT: CJ 10 GLU cc_start: 0.7504 (tp30) cc_final: 0.7103 (tp30) REVERT: CJ 66 LYS cc_start: 0.8330 (mtmt) cc_final: 0.7925 (tmtt) REVERT: CC 58 ARG cc_start: 0.6233 (mpt180) cc_final: 0.5892 (mtp85) REVERT: CD 15 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8452 (p) outliers start: 40 outliers final: 26 residues processed: 237 average time/residue: 2.6124 time to fit residues: 712.1833 Evaluate side-chains 220 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 179 SER Chi-restraints excluded: chain CM residue 58 SER Chi-restraints excluded: chain CL residue 88 THR Chi-restraints excluded: chain CA residue 104 ASP Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 279 GLU Chi-restraints excluded: chain CA residue 345 VAL Chi-restraints excluded: chain CA residue 348 LYS Chi-restraints excluded: chain CA residue 564 SER Chi-restraints excluded: chain CA residue 620 HIS Chi-restraints excluded: chain CB residue 62 SER 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 209 LEU Chi-restraints excluded: chain CB residue 231 HIS Chi-restraints excluded: chain CB residue 296 MET Chi-restraints excluded: chain CG residue 144 ILE Chi-restraints excluded: chain CG residue 160 VAL Chi-restraints excluded: chain CG residue 162 GLU Chi-restraints excluded: chain CG residue 169 HIS Chi-restraints excluded: chain CG residue 174 SER Chi-restraints excluded: chain CK residue 20 VAL Chi-restraints excluded: chain CK residue 22 LEU Chi-restraints excluded: chain CE residue 11 LYS Chi-restraints excluded: chain CE residue 130 LEU Chi-restraints excluded: chain CE residue 231 ILE Chi-restraints excluded: chain CE residue 321 CYS Chi-restraints excluded: chain CD residue 15 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 210 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 209 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 160 GLN ** CB 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 182 ASN CG 24 GLN CG 145 GLN CK 87 GLN CE 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.9222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 21071 Z= 0.163 Angle : 0.721 80.650 28321 Z= 0.304 Chirality : 0.046 1.552 2945 Planarity : 0.003 0.035 3521 Dihedral : 13.216 162.689 3596 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.99 % Favored : 95.80 % Rotamer: Outliers : 1.57 % Allowed : 19.99 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2379 helix: 1.81 (0.15), residues: 1295 sheet: -0.51 (0.39), residues: 176 loop : -0.96 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPCK 32 HIS 0.006 0.001 HISCG 99 PHE 0.020 0.001 PHECA 65 TYR 0.016 0.001 TYRCG 109 ARG 0.003 0.000 ARGCL 16 *********************** 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 241 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 208 time to evaluate : 3.467 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 118 LYS cc_start: 0.7974 (mttt) cc_final: 0.7453 (mtmt) REVERT: CH 125 SER cc_start: 0.8681 (t) cc_final: 0.8435 (m) REVERT: CM 58 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7849 (p) REVERT: CM 73 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7887 (mttt) REVERT: CL 38 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8381 (mt-10) REVERT: CL 82 LYS cc_start: 0.8734 (tttt) cc_final: 0.8044 (tppt) REVERT: CA 295 MET cc_start: 0.7857 (mmm) cc_final: 0.7602 (mmm) REVERT: CA 486 ASP cc_start: 0.7953 (t70) cc_final: 0.7587 (t0) REVERT: CA 625 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7606 (mm-30) REVERT: CA 633 LYS cc_start: 0.7825 (pttt) cc_final: 0.7517 (ttpp) REVERT: CI 31 GLU cc_start: 0.8218 (tt0) cc_final: 0.7591 (mp0) REVERT: CI 33 GLN cc_start: 0.7251 (tm-30) cc_final: 0.7018 (tt0) REVERT: CI 64 ARG cc_start: 0.8755 (mmt180) cc_final: 0.7116 (ptm160) REVERT: CI 84 LYS cc_start: 0.6557 (tttt) cc_final: 0.5825 (mttt) REVERT: CI 111 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7734 (mt-10) REVERT: CB 38 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7758 (mm-30) REVERT: CB 66 LYS cc_start: 0.8337 (mttt) cc_final: 0.7899 (mptp) REVERT: CB 123 ARG cc_start: 0.7884 (ttp-110) cc_final: 0.7655 (ttp-110) REVERT: CB 139 THR cc_start: 0.8361 (t) cc_final: 0.8020 (p) REVERT: CB 277 MET cc_start: 0.8039 (tpt) cc_final: 0.7519 (tpt) REVERT: CB 306 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7032 (ttm-80) REVERT: CF 89 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8008 (tm-30) REVERT: CF 127 ILE cc_start: 0.8710 (pp) cc_final: 0.8400 (mt) REVERT: CF 204 LEU cc_start: 0.7787 (tp) cc_final: 0.7404 (mp) REVERT: CF 242 ASP cc_start: 0.8438 (t70) cc_final: 0.8111 (t0) REVERT: CG 87 ASP cc_start: 0.7774 (m-30) cc_final: 0.7452 (m-30) REVERT: CG 180 ASN cc_start: 0.8450 (m110) cc_final: 0.8166 (m110) REVERT: CG 191 VAL cc_start: 0.8494 (t) cc_final: 0.8250 (p) REVERT: CK 4 ASP cc_start: 0.7034 (p0) cc_final: 0.6697 (p0) REVERT: CK 9 GLN cc_start: 0.6889 (tm-30) cc_final: 0.6428 (mt0) REVERT: CK 54 LYS cc_start: 0.8186 (mttm) cc_final: 0.7620 (mtmt) REVERT: CE 27 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6897 (tm-30) REVERT: CE 54 ASN cc_start: 0.7208 (m-40) cc_final: 0.6540 (m-40) REVERT: CE 130 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7346 (mm) REVERT: CE 275 GLU cc_start: 0.6788 (tt0) cc_final: 0.5691 (mp0) REVERT: CJ 10 GLU cc_start: 0.7513 (tp30) cc_final: 0.7263 (tp30) REVERT: CJ 66 LYS cc_start: 0.8303 (mtmt) cc_final: 0.7929 (tmtt) REVERT: CD 15 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8470 (p) outliers start: 33 outliers final: 24 residues processed: 233 average time/residue: 2.8981 time to fit residues: 777.7923 Evaluate side-chains 227 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CM residue 58 SER Chi-restraints excluded: chain CL residue 88 THR Chi-restraints excluded: chain CA residue 104 ASP Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 279 GLU Chi-restraints excluded: chain CA residue 345 VAL Chi-restraints excluded: chain CA residue 348 LYS Chi-restraints excluded: chain CA residue 564 SER Chi-restraints excluded: chain CA residue 602 ILE Chi-restraints excluded: chain CA residue 620 HIS Chi-restraints excluded: chain CB residue 62 SER 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 209 LEU 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 CG residue 144 ILE Chi-restraints excluded: chain CG residue 160 VAL Chi-restraints excluded: chain CG residue 162 GLU Chi-restraints excluded: chain CG residue 169 HIS Chi-restraints excluded: chain CG residue 174 SER Chi-restraints excluded: chain CK residue 20 VAL Chi-restraints excluded: chain CE residue 11 LYS Chi-restraints excluded: chain CE residue 130 LEU Chi-restraints excluded: chain CE residue 231 ILE Chi-restraints excluded: chain CD residue 15 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 105 HIS CH 160 GLN CA 397 ASN ** CB 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.9541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 21071 Z= 0.293 Angle : 0.760 80.474 28321 Z= 0.330 Chirality : 0.048 1.558 2945 Planarity : 0.003 0.037 3521 Dihedral : 13.642 165.935 3596 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.62 % Rotamer: Outliers : 1.52 % Allowed : 20.13 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2379 helix: 1.63 (0.14), residues: 1291 sheet: -0.47 (0.40), residues: 171 loop : -1.04 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPCK 32 HIS 0.007 0.001 HISCG 99 PHE 0.024 0.002 PHECA 65 TYR 0.017 0.001 TYRCG 109 ARG 0.004 0.001 ARGCG 114 ********************** 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 fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 3.254 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 118 LYS cc_start: 0.8026 (mttt) cc_final: 0.7503 (mtmt) REVERT: CH 125 SER cc_start: 0.8660 (t) cc_final: 0.8398 (m) REVERT: CM 58 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7887 (p) REVERT: CM 73 LYS cc_start: 0.8379 (mtmt) cc_final: 0.7907 (mttt) REVERT: CL 38 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8421 (mt-10) REVERT: CA 295 MET cc_start: 0.7895 (mmm) cc_final: 0.7603 (mmm) REVERT: CA 486 ASP cc_start: 0.7999 (t70) cc_final: 0.7667 (t0) REVERT: CA 620 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6148 (p-80) REVERT: CA 625 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7776 (mm-30) REVERT: CA 633 LYS cc_start: 0.7849 (pttt) cc_final: 0.7597 (ttpp) REVERT: CI 33 GLN cc_start: 0.7186 (tm-30) cc_final: 0.6935 (tt0) REVERT: CI 64 ARG cc_start: 0.8779 (mmt180) cc_final: 0.7173 (ptm160) REVERT: CI 84 LYS cc_start: 0.6554 (tttt) cc_final: 0.5863 (mttt) REVERT: CB 38 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7703 (mm-30) REVERT: CB 66 LYS cc_start: 0.8351 (mttt) cc_final: 0.7934 (mptp) REVERT: CB 123 ARG cc_start: 0.7940 (ttp-110) cc_final: 0.7735 (ttp-110) REVERT: CB 306 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7067 (ttm-80) REVERT: CF 89 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8048 (tm-30) REVERT: CF 127 ILE cc_start: 0.8729 (pp) cc_final: 0.8400 (mt) REVERT: CF 204 LEU cc_start: 0.7786 (tp) cc_final: 0.7363 (mp) REVERT: CF 242 ASP cc_start: 0.8446 (t70) cc_final: 0.8093 (t0) REVERT: CG 87 ASP cc_start: 0.7820 (m-30) cc_final: 0.7498 (m-30) REVERT: CG 180 ASN cc_start: 0.8439 (m110) cc_final: 0.8173 (m110) REVERT: CG 191 VAL cc_start: 0.8619 (t) cc_final: 0.8371 (p) REVERT: CK 4 ASP cc_start: 0.7173 (p0) cc_final: 0.6791 (p0) REVERT: CK 9 GLN cc_start: 0.6954 (tm-30) cc_final: 0.6515 (mt0) REVERT: CK 54 LYS cc_start: 0.8195 (mttm) cc_final: 0.7592 (mtmt) REVERT: CE 27 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6983 (tm-30) REVERT: CE 54 ASN cc_start: 0.7153 (m-40) cc_final: 0.6599 (m-40) REVERT: CE 130 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7391 (mm) REVERT: CJ 10 GLU cc_start: 0.7547 (tp30) cc_final: 0.7223 (tp30) REVERT: CJ 66 LYS cc_start: 0.8399 (mtmt) cc_final: 0.7998 (tmtt) REVERT: CD 15 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8469 (p) outliers start: 32 outliers final: 20 residues processed: 223 average time/residue: 2.7310 time to fit residues: 699.5909 Evaluate side-chains 217 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 3.140 ------------------------------------------------------------------------------- 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 88 THR Chi-restraints excluded: chain CA residue 104 ASP Chi-restraints excluded: chain CA residue 253 SER Chi-restraints excluded: chain CA residue 279 GLU Chi-restraints excluded: chain CA residue 345 VAL Chi-restraints excluded: chain CA residue 564 SER 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 209 LEU 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 CG residue 144 ILE Chi-restraints excluded: chain CG residue 160 VAL Chi-restraints excluded: chain CG residue 174 SER Chi-restraints excluded: chain CE residue 130 LEU Chi-restraints excluded: chain CE residue 231 ILE Chi-restraints excluded: chain CE residue 321 CYS Chi-restraints excluded: chain CD residue 15 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 171 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CB 57 ASN CG 145 GLN CK 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.115119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.103593 restraints weight = 95029.472| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.66 r_work: 0.3311 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.9673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 21071 Z= 0.237 Angle : 0.743 80.696 28321 Z= 0.318 Chirality : 0.047 1.535 2945 Planarity : 0.003 0.036 3521 Dihedral : 13.499 163.572 3596 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.29 % Favored : 95.54 % Rotamer: Outliers : 1.62 % Allowed : 19.90 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.17), residues: 2379 helix: 1.66 (0.14), residues: 1290 sheet: -0.42 (0.40), residues: 171 loop : -1.00 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPCA 405 HIS 0.006 0.001 HISCG 99 PHE 0.021 0.001 PHECA 65 TYR 0.015 0.001 TYRCG 109 ARG 0.003 0.000 ARGCH 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14191.65 seconds wall clock time: 250 minutes 42.16 seconds (15042.16 seconds total)