Starting phenix.real_space_refine on Mon Mar 18 08:41:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn0_30776/03_2024/7dn0_30776_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn0_30776/03_2024/7dn0_30776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn0_30776/03_2024/7dn0_30776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn0_30776/03_2024/7dn0_30776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn0_30776/03_2024/7dn0_30776_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dn0_30776/03_2024/7dn0_30776_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 4 5.21 5 S 134 5.16 5 C 12822 2.51 5 N 3460 2.21 5 O 3918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 3": "OE1" <-> "OE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D GLU 434": "OE1" <-> "OE2" Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C GLU 220": "OE1" <-> "OE2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C GLU 434": "OE1" <-> "OE2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E GLU 345": "OE1" <-> "OE2" Residue "E GLU 386": "OE1" <-> "OE2" Residue "E GLU 411": "OE1" <-> "OE2" Residue "E GLU 417": "OE1" <-> "OE2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 71": "OE1" <-> "OE2" Residue "F GLU 183": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F GLU 330": "OE1" <-> "OE2" Residue "F GLU 411": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20356 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3346 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3346 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3346 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3346 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "F" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'G2P': 1, 'TAJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'G2P': 1, 'TAJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.76, per 1000 atoms: 0.58 Number of scatterers: 20356 At special positions: 0 Unit cell: (124.2, 103.95, 166.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 134 16.00 P 18 15.00 Mg 4 11.99 O 3918 8.00 N 3460 7.00 C 12822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.44 Conformation dependent library (CDL) restraints added in 3.6 seconds 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4756 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 17 sheets defined 42.9% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'D' and resid 10 through 27 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 115 through 125 Processing helix chain 'D' and resid 145 through 160 removed outlier: 4.377A pdb=" N THR D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.603A pdb=" N LEU D 195 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 224 through 241 removed outlier: 4.687A pdb=" N SER D 241 " --> pdb=" O SER D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 259 Processing helix chain 'D' and resid 288 through 294 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 384 through 399 Processing helix chain 'D' and resid 405 through 409 Processing helix chain 'D' and resid 416 through 436 Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.713A pdb=" N HIS A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 73 through 76 No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.444A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.667A pdb=" N LEU A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 241 removed outlier: 4.692A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.999A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.239A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 384 through 400 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 417 through 436 Processing helix chain 'B' and resid 11 through 27 Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 75 through 78 No H-bonds generated for 'chain 'B' and resid 75 through 78' Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 115 through 125 Processing helix chain 'B' and resid 145 through 160 removed outlier: 4.589A pdb=" N THR B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.616A pdb=" N LEU B 195 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 224 through 241 removed outlier: 4.726A pdb=" N SER B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 removed outlier: 4.502A pdb=" N GLN B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 383 through 400 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 415 through 436 removed outlier: 3.564A pdb=" N VAL B 435 " --> pdb=" O TYR B 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 27 Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.982A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 78' Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 115 through 126 Processing helix chain 'C' and resid 145 through 160 removed outlier: 4.646A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 193 Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 224 through 243 removed outlier: 4.783A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 removed outlier: 3.550A pdb=" N PHE C 255 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN C 256 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU C 259 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 4.211A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 382 through 400 removed outlier: 3.651A pdb=" N ALA C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.436A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 436 Processing helix chain 'E' and resid 11 through 27 Processing helix chain 'E' and resid 42 through 47 No H-bonds generated for 'chain 'E' and resid 42 through 47' Processing helix chain 'E' and resid 49 through 51 No H-bonds generated for 'chain 'E' and resid 49 through 51' Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 111 through 127 removed outlier: 5.152A pdb=" N ASP E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 160 Processing helix chain 'E' and resid 183 through 196 removed outlier: 4.328A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 224 through 242 removed outlier: 5.630A pdb=" N CYS E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU E 242 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 288 through 295 Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 338 Processing helix chain 'E' and resid 340 through 342 No H-bonds generated for 'chain 'E' and resid 340 through 342' Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.983A pdb=" N GLU E 393 " --> pdb=" O ARG E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 removed outlier: 3.820A pdb=" N GLU E 411 " --> pdb=" O TRP E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 434 Processing helix chain 'F' and resid 12 through 28 Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 111 through 128 removed outlier: 4.974A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 Processing helix chain 'F' and resid 183 through 194 Processing helix chain 'F' and resid 207 through 215 Processing helix chain 'F' and resid 224 through 242 removed outlier: 5.404A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 259 Processing helix chain 'F' and resid 281 through 283 No H-bonds generated for 'chain 'F' and resid 281 through 283' Processing helix chain 'F' and resid 288 through 295 Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 307 through 309 No H-bonds generated for 'chain 'F' and resid 307 through 309' Processing helix chain 'F' and resid 325 through 338 Processing helix chain 'F' and resid 340 through 342 No H-bonds generated for 'chain 'F' and resid 340 through 342' Processing helix chain 'F' and resid 383 through 400 removed outlier: 4.692A pdb=" N GLU F 393 " --> pdb=" O ARG F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 409 No H-bonds generated for 'chain 'F' and resid 406 through 409' Processing helix chain 'F' and resid 415 through 434 Processing sheet with id= A, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.845A pdb=" N SER D 6 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL D 68 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N HIS D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N SER D 140 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER D 165 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N VAL D 137 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU D 167 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N HIS D 139 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N PHE D 169 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS D 200 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N SER D 170 " --> pdb=" O CYS D 200 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE D 202 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR D 172 " --> pdb=" O PHE D 202 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL D 204 " --> pdb=" O TYR D 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'D' and resid 269 through 273 removed outlier: 6.298A pdb=" N LYS D 352 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N TYR D 319 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY D 354 " --> pdb=" O TYR D 319 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.172A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE A 5 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE A 135 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE A 7 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL A 9 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N HIS A 139 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= F, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.269A pdb=" N LYS A 352 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N TYR A 319 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY A 354 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.950A pdb=" N ILE B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE B 67 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N VAL B 66 " --> pdb=" O CYS B 4 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER B 6 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL B 68 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY B 134 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE B 7 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 136 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL B 9 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE B 138 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N SER B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL B 137 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 167 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N HIS B 139 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR B 172 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL B 204 " --> pdb=" O TYR B 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= I, first strand: chain 'B' and resid 269 through 273 removed outlier: 6.244A pdb=" N LYS B 352 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TYR B 319 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 354 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.163A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLY C 134 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ILE C 7 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU C 136 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL C 9 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE C 138 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N VAL C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N HIS C 139 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE C 169 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TYR C 172 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL C 204 " --> pdb=" O TYR C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= L, first strand: chain 'C' and resid 269 through 273 removed outlier: 6.221A pdb=" N LYS C 352 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N TYR C 319 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY C 354 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.642A pdb=" N VAL E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU E 67 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ILE E 66 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N HIS E 6 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL E 68 " --> pdb=" O HIS E 6 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLN E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY E 134 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ILE E 7 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN E 136 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ALA E 9 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR E 138 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN E 167 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N HIS E 139 " --> pdb=" O ASN E 167 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU E 200 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER E 170 " --> pdb=" O GLU E 200 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE E 267 " --> pdb=" O SER E 381 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N SER E 381 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 53 through 56 Processing sheet with id= O, first strand: chain 'F' and resid 92 through 94 removed outlier: 8.559A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL F 5 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE F 7 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA F 9 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N HIS F 139 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE F 165 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LEU F 137 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASN F 167 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N HIS F 139 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE F 169 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU F 200 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N SER F 170 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR F 202 " --> pdb=" O SER F 170 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.582A pdb=" N LYS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 269 through 273 774 hydrogen bonds defined for protein. 2055 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: 5.98 Time building geometry restraints manager: 9.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3428 1.31 - 1.43: 5598 1.43 - 1.56: 11565 1.56 - 1.69: 35 1.69 - 1.81: 208 Bond restraints: 20834 Sorted by residual: bond pdb=" C1' GTP A 501 " pdb=" C2' GTP A 501 " ideal model delta sigma weight residual 1.524 1.277 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C1' GTP C 501 " pdb=" C2' GTP C 501 " ideal model delta sigma weight residual 1.524 1.277 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C1' GTP B 501 " pdb=" C2' GTP B 501 " ideal model delta sigma weight residual 1.524 1.278 0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C1' GTP D 501 " pdb=" C2' GTP D 501 " ideal model delta sigma weight residual 1.524 1.284 0.240 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C1' GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sigma weight residual 1.410 1.615 -0.205 2.00e-02 2.50e+03 1.05e+02 ... (remaining 20829 not shown) Histogram of bond angle deviations from ideal: 59.51 - 75.99: 6 75.99 - 92.48: 0 92.48 - 108.96: 1890 108.96 - 125.44: 26121 125.44 - 141.93: 347 Bond angle restraints: 28364 Sorted by residual: angle pdb=" C PRO F 173 " pdb=" N SER F 174 " pdb=" CA SER F 174 " ideal model delta sigma weight residual 120.69 141.93 -21.24 2.95e+00 1.15e-01 5.18e+01 angle pdb=" C THR F 287 " pdb=" N VAL F 288 " pdb=" CA VAL F 288 " ideal model delta sigma weight residual 120.24 123.59 -3.35 6.30e-01 2.52e+00 2.83e+01 angle pdb=" PA G2P E 501 " pdb=" C3A G2P E 501 " pdb=" PB G2P E 501 " ideal model delta sigma weight residual 120.83 106.17 14.66 3.00e+00 1.11e-01 2.39e+01 angle pdb=" N SER B 340 " pdb=" CA SER B 340 " pdb=" C SER B 340 " ideal model delta sigma weight residual 111.28 105.97 5.31 1.09e+00 8.42e-01 2.37e+01 angle pdb=" C PHE A 87 " pdb=" N HIS A 88 " pdb=" CA HIS A 88 " ideal model delta sigma weight residual 120.67 126.76 -6.09 1.34e+00 5.57e-01 2.06e+01 ... (remaining 28359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.30: 12220 33.30 - 66.59: 348 66.59 - 99.89: 38 99.89 - 133.18: 4 133.18 - 166.48: 8 Dihedral angle restraints: 12618 sinusoidal: 5204 harmonic: 7414 Sorted by residual: dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -124.25 -166.48 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -55.83 160.42 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sinusoidal sigma weight residual 69.27 -134.98 -155.75 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 12615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2970 0.118 - 0.237: 147 0.237 - 0.355: 11 0.355 - 0.474: 0 0.474 - 0.592: 2 Chirality restraints: 3130 Sorted by residual: chirality pdb=" CBB TAJ E 502 " pdb=" CBA TAJ E 502 " pdb=" CBC TAJ E 502 " pdb=" CBD TAJ E 502 " both_signs ideal model delta sigma weight residual False 2.06 2.65 -0.59 2.00e-01 2.50e+01 8.77e+00 chirality pdb=" CBB TAJ F 502 " pdb=" CBA TAJ F 502 " pdb=" CBC TAJ F 502 " pdb=" CBD TAJ F 502 " both_signs ideal model delta sigma weight residual False 2.06 2.65 -0.59 2.00e-01 2.50e+01 8.75e+00 chirality pdb=" CAV TAJ F 502 " pdb=" CAQ TAJ F 502 " pdb=" CAU TAJ F 502 " pdb=" CAZ TAJ F 502 " both_signs ideal model delta sigma weight residual False 2.63 2.30 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 3127 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 397 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ALA E 397 " 0.056 2.00e-02 2.50e+03 pdb=" O ALA E 397 " -0.021 2.00e-02 2.50e+03 pdb=" N MET E 398 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 397 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.22e+00 pdb=" C LEU C 397 " 0.053 2.00e-02 2.50e+03 pdb=" O LEU C 397 " -0.020 2.00e-02 2.50e+03 pdb=" N MET C 398 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 397 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.18e+00 pdb=" C LEU A 397 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU A 397 " -0.020 2.00e-02 2.50e+03 pdb=" N MET A 398 " -0.018 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 244 2.64 - 3.21: 16907 3.21 - 3.77: 29659 3.77 - 4.34: 40275 4.34 - 4.90: 69799 Nonbonded interactions: 156884 Sorted by model distance: nonbonded pdb=" O1G GTP B 501 " pdb="MG MG B 502 " model vdw 2.080 2.170 nonbonded pdb=" O1G GTP C 501 " pdb="MG MG C 502 " model vdw 2.126 2.170 nonbonded pdb=" O1G GTP D 501 " pdb="MG MG D 502 " model vdw 2.130 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 2.147 2.170 nonbonded pdb=" O ASN B 186 " pdb=" OG1 THR B 190 " model vdw 2.256 2.440 ... (remaining 156879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 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: 0.020 Extract box with map and model: 2.150 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 55.130 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.010 0.247 20834 Z= 0.675 Angle : 0.966 21.236 28364 Z= 0.535 Chirality : 0.062 0.592 3130 Planarity : 0.008 0.070 3668 Dihedral : 16.615 166.481 7862 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.74 % Allowed : 8.80 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.21 (0.14), residues: 2544 helix: -1.84 (0.12), residues: 1120 sheet: -0.68 (0.26), residues: 384 loop : -2.97 (0.15), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 21 HIS 0.012 0.002 HIS B 266 PHE 0.025 0.003 PHE A 141 TYR 0.031 0.002 TYR D 432 ARG 0.007 0.001 ARG B 422 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 420 time to evaluate : 2.518 Fit side-chains REVERT: D 3 GLU cc_start: 0.7660 (mp0) cc_final: 0.7305 (mp0) REVERT: D 221 ARG cc_start: 0.8429 (mtt180) cc_final: 0.6327 (tpt170) REVERT: D 300 ASN cc_start: 0.8967 (m110) cc_final: 0.8763 (m110) REVERT: D 326 LYS cc_start: 0.7958 (tttt) cc_final: 0.7626 (tptt) REVERT: D 425 MET cc_start: 0.8224 (mmp) cc_final: 0.7936 (mmm) REVERT: A 31 GLN cc_start: 0.8160 (mt0) cc_final: 0.7262 (mm-40) REVERT: A 50 ASN cc_start: 0.8187 (t0) cc_final: 0.7447 (t0) REVERT: A 176 GLN cc_start: 0.7968 (mm110) cc_final: 0.7660 (mm-40) REVERT: A 197 HIS cc_start: 0.7638 (m90) cc_final: 0.7414 (m-70) REVERT: A 215 ARG cc_start: 0.7125 (ttm110) cc_final: 0.6908 (tmm160) REVERT: A 249 ASN cc_start: 0.8316 (p0) cc_final: 0.7948 (p0) REVERT: A 398 MET cc_start: 0.8201 (mtm) cc_final: 0.7891 (mtp) REVERT: A 435 VAL cc_start: 0.8023 (t) cc_final: 0.7774 (m) REVERT: B 52 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7187 (m-10) REVERT: B 123 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.7969 (tpp80) REVERT: B 176 GLN cc_start: 0.7980 (mm110) cc_final: 0.6803 (mt0) REVERT: B 214 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.7292 (ttp-170) REVERT: B 219 ILE cc_start: 0.8135 (mm) cc_final: 0.7922 (mt) REVERT: B 392 ASP cc_start: 0.7408 (m-30) cc_final: 0.7050 (m-30) REVERT: C 141 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.6827 (m-80) REVERT: C 149 PHE cc_start: 0.8131 (t80) cc_final: 0.7876 (t80) REVERT: C 176 GLN cc_start: 0.7403 (mm110) cc_final: 0.6853 (mt0) REVERT: C 178 SER cc_start: 0.8312 (m) cc_final: 0.7941 (p) REVERT: C 219 ILE cc_start: 0.8329 (mm) cc_final: 0.8100 (mt) REVERT: E 69 ASP cc_start: 0.8068 (t70) cc_final: 0.7830 (t0) REVERT: E 90 ASP cc_start: 0.7393 (t0) cc_final: 0.7090 (t0) REVERT: E 269 MET cc_start: 0.7783 (ptp) cc_final: 0.7573 (mtm) REVERT: E 302 MET cc_start: 0.8462 (mtt) cc_final: 0.8043 (mtm) REVERT: E 336 GLN cc_start: 0.7944 (tt0) cc_final: 0.7662 (mt0) REVERT: E 339 ASN cc_start: 0.8090 (p0) cc_final: 0.7431 (p0) REVERT: E 346 TRP cc_start: 0.8142 (p-90) cc_final: 0.7797 (p-90) REVERT: E 434 GLN cc_start: 0.8311 (tp40) cc_final: 0.8107 (tt0) REVERT: F 88 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7360 (ttp-170) REVERT: F 113 GLU cc_start: 0.6924 (mp0) cc_final: 0.6358 (mp0) REVERT: F 123 ARG cc_start: 0.8685 (ttm110) cc_final: 0.8016 (mtt180) REVERT: F 151 THR cc_start: 0.8793 (m) cc_final: 0.8556 (m) REVERT: F 166 MET cc_start: 0.7536 (ttt) cc_final: 0.7259 (ttt) REVERT: F 299 LYS cc_start: 0.8136 (pttt) cc_final: 0.7727 (pttt) REVERT: F 398 MET cc_start: 0.7782 (mtt) cc_final: 0.7574 (mtp) outliers start: 16 outliers final: 7 residues processed: 435 average time/residue: 0.3764 time to fit residues: 238.4337 Evaluate side-chains 331 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 322 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 5 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 197 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 228 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS D 107 HIS D 128 GLN D 197 HIS D 206 ASN D 258 ASN D 300 ASN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS A 206 ASN A 216 ASN A 226 ASN A 256 GLN A 301 GLN A 309 HIS A 372 GLN B 11 GLN B 50 ASN B 192 HIS B 283 HIS B 372 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 HIS C 358 GLN C 372 GLN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN E 139 HIS E 192 HIS E 206 ASN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN E 349 ASN E 406 HIS F 91 ASN F 139 HIS F 167 ASN F 206 ASN ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20834 Z= 0.152 Angle : 0.523 9.514 28364 Z= 0.265 Chirality : 0.043 0.150 3130 Planarity : 0.005 0.042 3668 Dihedral : 11.268 167.506 3195 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.13 % Allowed : 14.07 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.57 (0.16), residues: 2544 helix: -0.16 (0.15), residues: 1092 sheet: -0.27 (0.25), residues: 412 loop : -2.32 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.008 0.001 HIS E 139 PHE 0.013 0.001 PHE C 351 TYR 0.013 0.001 TYR A 103 ARG 0.004 0.000 ARG F 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 348 time to evaluate : 2.416 Fit side-chains REVERT: D 221 ARG cc_start: 0.8480 (mtt180) cc_final: 0.6397 (tpt170) REVERT: D 326 LYS cc_start: 0.7959 (tttt) cc_final: 0.7684 (tptt) REVERT: A 31 GLN cc_start: 0.8081 (mt0) cc_final: 0.7176 (mm110) REVERT: A 52 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.6825 (m-10) REVERT: A 176 GLN cc_start: 0.7918 (mm110) cc_final: 0.7588 (mm-40) REVERT: A 197 HIS cc_start: 0.7449 (m90) cc_final: 0.7223 (m-70) REVERT: A 249 ASN cc_start: 0.8318 (p0) cc_final: 0.7837 (p0) REVERT: A 391 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8453 (tt) REVERT: A 398 MET cc_start: 0.7392 (mtm) cc_final: 0.7146 (mtp) REVERT: B 52 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7121 (m-10) REVERT: B 123 ARG cc_start: 0.8258 (tpp-160) cc_final: 0.8005 (tpp80) REVERT: B 176 GLN cc_start: 0.7871 (mm110) cc_final: 0.6784 (mt0) REVERT: B 214 ARG cc_start: 0.7607 (ttp-170) cc_final: 0.7270 (ttp-170) REVERT: B 219 ILE cc_start: 0.8178 (mm) cc_final: 0.7898 (mt) REVERT: B 221 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7139 (mmt180) REVERT: B 334 THR cc_start: 0.8464 (t) cc_final: 0.8253 (m) REVERT: B 392 ASP cc_start: 0.7509 (m-30) cc_final: 0.7166 (m-30) REVERT: C 129 CYS cc_start: 0.6299 (m) cc_final: 0.6025 (m) REVERT: C 141 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6583 (m-10) REVERT: E 90 ASP cc_start: 0.7526 (t0) cc_final: 0.7185 (t0) REVERT: E 151 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7761 (m) REVERT: E 166 MET cc_start: 0.7511 (tpp) cc_final: 0.7271 (mtp) REVERT: E 301 MET cc_start: 0.8196 (mmp) cc_final: 0.7988 (mmm) REVERT: E 302 MET cc_start: 0.8466 (mtt) cc_final: 0.8259 (mtm) REVERT: E 339 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7217 (p0) REVERT: E 346 TRP cc_start: 0.8100 (p-90) cc_final: 0.7781 (p-90) REVERT: E 434 GLN cc_start: 0.8263 (tp40) cc_final: 0.8037 (tt0) REVERT: F 60 LYS cc_start: 0.8430 (mttm) cc_final: 0.7389 (tttp) REVERT: F 88 ARG cc_start: 0.7687 (ttp-110) cc_final: 0.7398 (ttp-170) REVERT: F 113 GLU cc_start: 0.6692 (mp0) cc_final: 0.6257 (mp0) REVERT: F 123 ARG cc_start: 0.8625 (ttm110) cc_final: 0.8060 (mtt180) REVERT: F 151 THR cc_start: 0.8427 (m) cc_final: 0.8151 (m) REVERT: F 299 LYS cc_start: 0.8048 (pttt) cc_final: 0.7618 (pttt) REVERT: F 398 MET cc_start: 0.8303 (mtt) cc_final: 0.8061 (mtp) outliers start: 46 outliers final: 23 residues processed: 382 average time/residue: 0.3393 time to fit residues: 197.2631 Evaluate side-chains 351 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 322 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 276 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 155 optimal weight: 0.0270 chunk 63 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN B 283 HIS ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN E 336 GLN E 339 ASN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 206 ASN F 282 GLN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20834 Z= 0.192 Angle : 0.525 9.655 28364 Z= 0.263 Chirality : 0.044 0.201 3130 Planarity : 0.004 0.041 3668 Dihedral : 10.965 169.641 3194 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.92 % Allowed : 16.67 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.19 (0.16), residues: 2544 helix: 0.29 (0.16), residues: 1090 sheet: -0.31 (0.26), residues: 408 loop : -2.17 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.006 0.001 HIS D 192 PHE 0.014 0.001 PHE F 272 TYR 0.010 0.001 TYR D 103 ARG 0.002 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 331 time to evaluate : 2.707 Fit side-chains REVERT: D 3 GLU cc_start: 0.7770 (mp0) cc_final: 0.7519 (mp0) REVERT: D 221 ARG cc_start: 0.8521 (mtt180) cc_final: 0.6409 (tpt170) REVERT: D 300 ASN cc_start: 0.8986 (m110) cc_final: 0.8584 (m110) REVERT: D 326 LYS cc_start: 0.8034 (tttt) cc_final: 0.7742 (tptt) REVERT: A 31 GLN cc_start: 0.8098 (mt0) cc_final: 0.7250 (mm-40) REVERT: A 52 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6877 (m-10) REVERT: A 176 GLN cc_start: 0.7970 (mm110) cc_final: 0.7709 (mm-40) REVERT: A 197 HIS cc_start: 0.7459 (m90) cc_final: 0.7203 (m-70) REVERT: A 249 ASN cc_start: 0.8319 (p0) cc_final: 0.7797 (p0) REVERT: A 326 LYS cc_start: 0.5296 (mttt) cc_final: 0.5051 (mttt) REVERT: A 391 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8424 (tt) REVERT: A 392 ASP cc_start: 0.7198 (m-30) cc_final: 0.6223 (m-30) REVERT: A 408 TYR cc_start: 0.7530 (m-80) cc_final: 0.7304 (m-80) REVERT: A 432 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.6863 (t80) REVERT: B 24 TYR cc_start: 0.8462 (m-10) cc_final: 0.8056 (m-10) REVERT: B 52 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.6796 (m-10) REVERT: B 123 ARG cc_start: 0.8161 (tpp-160) cc_final: 0.7913 (tpp80) REVERT: B 176 GLN cc_start: 0.7916 (mm110) cc_final: 0.6903 (mt0) REVERT: B 193 THR cc_start: 0.8338 (t) cc_final: 0.7903 (m) REVERT: B 214 ARG cc_start: 0.7538 (ttp-170) cc_final: 0.7246 (ttp-170) REVERT: B 219 ILE cc_start: 0.8222 (mm) cc_final: 0.7942 (mt) REVERT: B 221 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7343 (mmt180) REVERT: C 141 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6699 (m-10) REVERT: C 252 LEU cc_start: 0.8795 (mp) cc_final: 0.8532 (mp) REVERT: C 432 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7139 (t80) REVERT: E 90 ASP cc_start: 0.7509 (t0) cc_final: 0.7201 (t0) REVERT: E 151 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7829 (m) REVERT: E 302 MET cc_start: 0.8410 (mtt) cc_final: 0.8209 (mtm) REVERT: E 338 LYS cc_start: 0.8295 (tppt) cc_final: 0.7911 (mptt) REVERT: E 339 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7086 (p0) REVERT: E 346 TRP cc_start: 0.8143 (p-90) cc_final: 0.7846 (p-90) REVERT: F 88 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.7391 (ttp-170) REVERT: F 113 GLU cc_start: 0.6937 (mp0) cc_final: 0.6332 (mp0) REVERT: F 123 ARG cc_start: 0.8641 (ttm110) cc_final: 0.8124 (mtt180) REVERT: F 299 LYS cc_start: 0.8114 (pttt) cc_final: 0.7704 (pttt) REVERT: F 398 MET cc_start: 0.8552 (mtt) cc_final: 0.8341 (mtp) REVERT: F 425 MET cc_start: 0.7769 (mmm) cc_final: 0.7202 (tpt) outliers start: 63 outliers final: 41 residues processed: 373 average time/residue: 0.3473 time to fit residues: 192.6547 Evaluate side-chains 367 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 318 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 166 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 2.9990 chunk 172 optimal weight: 0.0030 chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 0.0370 chunk 109 optimal weight: 8.9990 chunk 153 optimal weight: 0.0270 chunk 230 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 overall best weight: 0.4266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN B 18 ASN B 91 GLN C 258 ASN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN E 349 ASN E 350 ASN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN F 349 ASN F 433 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20834 Z= 0.116 Angle : 0.471 9.437 28364 Z= 0.233 Chirality : 0.041 0.193 3130 Planarity : 0.004 0.040 3668 Dihedral : 10.473 172.277 3194 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.78 % Allowed : 17.96 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.68 (0.17), residues: 2544 helix: 0.72 (0.16), residues: 1092 sheet: -0.09 (0.25), residues: 430 loop : -1.91 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 103 HIS 0.003 0.000 HIS C 8 PHE 0.014 0.001 PHE F 296 TYR 0.012 0.001 TYR A 103 ARG 0.003 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 345 time to evaluate : 2.248 Fit side-chains REVERT: D 3 GLU cc_start: 0.7757 (mp0) cc_final: 0.7181 (mp0) REVERT: D 221 ARG cc_start: 0.8555 (mtt180) cc_final: 0.6425 (tpt170) REVERT: D 326 LYS cc_start: 0.8001 (tttt) cc_final: 0.7679 (tptt) REVERT: A 3 GLU cc_start: 0.7257 (mp0) cc_final: 0.7054 (mp0) REVERT: A 31 GLN cc_start: 0.8046 (mt0) cc_final: 0.7202 (mm110) REVERT: A 52 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.6904 (m-10) REVERT: A 176 GLN cc_start: 0.7787 (mm110) cc_final: 0.7565 (mm-40) REVERT: A 197 HIS cc_start: 0.7357 (m90) cc_final: 0.7094 (m-70) REVERT: A 249 ASN cc_start: 0.8272 (p0) cc_final: 0.7727 (p0) REVERT: A 313 MET cc_start: 0.7811 (ttm) cc_final: 0.7506 (ttp) REVERT: A 391 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8416 (tt) REVERT: A 392 ASP cc_start: 0.7133 (m-30) cc_final: 0.6223 (m-30) REVERT: A 432 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6812 (t80) REVERT: B 24 TYR cc_start: 0.8470 (m-10) cc_final: 0.8131 (m-10) REVERT: B 36 MET cc_start: 0.7925 (ptm) cc_final: 0.7712 (ptm) REVERT: B 123 ARG cc_start: 0.8106 (tpp-160) cc_final: 0.7882 (tpp80) REVERT: B 176 GLN cc_start: 0.7896 (mm110) cc_final: 0.6905 (mt0) REVERT: B 193 THR cc_start: 0.8203 (t) cc_final: 0.7788 (m) REVERT: B 214 ARG cc_start: 0.7456 (ttp-170) cc_final: 0.7132 (ttp-170) REVERT: B 219 ILE cc_start: 0.8213 (mm) cc_final: 0.7957 (mt) REVERT: B 221 ARG cc_start: 0.8064 (mtt180) cc_final: 0.7312 (mmt180) REVERT: C 141 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6514 (m-80) REVERT: C 149 PHE cc_start: 0.7925 (t80) cc_final: 0.7663 (t80) REVERT: C 432 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.7052 (t80) REVERT: E 151 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7561 (m) REVERT: E 166 MET cc_start: 0.7238 (mtp) cc_final: 0.6929 (mtp) REVERT: E 339 ASN cc_start: 0.7233 (p0) cc_final: 0.6647 (p0) REVERT: F 88 ARG cc_start: 0.7666 (ttp-110) cc_final: 0.7393 (ttp-170) REVERT: F 123 ARG cc_start: 0.8608 (ttm110) cc_final: 0.8059 (mtt180) REVERT: F 151 THR cc_start: 0.8363 (m) cc_final: 0.8077 (m) REVERT: F 299 LYS cc_start: 0.8012 (pttt) cc_final: 0.7624 (pttt) REVERT: F 337 ASN cc_start: 0.6248 (t160) cc_final: 0.5848 (p0) REVERT: F 425 MET cc_start: 0.7822 (mmm) cc_final: 0.7620 (mmm) outliers start: 60 outliers final: 32 residues processed: 388 average time/residue: 0.3403 time to fit residues: 197.7808 Evaluate side-chains 356 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 318 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 97 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 100 optimal weight: 0.4980 chunk 207 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 HIS ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN B 258 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20834 Z= 0.204 Angle : 0.519 9.194 28364 Z= 0.257 Chirality : 0.044 0.193 3130 Planarity : 0.004 0.044 3668 Dihedral : 10.589 170.952 3192 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.52 % Allowed : 17.27 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.63 (0.17), residues: 2544 helix: 0.84 (0.16), residues: 1088 sheet: -0.01 (0.26), residues: 406 loop : -1.97 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 21 HIS 0.006 0.001 HIS B 139 PHE 0.024 0.001 PHE F 296 TYR 0.016 0.001 TYR D 103 ARG 0.003 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 338 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 3 GLU cc_start: 0.7449 (mp0) cc_final: 0.6984 (mp0) REVERT: D 221 ARG cc_start: 0.8568 (mtt180) cc_final: 0.6435 (tpt170) REVERT: D 326 LYS cc_start: 0.8148 (tttt) cc_final: 0.7732 (tptt) REVERT: D 377 MET cc_start: 0.6125 (ttp) cc_final: 0.5871 (ttp) REVERT: A 26 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7563 (tt) REVERT: A 31 GLN cc_start: 0.8039 (mt0) cc_final: 0.7196 (mm110) REVERT: A 52 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.6939 (m-10) REVERT: A 176 GLN cc_start: 0.7968 (mm110) cc_final: 0.7695 (mm-40) REVERT: A 197 HIS cc_start: 0.7385 (m90) cc_final: 0.7084 (m-70) REVERT: A 249 ASN cc_start: 0.8280 (p0) cc_final: 0.7868 (p0) REVERT: A 391 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8439 (tt) REVERT: A 392 ASP cc_start: 0.7209 (m-30) cc_final: 0.6282 (m-30) REVERT: A 408 TYR cc_start: 0.7573 (m-80) cc_final: 0.7343 (m-80) REVERT: A 432 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.6813 (t80) REVERT: B 24 TYR cc_start: 0.8474 (m-10) cc_final: 0.8031 (m-10) REVERT: B 52 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.6728 (m-10) REVERT: B 123 ARG cc_start: 0.8210 (tpp-160) cc_final: 0.7951 (tpp80) REVERT: B 176 GLN cc_start: 0.7962 (mm110) cc_final: 0.7020 (mt0) REVERT: B 193 THR cc_start: 0.8435 (t) cc_final: 0.8064 (m) REVERT: B 214 ARG cc_start: 0.7448 (ttp-170) cc_final: 0.7125 (ttp-170) REVERT: B 219 ILE cc_start: 0.8257 (mm) cc_final: 0.7997 (mt) REVERT: B 221 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7384 (mmt180) REVERT: B 417 GLU cc_start: 0.7664 (mp0) cc_final: 0.7416 (mp0) REVERT: C 123 ARG cc_start: 0.7620 (tpp80) cc_final: 0.7371 (tpp80) REVERT: C 141 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6640 (m-80) REVERT: C 149 PHE cc_start: 0.8005 (t80) cc_final: 0.7710 (t80) REVERT: C 432 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7163 (t80) REVERT: E 90 ASP cc_start: 0.7597 (t0) cc_final: 0.7323 (t0) REVERT: E 149 MET cc_start: 0.8456 (tpp) cc_final: 0.8163 (tpt) REVERT: E 151 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7902 (m) REVERT: E 166 MET cc_start: 0.7336 (mtp) cc_final: 0.7061 (mtp) REVERT: E 338 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7859 (mptt) REVERT: E 339 ASN cc_start: 0.7582 (p0) cc_final: 0.7018 (p0) REVERT: E 346 TRP cc_start: 0.7981 (p-90) cc_final: 0.7633 (p-90) REVERT: F 88 ARG cc_start: 0.7646 (ttp-110) cc_final: 0.7342 (ttp-170) REVERT: F 113 GLU cc_start: 0.6980 (mp0) cc_final: 0.6460 (mp0) REVERT: F 123 ARG cc_start: 0.8628 (ttm110) cc_final: 0.8106 (mtt180) REVERT: F 151 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8201 (m) REVERT: F 299 LYS cc_start: 0.8192 (pttt) cc_final: 0.7747 (pttt) REVERT: F 329 ASP cc_start: 0.8130 (m-30) cc_final: 0.7859 (m-30) REVERT: F 425 MET cc_start: 0.7835 (mmm) cc_final: 0.7619 (mmm) outliers start: 76 outliers final: 57 residues processed: 395 average time/residue: 0.3368 time to fit residues: 200.4678 Evaluate side-chains 384 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 318 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 353 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 10.0000 chunk 219 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 143 optimal weight: 0.3980 chunk 60 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 202 optimal weight: 0.0050 chunk 112 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 GLN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20834 Z= 0.180 Angle : 0.513 9.465 28364 Z= 0.253 Chirality : 0.043 0.224 3130 Planarity : 0.004 0.037 3668 Dihedral : 10.530 172.108 3192 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.56 % Allowed : 18.29 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.51 (0.17), residues: 2544 helix: 0.93 (0.16), residues: 1094 sheet: -0.07 (0.25), residues: 438 loop : -1.90 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 21 HIS 0.005 0.001 HIS D 192 PHE 0.012 0.001 PHE E 319 TYR 0.014 0.001 TYR D 103 ARG 0.002 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 328 time to evaluate : 2.512 Fit side-chains revert: symmetry clash REVERT: D 221 ARG cc_start: 0.8569 (mtt180) cc_final: 0.6430 (tpt170) REVERT: D 326 LYS cc_start: 0.8151 (tttt) cc_final: 0.7732 (tptt) REVERT: D 377 MET cc_start: 0.6260 (ttp) cc_final: 0.6016 (ttp) REVERT: A 26 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7538 (tt) REVERT: A 31 GLN cc_start: 0.8047 (mt0) cc_final: 0.7163 (mm110) REVERT: A 52 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.6939 (m-10) REVERT: A 176 GLN cc_start: 0.8023 (mm110) cc_final: 0.7751 (mm-40) REVERT: A 197 HIS cc_start: 0.7351 (m90) cc_final: 0.7053 (m-70) REVERT: A 249 ASN cc_start: 0.8290 (p0) cc_final: 0.7868 (p0) REVERT: A 391 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8439 (tt) REVERT: A 392 ASP cc_start: 0.7197 (m-30) cc_final: 0.6282 (m-30) REVERT: A 408 TYR cc_start: 0.7639 (m-80) cc_final: 0.7422 (m-80) REVERT: A 432 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.6819 (t80) REVERT: B 24 TYR cc_start: 0.8458 (m-10) cc_final: 0.8021 (m-10) REVERT: B 52 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.6728 (m-10) REVERT: B 123 ARG cc_start: 0.8131 (tpp-160) cc_final: 0.7908 (tpp80) REVERT: B 176 GLN cc_start: 0.7949 (mm110) cc_final: 0.7012 (mt0) REVERT: B 193 THR cc_start: 0.8450 (t) cc_final: 0.8078 (m) REVERT: B 214 ARG cc_start: 0.7461 (ttp-170) cc_final: 0.7122 (ttp-170) REVERT: B 219 ILE cc_start: 0.8257 (mm) cc_final: 0.8002 (mt) REVERT: B 221 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7344 (mmt180) REVERT: B 417 GLU cc_start: 0.7662 (mp0) cc_final: 0.7408 (mp0) REVERT: B 424 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7484 (t0) REVERT: C 123 ARG cc_start: 0.7752 (tpp80) cc_final: 0.7506 (tpp80) REVERT: C 141 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6721 (m-80) REVERT: C 149 PHE cc_start: 0.8016 (t80) cc_final: 0.7692 (t80) REVERT: C 432 TYR cc_start: 0.7824 (OUTLIER) cc_final: 0.7174 (t80) REVERT: E 149 MET cc_start: 0.8460 (tpp) cc_final: 0.8182 (tpt) REVERT: E 151 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7581 (m) REVERT: E 166 MET cc_start: 0.7328 (mtp) cc_final: 0.7075 (mtp) REVERT: E 338 LYS cc_start: 0.8100 (ttmm) cc_final: 0.7751 (ttmm) REVERT: E 339 ASN cc_start: 0.7618 (p0) cc_final: 0.6983 (p0) REVERT: E 346 TRP cc_start: 0.7936 (p-90) cc_final: 0.7623 (p-90) REVERT: F 88 ARG cc_start: 0.7631 (ttp-110) cc_final: 0.7326 (ttp-170) REVERT: F 113 GLU cc_start: 0.7050 (mp0) cc_final: 0.6490 (mp0) REVERT: F 123 ARG cc_start: 0.8645 (ttm110) cc_final: 0.8429 (mtm-85) REVERT: F 151 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8155 (m) REVERT: F 248 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.6901 (tt) REVERT: F 299 LYS cc_start: 0.8218 (pttt) cc_final: 0.7739 (pttt) REVERT: F 337 ASN cc_start: 0.6483 (t0) cc_final: 0.6032 (p0) REVERT: F 425 MET cc_start: 0.7789 (mmm) cc_final: 0.7505 (mmm) outliers start: 77 outliers final: 57 residues processed: 388 average time/residue: 0.3491 time to fit residues: 205.3823 Evaluate side-chains 388 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 320 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 286 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN B 283 HIS ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN E 266 HIS F 6 HIS ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20834 Z= 0.298 Angle : 0.584 10.010 28364 Z= 0.292 Chirality : 0.046 0.226 3130 Planarity : 0.004 0.040 3668 Dihedral : 10.838 171.737 3192 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.21 % Allowed : 17.96 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2544 helix: 0.77 (0.16), residues: 1092 sheet: -0.04 (0.26), residues: 396 loop : -2.00 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 21 HIS 0.009 0.001 HIS D 192 PHE 0.020 0.002 PHE F 319 TYR 0.015 0.001 TYR B 103 ARG 0.005 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 324 time to evaluate : 2.286 Fit side-chains revert: symmetry clash REVERT: D 221 ARG cc_start: 0.8591 (mtt180) cc_final: 0.6434 (tpt170) REVERT: D 326 LYS cc_start: 0.8045 (tttt) cc_final: 0.7712 (tptt) REVERT: A 26 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7417 (tt) REVERT: A 31 GLN cc_start: 0.8097 (mt0) cc_final: 0.7218 (mm-40) REVERT: A 52 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.6993 (m-10) REVERT: A 176 GLN cc_start: 0.8051 (mm110) cc_final: 0.7795 (mm-40) REVERT: A 197 HIS cc_start: 0.7382 (m90) cc_final: 0.7073 (m-70) REVERT: A 249 ASN cc_start: 0.8244 (p0) cc_final: 0.7875 (p0) REVERT: A 285 GLN cc_start: 0.7151 (pp30) cc_final: 0.5624 (mm-40) REVERT: A 391 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8446 (tt) REVERT: A 392 ASP cc_start: 0.7257 (m-30) cc_final: 0.6379 (m-30) REVERT: A 408 TYR cc_start: 0.7669 (m-80) cc_final: 0.7452 (m-80) REVERT: A 432 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.6698 (t80) REVERT: B 52 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7143 (m-10) REVERT: B 123 ARG cc_start: 0.8257 (tpp-160) cc_final: 0.7991 (tpp80) REVERT: B 176 GLN cc_start: 0.8136 (mm110) cc_final: 0.7295 (mt0) REVERT: B 193 THR cc_start: 0.8531 (t) cc_final: 0.8199 (m) REVERT: B 214 ARG cc_start: 0.7470 (ttp-170) cc_final: 0.7230 (ttp-170) REVERT: B 219 ILE cc_start: 0.8274 (mm) cc_final: 0.7996 (mt) REVERT: B 221 ARG cc_start: 0.8133 (mtt180) cc_final: 0.7369 (mmt180) REVERT: B 417 GLU cc_start: 0.7666 (mp0) cc_final: 0.7334 (mp0) REVERT: B 424 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7513 (t0) REVERT: C 123 ARG cc_start: 0.7802 (tpp80) cc_final: 0.7529 (tpp80) REVERT: C 141 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.6925 (m-10) REVERT: C 149 PHE cc_start: 0.8008 (t80) cc_final: 0.7673 (t80) REVERT: C 219 ILE cc_start: 0.8008 (mm) cc_final: 0.7744 (mt) REVERT: C 432 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7253 (t80) REVERT: E 149 MET cc_start: 0.8421 (tpp) cc_final: 0.8149 (tpt) REVERT: E 166 MET cc_start: 0.7398 (mtp) cc_final: 0.7141 (mtp) REVERT: E 338 LYS cc_start: 0.7811 (ttmm) cc_final: 0.7468 (ttmm) REVERT: E 339 ASN cc_start: 0.7916 (p0) cc_final: 0.7262 (p0) REVERT: E 346 TRP cc_start: 0.7963 (p-90) cc_final: 0.7669 (p-90) REVERT: F 88 ARG cc_start: 0.7630 (ttp-110) cc_final: 0.7307 (ttp-170) REVERT: F 113 GLU cc_start: 0.7152 (mp0) cc_final: 0.6577 (mp0) REVERT: F 123 ARG cc_start: 0.8617 (ttm110) cc_final: 0.8008 (mtt180) REVERT: F 248 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.6980 (tt) REVERT: F 299 LYS cc_start: 0.8303 (pttt) cc_final: 0.7850 (pttt) REVERT: F 329 ASP cc_start: 0.8125 (m-30) cc_final: 0.7846 (m-30) REVERT: F 337 ASN cc_start: 0.6582 (t0) cc_final: 0.6143 (p0) outliers start: 91 outliers final: 67 residues processed: 396 average time/residue: 0.3356 time to fit residues: 200.7509 Evaluate side-chains 393 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 317 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 353 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.9990 chunk 96 optimal weight: 0.0070 chunk 145 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN B 283 HIS ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20834 Z= 0.145 Angle : 0.502 10.338 28364 Z= 0.247 Chirality : 0.042 0.234 3130 Planarity : 0.004 0.039 3668 Dihedral : 10.468 174.235 3192 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.43 % Allowed : 19.26 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.41 (0.17), residues: 2544 helix: 0.99 (0.16), residues: 1098 sheet: -0.06 (0.25), residues: 438 loop : -1.81 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 21 HIS 0.004 0.001 HIS B 139 PHE 0.011 0.001 PHE E 377 TYR 0.010 0.001 TYR D 103 ARG 0.003 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 332 time to evaluate : 2.521 Fit side-chains revert: symmetry clash REVERT: D 221 ARG cc_start: 0.8569 (mtt180) cc_final: 0.6437 (tpt170) REVERT: D 326 LYS cc_start: 0.8139 (tttt) cc_final: 0.7721 (tptt) REVERT: A 26 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7441 (tt) REVERT: A 31 GLN cc_start: 0.8051 (mt0) cc_final: 0.7146 (mm110) REVERT: A 52 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.6974 (m-10) REVERT: A 197 HIS cc_start: 0.7237 (m90) cc_final: 0.6929 (m-70) REVERT: A 249 ASN cc_start: 0.8294 (p0) cc_final: 0.7884 (p0) REVERT: A 391 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8416 (tt) REVERT: A 392 ASP cc_start: 0.7164 (m-30) cc_final: 0.6290 (m-30) REVERT: A 432 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.6722 (t80) REVERT: B 24 TYR cc_start: 0.8414 (m-10) cc_final: 0.8024 (m-10) REVERT: B 52 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.6763 (m-10) REVERT: B 123 ARG cc_start: 0.8130 (tpp-160) cc_final: 0.7905 (tpp80) REVERT: B 176 GLN cc_start: 0.8111 (mm110) cc_final: 0.7283 (mt0) REVERT: B 193 THR cc_start: 0.8437 (t) cc_final: 0.8126 (m) REVERT: B 214 ARG cc_start: 0.7487 (ttp-170) cc_final: 0.7136 (ttp-170) REVERT: B 219 ILE cc_start: 0.7966 (mm) cc_final: 0.7694 (mt) REVERT: B 221 ARG cc_start: 0.8062 (mtt180) cc_final: 0.7317 (mmt180) REVERT: C 141 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6685 (m-10) REVERT: C 149 PHE cc_start: 0.8030 (t80) cc_final: 0.7729 (t80) REVERT: C 432 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.7172 (t80) REVERT: E 123 ARG cc_start: 0.7867 (ttm110) cc_final: 0.7588 (mtm-85) REVERT: E 149 MET cc_start: 0.8420 (tpp) cc_final: 0.8178 (tpt) REVERT: E 166 MET cc_start: 0.7298 (mtp) cc_final: 0.7039 (mtp) REVERT: E 338 LYS cc_start: 0.7724 (ttmm) cc_final: 0.7390 (ttmm) REVERT: E 339 ASN cc_start: 0.7725 (p0) cc_final: 0.7079 (p0) REVERT: E 346 TRP cc_start: 0.7917 (p-90) cc_final: 0.7589 (p-90) REVERT: F 88 ARG cc_start: 0.7565 (ttp-110) cc_final: 0.7288 (ttp-170) REVERT: F 123 ARG cc_start: 0.8583 (ttm110) cc_final: 0.8042 (mtt180) REVERT: F 248 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6863 (tt) REVERT: F 299 LYS cc_start: 0.8238 (pttt) cc_final: 0.7764 (pttt) REVERT: F 337 ASN cc_start: 0.6465 (t0) cc_final: 0.6102 (p0) outliers start: 74 outliers final: 54 residues processed: 388 average time/residue: 0.3402 time to fit residues: 199.3835 Evaluate side-chains 389 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 327 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 353 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.2980 chunk 212 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 177 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 chunk 214 optimal weight: 0.1980 chunk 225 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 91 GLN C 18 ASN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN F 350 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20834 Z= 0.122 Angle : 0.482 10.649 28364 Z= 0.236 Chirality : 0.041 0.167 3130 Planarity : 0.004 0.038 3668 Dihedral : 10.055 175.713 3192 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.59 % Allowed : 20.19 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.10 (0.17), residues: 2544 helix: 1.22 (0.16), residues: 1096 sheet: 0.17 (0.25), residues: 436 loop : -1.65 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 103 HIS 0.004 0.000 HIS B 139 PHE 0.010 0.001 PHE E 377 TYR 0.011 0.001 TYR A 103 ARG 0.003 0.000 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 349 time to evaluate : 2.330 Fit side-chains revert: symmetry clash REVERT: D 221 ARG cc_start: 0.8519 (mtt180) cc_final: 0.6447 (tpt170) REVERT: D 326 LYS cc_start: 0.8141 (tttt) cc_final: 0.7715 (tptt) REVERT: A 26 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7352 (tt) REVERT: A 31 GLN cc_start: 0.8003 (mt0) cc_final: 0.7149 (mm110) REVERT: A 52 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.6914 (m-10) REVERT: A 197 HIS cc_start: 0.7184 (m90) cc_final: 0.6878 (m-70) REVERT: A 249 ASN cc_start: 0.8315 (p0) cc_final: 0.7906 (p0) REVERT: A 391 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8409 (tt) REVERT: A 392 ASP cc_start: 0.7198 (m-30) cc_final: 0.6331 (m-30) REVERT: A 432 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.6924 (t80) REVERT: B 24 TYR cc_start: 0.8366 (m-10) cc_final: 0.8009 (m-10) REVERT: B 52 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.6723 (m-10) REVERT: B 176 GLN cc_start: 0.8110 (mm110) cc_final: 0.7290 (mt0) REVERT: B 193 THR cc_start: 0.8447 (t) cc_final: 0.8048 (m) REVERT: B 214 ARG cc_start: 0.7502 (ttp-170) cc_final: 0.7164 (ttp-170) REVERT: B 219 ILE cc_start: 0.8019 (mm) cc_final: 0.7790 (mt) REVERT: B 221 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7304 (mmt180) REVERT: B 269 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7976 (pp) REVERT: C 141 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6459 (m-10) REVERT: C 149 PHE cc_start: 0.7883 (t80) cc_final: 0.7657 (t80) REVERT: C 178 SER cc_start: 0.8140 (m) cc_final: 0.7914 (p) REVERT: C 269 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7186 (pp) REVERT: C 432 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.7293 (t80) REVERT: E 123 ARG cc_start: 0.7796 (ttm110) cc_final: 0.7503 (mtm-85) REVERT: E 166 MET cc_start: 0.7206 (mtp) cc_final: 0.6911 (mtp) REVERT: E 235 MET cc_start: 0.7372 (mtm) cc_final: 0.7151 (mtp) REVERT: E 338 LYS cc_start: 0.7682 (ttmm) cc_final: 0.7382 (ttmm) REVERT: E 339 ASN cc_start: 0.7379 (p0) cc_final: 0.6839 (p0) REVERT: E 346 TRP cc_start: 0.7855 (p-90) cc_final: 0.7540 (p-90) REVERT: F 88 ARG cc_start: 0.7617 (ttp-110) cc_final: 0.7302 (ttp-170) REVERT: F 123 ARG cc_start: 0.8558 (ttm110) cc_final: 0.8211 (mtm180) REVERT: F 248 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6784 (tt) REVERT: F 299 LYS cc_start: 0.8148 (pttt) cc_final: 0.7625 (pttt) REVERT: F 425 MET cc_start: 0.7586 (mmm) cc_final: 0.7378 (mmm) outliers start: 56 outliers final: 40 residues processed: 393 average time/residue: 0.3336 time to fit residues: 197.7718 Evaluate side-chains 383 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 333 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 353 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 166 optimal weight: 0.6980 chunk 251 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 192 HIS ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20834 Z= 0.168 Angle : 0.508 9.107 28364 Z= 0.251 Chirality : 0.043 0.182 3130 Planarity : 0.004 0.038 3668 Dihedral : 10.166 175.585 3192 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.96 % Allowed : 20.00 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.11 (0.17), residues: 2544 helix: 1.23 (0.16), residues: 1094 sheet: 0.17 (0.25), residues: 438 loop : -1.66 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 21 HIS 0.012 0.001 HIS C 192 PHE 0.011 0.001 PHE F 319 TYR 0.020 0.001 TYR D 103 ARG 0.007 0.000 ARG C 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 334 time to evaluate : 2.333 Fit side-chains revert: symmetry clash REVERT: D 221 ARG cc_start: 0.8529 (mtt180) cc_final: 0.6446 (tpt170) REVERT: D 326 LYS cc_start: 0.8163 (tttt) cc_final: 0.7716 (tptt) REVERT: A 26 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7394 (tt) REVERT: A 31 GLN cc_start: 0.8024 (mt0) cc_final: 0.7161 (mm110) REVERT: A 52 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6928 (m-10) REVERT: A 197 HIS cc_start: 0.7204 (m90) cc_final: 0.6876 (m-70) REVERT: A 249 ASN cc_start: 0.8318 (p0) cc_final: 0.7906 (p0) REVERT: A 391 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8410 (tt) REVERT: A 392 ASP cc_start: 0.7200 (m-30) cc_final: 0.6360 (m-30) REVERT: A 408 TYR cc_start: 0.7640 (m-80) cc_final: 0.7434 (m-80) REVERT: A 432 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.6907 (t80) REVERT: B 24 TYR cc_start: 0.8430 (m-10) cc_final: 0.8015 (m-10) REVERT: B 52 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.6763 (m-10) REVERT: B 76 ASP cc_start: 0.7773 (m-30) cc_final: 0.7192 (t0) REVERT: B 176 GLN cc_start: 0.8116 (mm110) cc_final: 0.7285 (mt0) REVERT: B 193 THR cc_start: 0.8485 (t) cc_final: 0.8151 (m) REVERT: B 219 ILE cc_start: 0.7986 (mm) cc_final: 0.7749 (mt) REVERT: B 221 ARG cc_start: 0.8017 (mtt180) cc_final: 0.7307 (mmt180) REVERT: B 269 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8014 (pp) REVERT: C 113 GLU cc_start: 0.6648 (pm20) cc_final: 0.6389 (pm20) REVERT: C 141 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6587 (m-10) REVERT: C 178 SER cc_start: 0.8329 (m) cc_final: 0.8116 (p) REVERT: C 432 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.7336 (t80) REVERT: E 123 ARG cc_start: 0.7835 (ttm110) cc_final: 0.7580 (mtm-85) REVERT: E 166 MET cc_start: 0.7264 (mtp) cc_final: 0.6989 (mtp) REVERT: E 338 LYS cc_start: 0.7623 (ttmm) cc_final: 0.7326 (ttmm) REVERT: E 339 ASN cc_start: 0.7472 (p0) cc_final: 0.6908 (p0) REVERT: E 346 TRP cc_start: 0.7879 (p-90) cc_final: 0.7585 (p-90) REVERT: F 88 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7267 (ttp-170) REVERT: F 123 ARG cc_start: 0.8587 (ttm110) cc_final: 0.8035 (mtt180) REVERT: F 149 MET cc_start: 0.8697 (mmm) cc_final: 0.8370 (tpt) REVERT: F 193 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: F 248 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6838 (tt) REVERT: F 299 LYS cc_start: 0.8213 (pttt) cc_final: 0.7704 (pttt) outliers start: 64 outliers final: 52 residues processed: 383 average time/residue: 0.3425 time to fit residues: 198.6573 Evaluate side-chains 391 residues out of total 2182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 329 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 192 HIS Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 ASN Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 353 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 205 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.147708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129263 restraints weight = 25184.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131816 restraints weight = 15444.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.133527 restraints weight = 10916.802| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20834 Z= 0.188 Angle : 0.522 9.507 28364 Z= 0.258 Chirality : 0.043 0.183 3130 Planarity : 0.004 0.038 3668 Dihedral : 10.254 175.450 3192 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.01 % Allowed : 20.14 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.14 (0.17), residues: 2544 helix: 1.19 (0.16), residues: 1094 sheet: 0.13 (0.25), residues: 438 loop : -1.66 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 21 HIS 0.011 0.001 HIS C 192 PHE 0.012 0.001 PHE F 319 TYR 0.019 0.001 TYR D 103 ARG 0.008 0.000 ARG C 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4173.95 seconds wall clock time: 78 minutes 34.67 seconds (4714.67 seconds total)