Starting phenix.real_space_refine on Thu Feb 15 15:51:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phh_13416/02_2024/7phh_13416_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phh_13416/02_2024/7phh_13416.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phh_13416/02_2024/7phh_13416_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phh_13416/02_2024/7phh_13416_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phh_13416/02_2024/7phh_13416_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phh_13416/02_2024/7phh_13416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phh_13416/02_2024/7phh_13416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phh_13416/02_2024/7phh_13416_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phh_13416/02_2024/7phh_13416_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.082 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 Zn 4 6.06 5 P 8 5.49 5 S 68 5.16 5 C 8376 2.51 5 N 2092 2.21 5 O 2168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D GLU 380": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12720 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3101 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 22, 'TRANS': 373} Chain breaks: 3 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 100 Chain: "C" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3101 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 22, 'TRANS': 373} Chain breaks: 3 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 100 Chain: "B" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3101 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 22, 'TRANS': 373} Chain breaks: 3 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 100 Chain: "D" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3101 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 22, 'TRANS': 373} Chain breaks: 3 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 100 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {' K': 4, ' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 791 SG CYS A 104 50.120 68.370 76.120 1.00107.92 S ATOM 797 SG CYS A 105 50.638 65.305 77.854 1.00105.62 S ATOM 6824 SG CYS B 83 54.203 67.163 78.031 1.00103.76 S ATOM 3892 SG CYS C 104 79.236 60.937 76.084 1.00107.92 S ATOM 3898 SG CYS C 105 78.744 64.004 77.820 1.00105.62 S ATOM 9925 SG CYS D 83 75.152 62.201 78.008 1.00103.76 S ATOM 3723 SG CYS C 83 67.265 75.204 78.005 1.00103.76 S ATOM 6993 SG CYS B 104 68.379 79.245 76.123 1.00107.92 S ATOM 6999 SG CYS B 105 65.315 78.727 77.859 1.00105.62 S ATOM 622 SG CYS A 83 62.208 54.199 78.025 1.00103.76 S ATOM 10094 SG CYS D 104 60.978 50.121 76.072 1.00107.92 S ATOM 10100 SG CYS D 105 64.041 50.636 77.810 1.00105.62 S Time building chain proxies: 6.87, per 1000 atoms: 0.54 Number of scatterers: 12720 At special positions: 0 Unit cell: (130.2, 130.2, 120.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 K 4 19.00 S 68 16.00 P 8 15.00 O 2168 8.00 N 2092 7.00 C 8376 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=0, symmetry=0 Time building additional restraints: 5.23 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" SG CYS B 83 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 105 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 104 " pdb="ZN ZN A 603 " - pdb=" ND1 HIS A 77 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS C 83 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 105 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 104 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 77 " pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" SG CYS D 83 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 105 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 104 " pdb="ZN ZN C 603 " - pdb=" ND1 HIS C 77 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" SG CYS A 83 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 105 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 77 " Number of angles added : 12 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 4 sheets defined 61.9% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 61 through 73 removed outlier: 4.708A pdb=" N HIS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 112 through 118 Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.966A pdb=" N LEU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 187 through 210 Processing helix chain 'A' and resid 243 through 265 Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 277 through 294 Proline residue: A 288 - end of helix removed outlier: 3.516A pdb=" N LEU A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 327 removed outlier: 3.757A pdb=" N ASP A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N PHE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N HIS A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 342 through 368 removed outlier: 3.826A pdb=" N ARG A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 61 through 73 removed outlier: 4.709A pdb=" N HIS C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 112 through 118 Processing helix chain 'C' and resid 173 through 179 removed outlier: 3.966A pdb=" N LEU C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 187 through 210 Processing helix chain 'C' and resid 243 through 265 Processing helix chain 'C' and resid 270 through 275 Processing helix chain 'C' and resid 277 through 294 Proline residue: C 288 - end of helix removed outlier: 3.517A pdb=" N LEU C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL C 293 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY C 294 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 327 removed outlier: 3.757A pdb=" N ASP C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL C 316 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE C 318 " --> pdb=" O ARG C 314 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N PHE C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N HIS C 327 " --> pdb=" O LYS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 Processing helix chain 'C' and resid 342 through 368 removed outlier: 3.826A pdb=" N ARG C 368 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 398 Processing helix chain 'C' and resid 411 through 429 Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 61 through 73 removed outlier: 4.709A pdb=" N HIS B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 173 through 179 removed outlier: 3.966A pdb=" N LEU B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 187 through 210 Processing helix chain 'B' and resid 243 through 265 Processing helix chain 'B' and resid 270 through 275 Processing helix chain 'B' and resid 277 through 294 Proline residue: B 288 - end of helix removed outlier: 3.517A pdb=" N LEU B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU B 292 " --> pdb=" O PRO B 288 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY B 294 " --> pdb=" O TYR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 327 removed outlier: 3.758A pdb=" N ASP B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL B 316 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ILE B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N PHE B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N HIS B 327 " --> pdb=" O LYS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 Processing helix chain 'B' and resid 342 through 368 removed outlier: 3.826A pdb=" N ARG B 368 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 61 through 73 removed outlier: 4.709A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 94 Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 112 through 118 Processing helix chain 'D' and resid 173 through 179 removed outlier: 3.966A pdb=" N LEU D 179 " --> pdb=" O ARG D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 187 through 210 Processing helix chain 'D' and resid 243 through 265 Processing helix chain 'D' and resid 270 through 275 Processing helix chain 'D' and resid 277 through 294 Proline residue: D 288 - end of helix removed outlier: 3.517A pdb=" N LEU D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY D 294 " --> pdb=" O TYR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 327 removed outlier: 3.757A pdb=" N ASP D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL D 316 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE D 318 " --> pdb=" O ARG D 314 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE D 321 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N PHE D 322 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N HIS D 327 " --> pdb=" O LYS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 340 Processing helix chain 'D' and resid 342 through 368 removed outlier: 3.827A pdb=" N ARG D 368 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 398 Processing helix chain 'D' and resid 411 through 429 Processing helix chain 'D' and resid 432 through 451 Processing sheet with id= A, first strand: chain 'A' and resid 17 through 22 Processing sheet with id= B, first strand: chain 'C' and resid 17 through 22 Processing sheet with id= C, first strand: chain 'B' and resid 17 through 22 Processing sheet with id= D, first strand: chain 'D' and resid 17 through 22 648 hydrogen bonds defined for protein. 1932 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: 3.53 Time building geometry restraints manager: 5.57 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: 1916 1.31 - 1.43: 3797 1.43 - 1.56: 7246 1.56 - 1.68: 21 1.68 - 1.81: 104 Bond restraints: 13084 Sorted by residual: bond pdb=" N PCF D 603 " pdb=" C12 PCF D 603 " ideal model delta sigma weight residual 1.447 1.480 -0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" N PCF C 602 " pdb=" C12 PCF C 602 " ideal model delta sigma weight residual 1.447 1.479 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" N PCF A 602 " pdb=" C12 PCF A 602 " ideal model delta sigma weight residual 1.447 1.479 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" N PCF B 603 " pdb=" C12 PCF B 603 " ideal model delta sigma weight residual 1.447 1.479 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" CG LEU B 401 " pdb=" CD1 LEU B 401 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.39e+00 ... (remaining 13079 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.89: 332 105.89 - 112.94: 7105 112.94 - 119.98: 4484 119.98 - 127.02: 5647 127.02 - 134.07: 244 Bond angle restraints: 17812 Sorted by residual: angle pdb=" N PCF B 603 " pdb=" C12 PCF B 603 " pdb=" C11 PCF B 603 " ideal model delta sigma weight residual 109.46 116.99 -7.53 3.00e+00 1.11e-01 6.31e+00 angle pdb=" N PCF A 602 " pdb=" C12 PCF A 602 " pdb=" C11 PCF A 602 " ideal model delta sigma weight residual 109.46 116.96 -7.50 3.00e+00 1.11e-01 6.25e+00 angle pdb=" N PCF C 602 " pdb=" C12 PCF C 602 " pdb=" C11 PCF C 602 " ideal model delta sigma weight residual 109.46 116.92 -7.46 3.00e+00 1.11e-01 6.19e+00 angle pdb=" N PCF D 603 " pdb=" C12 PCF D 603 " pdb=" C11 PCF D 603 " ideal model delta sigma weight residual 109.46 116.91 -7.45 3.00e+00 1.11e-01 6.17e+00 angle pdb=" C SER C 7 " pdb=" N GLU C 8 " pdb=" CA GLU C 8 " ideal model delta sigma weight residual 121.54 125.86 -4.32 1.91e+00 2.74e-01 5.13e+00 ... (remaining 17807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.37: 7076 23.37 - 46.74: 408 46.74 - 70.11: 60 70.11 - 93.48: 12 93.48 - 116.84: 4 Dihedral angle restraints: 7560 sinusoidal: 2936 harmonic: 4624 Sorted by residual: dihedral pdb=" N PCF A 602 " pdb=" C11 PCF A 602 " pdb=" C12 PCF A 602 " pdb=" O13 PCF A 602 " ideal model delta sinusoidal sigma weight residual -167.95 -51.11 -116.84 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" N PCF D 603 " pdb=" C11 PCF D 603 " pdb=" C12 PCF D 603 " pdb=" O13 PCF D 603 " ideal model delta sinusoidal sigma weight residual -167.95 -51.11 -116.84 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" N PCF B 603 " pdb=" C11 PCF B 603 " pdb=" C12 PCF B 603 " pdb=" O13 PCF B 603 " ideal model delta sinusoidal sigma weight residual -167.95 -51.15 -116.80 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 7557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1306 0.041 - 0.081: 461 0.081 - 0.122: 156 0.122 - 0.163: 33 0.163 - 0.203: 4 Chirality restraints: 1960 Sorted by residual: chirality pdb=" C2 PCF A 602 " pdb=" C1 PCF A 602 " pdb=" C3 PCF A 602 " pdb=" O21 PCF A 602 " both_signs ideal model delta sigma weight residual False -2.53 -2.33 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C2 PCF D 603 " pdb=" C1 PCF D 603 " pdb=" C3 PCF D 603 " pdb=" O21 PCF D 603 " both_signs ideal model delta sigma weight residual False -2.53 -2.33 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C2 PCF B 603 " pdb=" C1 PCF B 603 " pdb=" C3 PCF B 603 " pdb=" O21 PCF B 603 " both_signs ideal model delta sigma weight residual False -2.53 -2.33 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1957 not shown) Planarity restraints: 2212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 174 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C PRO C 174 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO C 174 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG C 175 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 174 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C PRO A 174 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO A 174 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 175 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 174 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C PRO B 174 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO B 174 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG B 175 " -0.010 2.00e-02 2.50e+03 ... (remaining 2209 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.66: 122 2.66 - 3.28: 14265 3.28 - 3.90: 24526 3.90 - 4.52: 32357 4.52 - 5.14: 51010 Nonbonded interactions: 122280 Sorted by model distance: nonbonded pdb=" OG1 THR B 32 " pdb=" OH TYR B 71 " model vdw 2.045 2.440 nonbonded pdb=" OG1 THR C 32 " pdb=" OH TYR C 71 " model vdw 2.045 2.440 nonbonded pdb=" OG1 THR A 32 " pdb=" OH TYR A 71 " model vdw 2.045 2.440 nonbonded pdb=" OG1 THR D 32 " pdb=" OH TYR D 71 " model vdw 2.045 2.440 nonbonded pdb=" O ASP C 182 " pdb=" OG SER C 185 " model vdw 2.189 2.440 ... (remaining 122275 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' and (resid 7 through 464 or resid 602)) selection = (chain 'B' and (resid 7 through 464 or (resid 602 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or na \ me O31 or name O32 or name P )))) selection = (chain 'C' and (resid 7 through 464 or resid 602)) selection = (chain 'D' and (resid 7 through 464 or (resid 602 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or na \ me O31 or name O32 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.630 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 37.560 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 13084 Z= 0.458 Angle : 0.711 7.756 17812 Z= 0.377 Chirality : 0.047 0.203 1960 Planarity : 0.005 0.040 2212 Dihedral : 15.366 116.845 4560 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.96 % Allowed : 11.82 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1552 helix: -0.31 (0.15), residues: 940 sheet: 0.91 (0.88), residues: 40 loop : -0.94 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 255 HIS 0.005 0.002 HIS B 77 PHE 0.019 0.002 PHE D 384 TYR 0.013 0.002 TYR D 109 ARG 0.009 0.001 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 214 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7186 (ttm110) cc_final: 0.6657 (tmt170) REVERT: A 36 TRP cc_start: 0.6803 (m100) cc_final: 0.6263 (m100) REVERT: A 214 ARG cc_start: 0.7330 (ttm170) cc_final: 0.6962 (ttt180) REVERT: A 247 TYR cc_start: 0.5763 (m-80) cc_final: 0.5377 (m-10) REVERT: A 457 LYS cc_start: 0.6205 (tmtm) cc_final: 0.5912 (tptt) REVERT: A 458 LYS cc_start: 0.7267 (tttt) cc_final: 0.6594 (ttpt) REVERT: C 9 ARG cc_start: 0.7309 (ttm110) cc_final: 0.6837 (tmt170) REVERT: C 36 TRP cc_start: 0.6832 (m100) cc_final: 0.6516 (m100) REVERT: C 75 LYS cc_start: 0.8178 (mttp) cc_final: 0.7913 (mttp) REVERT: C 247 TYR cc_start: 0.6040 (m-80) cc_final: 0.5502 (m-10) REVERT: C 311 ARG cc_start: 0.5420 (mmm-85) cc_final: 0.5082 (mtp85) REVERT: C 458 LYS cc_start: 0.7091 (tttt) cc_final: 0.6779 (mtpt) REVERT: B 9 ARG cc_start: 0.7298 (ttm110) cc_final: 0.6703 (tmt170) REVERT: B 36 TRP cc_start: 0.6839 (m100) cc_final: 0.6276 (m100) REVERT: B 214 ARG cc_start: 0.7302 (ttm170) cc_final: 0.7032 (mtp85) REVERT: B 247 TYR cc_start: 0.5962 (m-80) cc_final: 0.5505 (m-10) REVERT: B 311 ARG cc_start: 0.5561 (mmm-85) cc_final: 0.5300 (mtm110) REVERT: B 457 LYS cc_start: 0.6217 (tmtm) cc_final: 0.5943 (tptt) REVERT: B 458 LYS cc_start: 0.7296 (tttt) cc_final: 0.6627 (ttpt) REVERT: D 9 ARG cc_start: 0.7308 (ttm110) cc_final: 0.6806 (tmt170) REVERT: D 36 TRP cc_start: 0.6701 (m100) cc_final: 0.6134 (m100) REVERT: D 214 ARG cc_start: 0.7287 (ttm170) cc_final: 0.7033 (mtp85) REVERT: D 247 TYR cc_start: 0.5737 (m-80) cc_final: 0.5418 (m-10) REVERT: D 311 ARG cc_start: 0.5724 (mmm-85) cc_final: 0.5485 (mtm110) REVERT: D 430 MET cc_start: 0.7513 (mmt) cc_final: 0.7265 (mmt) REVERT: D 458 LYS cc_start: 0.7283 (tttt) cc_final: 0.6633 (ttpt) outliers start: 12 outliers final: 4 residues processed: 222 average time/residue: 0.3335 time to fit residues: 98.0272 Evaluate side-chains 164 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 160 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain D residue 315 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 141 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN B 437 ASN D 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13084 Z= 0.236 Angle : 0.525 6.445 17812 Z= 0.261 Chirality : 0.040 0.125 1960 Planarity : 0.005 0.042 2212 Dihedral : 10.044 71.090 1912 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.88 % Allowed : 15.27 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1552 helix: 1.18 (0.16), residues: 960 sheet: None (None), residues: 0 loop : -0.37 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 255 HIS 0.004 0.001 HIS C 327 PHE 0.011 0.001 PHE C 289 TYR 0.009 0.001 TYR B 48 ARG 0.004 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7203 (ttm110) cc_final: 0.6722 (tmt170) REVERT: A 36 TRP cc_start: 0.6878 (m100) cc_final: 0.6261 (m100) REVERT: A 214 ARG cc_start: 0.7456 (ttm170) cc_final: 0.7044 (ttt180) REVERT: A 247 TYR cc_start: 0.5732 (m-80) cc_final: 0.5427 (m-10) REVERT: A 457 LYS cc_start: 0.6108 (tmtm) cc_final: 0.5765 (tptt) REVERT: C 9 ARG cc_start: 0.7239 (ttm110) cc_final: 0.6779 (tmt170) REVERT: C 36 TRP cc_start: 0.6966 (m100) cc_final: 0.6345 (m100) REVERT: C 75 LYS cc_start: 0.8289 (mttp) cc_final: 0.8008 (mttp) REVERT: C 247 TYR cc_start: 0.5970 (m-80) cc_final: 0.5547 (m-10) REVERT: C 458 LYS cc_start: 0.7128 (tttt) cc_final: 0.6827 (mtpt) REVERT: B 9 ARG cc_start: 0.7228 (ttm110) cc_final: 0.6712 (tmt170) REVERT: B 36 TRP cc_start: 0.6922 (m100) cc_final: 0.6304 (m100) REVERT: B 214 ARG cc_start: 0.7406 (ttm170) cc_final: 0.6952 (ttt180) REVERT: B 247 TYR cc_start: 0.5799 (m-80) cc_final: 0.5429 (m-10) REVERT: B 457 LYS cc_start: 0.6110 (tmtm) cc_final: 0.5759 (tptt) REVERT: D 9 ARG cc_start: 0.7248 (ttm110) cc_final: 0.6821 (tmt170) REVERT: D 36 TRP cc_start: 0.6828 (m100) cc_final: 0.6220 (m100) REVERT: D 214 ARG cc_start: 0.7449 (ttm170) cc_final: 0.7114 (mtp85) REVERT: D 247 TYR cc_start: 0.5715 (m-80) cc_final: 0.5425 (m-10) REVERT: D 311 ARG cc_start: 0.5608 (mmm-85) cc_final: 0.5367 (mtm110) outliers start: 11 outliers final: 8 residues processed: 171 average time/residue: 0.3230 time to fit residues: 74.5538 Evaluate side-chains 163 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 349 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 0.1980 chunk 126 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN C 437 ASN B 437 ASN D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13084 Z= 0.298 Angle : 0.530 6.528 17812 Z= 0.265 Chirality : 0.042 0.142 1960 Planarity : 0.005 0.046 2212 Dihedral : 9.333 70.417 1912 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.25 % Allowed : 16.40 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.21), residues: 1552 helix: 1.40 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -0.23 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 255 HIS 0.003 0.001 HIS C 327 PHE 0.013 0.001 PHE A 289 TYR 0.009 0.001 TYR C 48 ARG 0.005 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7285 (ttm110) cc_final: 0.6742 (tmt170) REVERT: A 36 TRP cc_start: 0.7012 (m100) cc_final: 0.6776 (m100) REVERT: A 67 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.5995 (mp) REVERT: A 214 ARG cc_start: 0.7440 (ttm170) cc_final: 0.7026 (ttt180) REVERT: A 247 TYR cc_start: 0.5760 (m-80) cc_final: 0.5448 (m-10) REVERT: A 275 LYS cc_start: 0.5214 (tptp) cc_final: 0.4911 (tptp) REVERT: A 457 LYS cc_start: 0.6154 (tmtm) cc_final: 0.5890 (tptt) REVERT: C 9 ARG cc_start: 0.7306 (ttm110) cc_final: 0.6769 (tmt170) REVERT: C 36 TRP cc_start: 0.7026 (m100) cc_final: 0.6398 (m100) REVERT: C 67 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6007 (mp) REVERT: C 247 TYR cc_start: 0.5996 (m-80) cc_final: 0.5577 (m-10) REVERT: C 458 LYS cc_start: 0.7160 (tttt) cc_final: 0.6793 (mtpt) REVERT: B 9 ARG cc_start: 0.7313 (ttm110) cc_final: 0.6732 (tmt170) REVERT: B 36 TRP cc_start: 0.7034 (m100) cc_final: 0.6369 (m100) REVERT: B 67 ILE cc_start: 0.6586 (OUTLIER) cc_final: 0.6004 (mp) REVERT: B 214 ARG cc_start: 0.7446 (ttm170) cc_final: 0.7195 (ttm-80) REVERT: B 247 TYR cc_start: 0.5884 (m-80) cc_final: 0.5468 (m-10) REVERT: B 457 LYS cc_start: 0.6152 (tmtm) cc_final: 0.5893 (tptt) REVERT: D 9 ARG cc_start: 0.7280 (ttm110) cc_final: 0.6792 (tmt170) REVERT: D 36 TRP cc_start: 0.6897 (m100) cc_final: 0.6299 (m100) REVERT: D 67 ILE cc_start: 0.6603 (OUTLIER) cc_final: 0.6023 (mp) REVERT: D 214 ARG cc_start: 0.7461 (ttm170) cc_final: 0.7118 (mtp85) REVERT: D 247 TYR cc_start: 0.5786 (m-80) cc_final: 0.5480 (m-10) REVERT: D 275 LYS cc_start: 0.5281 (tptp) cc_final: 0.4884 (tptp) REVERT: D 311 ARG cc_start: 0.5747 (mmm-85) cc_final: 0.5385 (mtm110) outliers start: 28 outliers final: 10 residues processed: 173 average time/residue: 0.3030 time to fit residues: 71.7657 Evaluate side-chains 158 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 349 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 40.0000 chunk 106 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 95 optimal weight: 50.0000 chunk 142 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 134 optimal weight: 40.0000 chunk 40 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN C 437 ASN B 437 ASN D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 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 0.040 13084 Z= 0.197 Angle : 0.477 6.046 17812 Z= 0.237 Chirality : 0.038 0.120 1960 Planarity : 0.004 0.046 2212 Dihedral : 8.606 63.444 1912 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.57 % Allowed : 15.68 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.21), residues: 1552 helix: 1.76 (0.17), residues: 956 sheet: None (None), residues: 0 loop : -0.05 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 255 HIS 0.002 0.001 HIS C 327 PHE 0.017 0.001 PHE A 93 TYR 0.008 0.001 TYR A 48 ARG 0.004 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 157 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7219 (ttm110) cc_final: 0.6701 (tmt170) REVERT: A 36 TRP cc_start: 0.6998 (m100) cc_final: 0.6427 (m100) REVERT: A 67 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.5985 (mp) REVERT: A 214 ARG cc_start: 0.7436 (ttm170) cc_final: 0.7044 (ttt180) REVERT: A 247 TYR cc_start: 0.5730 (m-80) cc_final: 0.5434 (m-10) REVERT: A 275 LYS cc_start: 0.5215 (tptp) cc_final: 0.4901 (tptp) REVERT: A 457 LYS cc_start: 0.6087 (tmtm) cc_final: 0.5811 (tptt) REVERT: C 9 ARG cc_start: 0.7252 (ttm110) cc_final: 0.6800 (tmt170) REVERT: C 36 TRP cc_start: 0.7014 (m100) cc_final: 0.6444 (m100) REVERT: C 67 ILE cc_start: 0.6519 (OUTLIER) cc_final: 0.6000 (mp) REVERT: C 214 ARG cc_start: 0.7458 (ttm170) cc_final: 0.7083 (ttt180) REVERT: C 247 TYR cc_start: 0.5973 (m-80) cc_final: 0.5567 (m-10) REVERT: C 458 LYS cc_start: 0.7190 (tttt) cc_final: 0.6774 (mtpt) REVERT: B 9 ARG cc_start: 0.7315 (ttm110) cc_final: 0.6750 (tmt170) REVERT: B 36 TRP cc_start: 0.6996 (m100) cc_final: 0.6429 (m100) REVERT: B 67 ILE cc_start: 0.6511 (OUTLIER) cc_final: 0.5995 (mp) REVERT: B 214 ARG cc_start: 0.7457 (ttm170) cc_final: 0.7212 (ttm-80) REVERT: B 247 TYR cc_start: 0.5794 (m-80) cc_final: 0.5405 (m-10) REVERT: B 457 LYS cc_start: 0.6078 (tmtm) cc_final: 0.5854 (tptt) REVERT: D 9 ARG cc_start: 0.7236 (ttm110) cc_final: 0.6786 (tmt170) REVERT: D 36 TRP cc_start: 0.7003 (m100) cc_final: 0.6402 (m100) REVERT: D 67 ILE cc_start: 0.6528 (OUTLIER) cc_final: 0.6013 (mp) REVERT: D 214 ARG cc_start: 0.7446 (ttm170) cc_final: 0.6971 (ttt180) REVERT: D 247 TYR cc_start: 0.5746 (m-80) cc_final: 0.5507 (m-10) outliers start: 32 outliers final: 12 residues processed: 183 average time/residue: 0.2990 time to fit residues: 75.1251 Evaluate side-chains 161 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 316 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 40.0000 chunk 128 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN C 437 ASN B 437 ASN D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 13084 Z= 0.409 Angle : 0.571 7.410 17812 Z= 0.287 Chirality : 0.043 0.135 1960 Planarity : 0.005 0.050 2212 Dihedral : 9.037 62.592 1912 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.30 % Allowed : 15.03 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.21), residues: 1552 helix: 1.28 (0.16), residues: 960 sheet: -0.55 (0.70), residues: 40 loop : -0.23 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 255 HIS 0.004 0.001 HIS D 77 PHE 0.012 0.002 PHE C 315 TYR 0.009 0.002 TYR B 70 ARG 0.006 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7297 (ttm110) cc_final: 0.6761 (tmt170) REVERT: A 36 TRP cc_start: 0.7045 (m100) cc_final: 0.6810 (m100) REVERT: A 67 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6000 (mp) REVERT: A 214 ARG cc_start: 0.7453 (ttm170) cc_final: 0.6969 (ttt180) REVERT: A 247 TYR cc_start: 0.5909 (m-80) cc_final: 0.5479 (m-10) REVERT: A 275 LYS cc_start: 0.5151 (tptp) cc_final: 0.4829 (tptp) REVERT: A 457 LYS cc_start: 0.6108 (tmtm) cc_final: 0.5774 (tptt) REVERT: C 9 ARG cc_start: 0.7370 (ttm110) cc_final: 0.6830 (tmt170) REVERT: C 36 TRP cc_start: 0.7042 (m100) cc_final: 0.6784 (m100) REVERT: C 67 ILE cc_start: 0.6635 (OUTLIER) cc_final: 0.6012 (mp) REVERT: C 214 ARG cc_start: 0.7500 (ttm170) cc_final: 0.7113 (ttt180) REVERT: C 247 TYR cc_start: 0.5903 (m-80) cc_final: 0.5438 (m-10) REVERT: C 458 LYS cc_start: 0.7156 (tttt) cc_final: 0.6684 (mtpt) REVERT: B 9 ARG cc_start: 0.7346 (ttm110) cc_final: 0.6777 (tmt170) REVERT: B 36 TRP cc_start: 0.7021 (m100) cc_final: 0.6797 (m100) REVERT: B 67 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6026 (mp) REVERT: B 214 ARG cc_start: 0.7467 (ttm170) cc_final: 0.7192 (ttm-80) REVERT: B 247 TYR cc_start: 0.5898 (m-80) cc_final: 0.5465 (m-10) REVERT: B 262 MET cc_start: 0.6048 (mmt) cc_final: 0.5622 (tpp) REVERT: B 457 LYS cc_start: 0.6129 (tmtm) cc_final: 0.5799 (tptt) REVERT: D 9 ARG cc_start: 0.7351 (ttm110) cc_final: 0.6840 (tmt170) REVERT: D 36 TRP cc_start: 0.7047 (m100) cc_final: 0.6401 (m100) REVERT: D 67 ILE cc_start: 0.6638 (OUTLIER) cc_final: 0.6006 (mp) REVERT: D 214 ARG cc_start: 0.7460 (ttm170) cc_final: 0.7110 (mtp85) REVERT: D 247 TYR cc_start: 0.5991 (m-80) cc_final: 0.5578 (m-10) REVERT: D 275 LYS cc_start: 0.5191 (tptp) cc_final: 0.4849 (tptp) outliers start: 41 outliers final: 21 residues processed: 172 average time/residue: 0.2999 time to fit residues: 71.0942 Evaluate side-chains 165 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 69 optimal weight: 0.0470 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN C 279 ASN C 437 ASN B 279 ASN B 437 ASN D 437 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13084 Z= 0.181 Angle : 0.475 6.775 17812 Z= 0.236 Chirality : 0.038 0.123 1960 Planarity : 0.004 0.048 2212 Dihedral : 8.208 59.471 1912 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.61 % Allowed : 16.72 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.21), residues: 1552 helix: 1.70 (0.17), residues: 960 sheet: None (None), residues: 0 loop : 0.05 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 255 HIS 0.002 0.000 HIS C 327 PHE 0.022 0.001 PHE A 93 TYR 0.007 0.001 TYR B 365 ARG 0.005 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7201 (ttm110) cc_final: 0.6767 (tmt170) REVERT: A 36 TRP cc_start: 0.7058 (m100) cc_final: 0.6560 (m100) REVERT: A 67 ILE cc_start: 0.6468 (OUTLIER) cc_final: 0.5964 (mp) REVERT: A 214 ARG cc_start: 0.7444 (ttm170) cc_final: 0.7014 (ttt180) REVERT: A 247 TYR cc_start: 0.5785 (m-80) cc_final: 0.5443 (m-10) REVERT: A 457 LYS cc_start: 0.5976 (tmtm) cc_final: 0.5689 (tptt) REVERT: C 9 ARG cc_start: 0.7199 (ttm110) cc_final: 0.6788 (tmt170) REVERT: C 36 TRP cc_start: 0.7088 (m100) cc_final: 0.6530 (m100) REVERT: C 67 ILE cc_start: 0.6475 (OUTLIER) cc_final: 0.5967 (mp) REVERT: C 214 ARG cc_start: 0.7494 (ttm170) cc_final: 0.7163 (ttt180) REVERT: C 247 TYR cc_start: 0.5855 (m-80) cc_final: 0.5459 (m-10) REVERT: C 458 LYS cc_start: 0.7049 (tttt) cc_final: 0.6585 (mtpt) REVERT: B 9 ARG cc_start: 0.7257 (ttm110) cc_final: 0.6793 (tmt170) REVERT: B 36 TRP cc_start: 0.7068 (m100) cc_final: 0.6566 (m100) REVERT: B 67 ILE cc_start: 0.6482 (OUTLIER) cc_final: 0.5979 (mp) REVERT: B 214 ARG cc_start: 0.7470 (ttm170) cc_final: 0.7222 (ttm-80) REVERT: B 247 TYR cc_start: 0.5738 (m-80) cc_final: 0.5387 (m-10) REVERT: B 457 LYS cc_start: 0.6028 (tmtm) cc_final: 0.5787 (tptt) REVERT: D 9 ARG cc_start: 0.7206 (ttm110) cc_final: 0.6791 (tmt170) REVERT: D 36 TRP cc_start: 0.7035 (m100) cc_final: 0.6570 (m100) REVERT: D 67 ILE cc_start: 0.6486 (OUTLIER) cc_final: 0.5989 (mp) REVERT: D 214 ARG cc_start: 0.7461 (ttm170) cc_final: 0.6981 (ttt180) REVERT: D 247 TYR cc_start: 0.5812 (m-80) cc_final: 0.5500 (m-10) outliers start: 20 outliers final: 11 residues processed: 163 average time/residue: 0.3313 time to fit residues: 73.0888 Evaluate side-chains 156 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 316 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.9990 chunk 17 optimal weight: 40.0000 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 84 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 69 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN C 437 ASN B 437 ASN D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13084 Z= 0.203 Angle : 0.481 6.377 17812 Z= 0.239 Chirality : 0.039 0.124 1960 Planarity : 0.004 0.048 2212 Dihedral : 8.017 59.629 1912 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.85 % Allowed : 17.28 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.21), residues: 1552 helix: 1.74 (0.17), residues: 960 sheet: None (None), residues: 0 loop : 0.15 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 255 HIS 0.002 0.001 HIS B 383 PHE 0.020 0.001 PHE A 93 TYR 0.007 0.001 TYR B 365 ARG 0.005 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7194 (ttm110) cc_final: 0.6778 (tmt170) REVERT: A 36 TRP cc_start: 0.7072 (m100) cc_final: 0.6555 (m100) REVERT: A 67 ILE cc_start: 0.6468 (OUTLIER) cc_final: 0.5906 (mp) REVERT: A 214 ARG cc_start: 0.7431 (ttm170) cc_final: 0.6990 (ttt180) REVERT: A 247 TYR cc_start: 0.5832 (m-80) cc_final: 0.5445 (m-10) REVERT: A 262 MET cc_start: 0.6510 (tpp) cc_final: 0.6025 (ttt) REVERT: A 457 LYS cc_start: 0.6014 (tmtm) cc_final: 0.5755 (tptt) REVERT: C 9 ARG cc_start: 0.7247 (ttm110) cc_final: 0.6783 (tmt170) REVERT: C 36 TRP cc_start: 0.7075 (m100) cc_final: 0.6572 (m100) REVERT: C 67 ILE cc_start: 0.6478 (OUTLIER) cc_final: 0.5913 (mp) REVERT: C 214 ARG cc_start: 0.7474 (ttm170) cc_final: 0.7141 (ttt180) REVERT: C 247 TYR cc_start: 0.5899 (m-80) cc_final: 0.5492 (m-10) REVERT: C 458 LYS cc_start: 0.7068 (tttt) cc_final: 0.6598 (mtpt) REVERT: B 9 ARG cc_start: 0.7211 (ttm110) cc_final: 0.6774 (tmt170) REVERT: B 36 TRP cc_start: 0.7076 (m100) cc_final: 0.6566 (m100) REVERT: B 67 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.5924 (mp) REVERT: B 214 ARG cc_start: 0.7444 (ttm170) cc_final: 0.7215 (ttm-80) REVERT: B 247 TYR cc_start: 0.5752 (m-80) cc_final: 0.5400 (m-10) REVERT: B 457 LYS cc_start: 0.6020 (tmtm) cc_final: 0.5767 (tptt) REVERT: D 9 ARG cc_start: 0.7230 (ttm110) cc_final: 0.6795 (tmt170) REVERT: D 36 TRP cc_start: 0.7050 (m100) cc_final: 0.6565 (m100) REVERT: D 67 ILE cc_start: 0.6487 (OUTLIER) cc_final: 0.5931 (mp) REVERT: D 214 ARG cc_start: 0.7445 (ttm170) cc_final: 0.6977 (ttt180) REVERT: D 247 TYR cc_start: 0.5859 (m-80) cc_final: 0.5567 (m-10) outliers start: 23 outliers final: 15 residues processed: 158 average time/residue: 0.3283 time to fit residues: 70.1124 Evaluate side-chains 156 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 50.0000 chunk 102 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN C 437 ASN B 437 ASN D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13084 Z= 0.316 Angle : 0.523 6.455 17812 Z= 0.261 Chirality : 0.041 0.128 1960 Planarity : 0.005 0.050 2212 Dihedral : 8.351 59.616 1912 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.09 % Allowed : 17.12 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.21), residues: 1552 helix: 1.54 (0.17), residues: 960 sheet: -0.63 (0.71), residues: 40 loop : 0.11 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 255 HIS 0.003 0.001 HIS B 77 PHE 0.021 0.001 PHE C 93 TYR 0.007 0.001 TYR D 70 ARG 0.007 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7283 (ttm110) cc_final: 0.6788 (tmt170) REVERT: A 36 TRP cc_start: 0.7065 (m100) cc_final: 0.6549 (m100) REVERT: A 67 ILE cc_start: 0.6570 (OUTLIER) cc_final: 0.5978 (mp) REVERT: A 214 ARG cc_start: 0.7427 (ttm170) cc_final: 0.6957 (ttt180) REVERT: A 247 TYR cc_start: 0.5882 (m-80) cc_final: 0.5468 (m-10) REVERT: A 262 MET cc_start: 0.6588 (tpp) cc_final: 0.6112 (ttt) REVERT: A 457 LYS cc_start: 0.5970 (tmtm) cc_final: 0.5631 (tptt) REVERT: C 9 ARG cc_start: 0.7265 (ttm110) cc_final: 0.6793 (tmt170) REVERT: C 36 TRP cc_start: 0.7116 (m100) cc_final: 0.6585 (m100) REVERT: C 67 ILE cc_start: 0.6571 (OUTLIER) cc_final: 0.5976 (mp) REVERT: C 214 ARG cc_start: 0.7479 (ttm170) cc_final: 0.7140 (ttt180) REVERT: C 247 TYR cc_start: 0.5913 (m-80) cc_final: 0.5464 (m-10) REVERT: C 458 LYS cc_start: 0.7091 (tttt) cc_final: 0.6591 (mtpt) REVERT: B 9 ARG cc_start: 0.7288 (ttm110) cc_final: 0.6799 (tmt170) REVERT: B 36 TRP cc_start: 0.7060 (m100) cc_final: 0.6546 (m100) REVERT: B 67 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.5991 (mp) REVERT: B 214 ARG cc_start: 0.7446 (ttm170) cc_final: 0.7210 (ttm-80) REVERT: B 247 TYR cc_start: 0.5812 (m-80) cc_final: 0.5389 (m-10) REVERT: B 262 MET cc_start: 0.6490 (tpp) cc_final: 0.6002 (ttt) REVERT: B 457 LYS cc_start: 0.6032 (tmtm) cc_final: 0.5708 (tptt) REVERT: D 9 ARG cc_start: 0.7260 (ttm110) cc_final: 0.6809 (tmt170) REVERT: D 36 TRP cc_start: 0.7056 (m100) cc_final: 0.6554 (m100) REVERT: D 67 ILE cc_start: 0.6587 (OUTLIER) cc_final: 0.6001 (mp) REVERT: D 214 ARG cc_start: 0.7432 (ttm170) cc_final: 0.6959 (ttt180) REVERT: D 247 TYR cc_start: 0.5924 (m-80) cc_final: 0.5578 (m-10) outliers start: 26 outliers final: 20 residues processed: 161 average time/residue: 0.3118 time to fit residues: 68.5864 Evaluate side-chains 159 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 0.0470 chunk 132 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN C 437 ASN B 437 ASN D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13084 Z= 0.317 Angle : 0.526 6.423 17812 Z= 0.263 Chirality : 0.041 0.129 1960 Planarity : 0.005 0.050 2212 Dihedral : 8.486 59.571 1912 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.09 % Allowed : 17.52 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1552 helix: 1.41 (0.17), residues: 980 sheet: -0.66 (0.71), residues: 40 loop : 0.06 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 255 HIS 0.003 0.001 HIS B 77 PHE 0.024 0.001 PHE C 93 TYR 0.007 0.001 TYR B 70 ARG 0.009 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7287 (ttm110) cc_final: 0.6791 (tmt170) REVERT: A 36 TRP cc_start: 0.7066 (m100) cc_final: 0.6530 (m100) REVERT: A 67 ILE cc_start: 0.6578 (OUTLIER) cc_final: 0.5989 (mp) REVERT: A 214 ARG cc_start: 0.7427 (ttm170) cc_final: 0.6954 (ttt180) REVERT: A 247 TYR cc_start: 0.5856 (m-80) cc_final: 0.5435 (m-10) REVERT: A 262 MET cc_start: 0.6639 (tpp) cc_final: 0.6162 (ttt) REVERT: A 457 LYS cc_start: 0.6006 (tmtm) cc_final: 0.5656 (tptt) REVERT: C 9 ARG cc_start: 0.7281 (ttm110) cc_final: 0.6798 (tmt170) REVERT: C 36 TRP cc_start: 0.7140 (m100) cc_final: 0.6608 (m100) REVERT: C 67 ILE cc_start: 0.6583 (OUTLIER) cc_final: 0.5992 (mp) REVERT: C 214 ARG cc_start: 0.7502 (ttm170) cc_final: 0.7154 (ttt180) REVERT: C 247 TYR cc_start: 0.5933 (m-80) cc_final: 0.5440 (m-10) REVERT: B 9 ARG cc_start: 0.7306 (ttm110) cc_final: 0.6804 (tmt170) REVERT: B 36 TRP cc_start: 0.7049 (m100) cc_final: 0.6522 (m100) REVERT: B 67 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6004 (mp) REVERT: B 214 ARG cc_start: 0.7448 (ttm170) cc_final: 0.7184 (ttm-80) REVERT: B 247 TYR cc_start: 0.5813 (m-80) cc_final: 0.5388 (m-10) REVERT: B 262 MET cc_start: 0.6519 (tpp) cc_final: 0.6105 (ttt) REVERT: B 457 LYS cc_start: 0.5972 (tmtm) cc_final: 0.5642 (tptt) REVERT: D 9 ARG cc_start: 0.7267 (ttm110) cc_final: 0.6810 (tmt170) REVERT: D 36 TRP cc_start: 0.7117 (m100) cc_final: 0.6603 (m100) REVERT: D 67 ILE cc_start: 0.6595 (OUTLIER) cc_final: 0.6010 (mp) REVERT: D 214 ARG cc_start: 0.7434 (ttm170) cc_final: 0.6956 (ttt180) REVERT: D 247 TYR cc_start: 0.5900 (m-80) cc_final: 0.5492 (m-10) outliers start: 26 outliers final: 20 residues processed: 158 average time/residue: 0.3200 time to fit residues: 68.4838 Evaluate side-chains 159 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 95 optimal weight: 50.0000 chunk 75 optimal weight: 0.7980 chunk 98 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN C 437 ASN B 437 ASN D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13084 Z= 0.176 Angle : 0.474 6.936 17812 Z= 0.236 Chirality : 0.038 0.126 1960 Planarity : 0.005 0.049 2212 Dihedral : 7.946 59.469 1912 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.37 % Allowed : 18.41 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.22), residues: 1552 helix: 1.71 (0.17), residues: 984 sheet: None (None), residues: 0 loop : 0.33 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 255 HIS 0.002 0.000 HIS A 383 PHE 0.025 0.001 PHE C 93 TYR 0.007 0.001 TYR A 365 ARG 0.008 0.000 ARG C 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7168 (ttm110) cc_final: 0.6746 (tmt170) REVERT: A 36 TRP cc_start: 0.7038 (m100) cc_final: 0.6584 (m100) REVERT: A 67 ILE cc_start: 0.6482 (OUTLIER) cc_final: 0.6010 (mp) REVERT: A 214 ARG cc_start: 0.7417 (ttm170) cc_final: 0.6962 (ttt180) REVERT: A 262 MET cc_start: 0.6626 (tpp) cc_final: 0.6144 (ttt) REVERT: A 457 LYS cc_start: 0.5962 (tmtm) cc_final: 0.5681 (tptt) REVERT: C 9 ARG cc_start: 0.7191 (ttm110) cc_final: 0.6810 (tmt170) REVERT: C 36 TRP cc_start: 0.7113 (m100) cc_final: 0.6642 (m100) REVERT: C 67 ILE cc_start: 0.6489 (OUTLIER) cc_final: 0.6016 (mp) REVERT: C 214 ARG cc_start: 0.7513 (ttm170) cc_final: 0.7173 (ttt180) REVERT: C 247 TYR cc_start: 0.5936 (m-80) cc_final: 0.5464 (m-10) REVERT: B 9 ARG cc_start: 0.7212 (ttm110) cc_final: 0.6804 (tmt170) REVERT: B 36 TRP cc_start: 0.7024 (m100) cc_final: 0.6580 (m100) REVERT: B 67 ILE cc_start: 0.6498 (OUTLIER) cc_final: 0.6029 (mp) REVERT: B 214 ARG cc_start: 0.7438 (ttm170) cc_final: 0.7003 (ttt180) REVERT: B 247 TYR cc_start: 0.5802 (m-80) cc_final: 0.5475 (m-10) REVERT: B 262 MET cc_start: 0.6498 (tpp) cc_final: 0.6102 (ttt) REVERT: B 457 LYS cc_start: 0.5963 (tmtm) cc_final: 0.5697 (tptt) REVERT: D 9 ARG cc_start: 0.7185 (ttm110) cc_final: 0.6819 (tmt170) REVERT: D 36 TRP cc_start: 0.7052 (m100) cc_final: 0.6569 (m100) REVERT: D 67 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6036 (mp) REVERT: D 214 ARG cc_start: 0.7419 (ttm170) cc_final: 0.6970 (ttt180) REVERT: D 247 TYR cc_start: 0.5920 (m-80) cc_final: 0.5574 (m-10) outliers start: 17 outliers final: 11 residues processed: 149 average time/residue: 0.3152 time to fit residues: 63.2759 Evaluate side-chains 146 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN C 437 ASN B 437 ASN D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.187543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.140003 restraints weight = 14516.924| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.61 r_work: 0.3381 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13084 Z= 0.361 Angle : 0.545 6.674 17812 Z= 0.274 Chirality : 0.042 0.187 1960 Planarity : 0.005 0.053 2212 Dihedral : 8.479 59.155 1912 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.01 % Allowed : 18.09 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.21), residues: 1552 helix: 1.35 (0.17), residues: 984 sheet: -0.64 (0.72), residues: 40 loop : 0.20 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 255 HIS 0.004 0.001 HIS B 77 PHE 0.035 0.002 PHE B 93 TYR 0.007 0.001 TYR D 70 ARG 0.011 0.001 ARG A 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2595.80 seconds wall clock time: 47 minutes 49.95 seconds (2869.95 seconds total)