Starting phenix.real_space_refine on Fri Mar 15 20:39:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phi_13417/03_2024/7phi_13417_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phi_13417/03_2024/7phi_13417.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phi_13417/03_2024/7phi_13417_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phi_13417/03_2024/7phi_13417_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phi_13417/03_2024/7phi_13417_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phi_13417/03_2024/7phi_13417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phi_13417/03_2024/7phi_13417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phi_13417/03_2024/7phi_13417_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phi_13417/03_2024/7phi_13417_updated.pdb" } resolution = 3.1 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= 0.013 sd= 0.099 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 8328 2.51 5 N 2108 2.21 5 O 2188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 51": "NH1" <-> "NH2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D GLU 380": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12708 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'PCF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 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: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 123 Unusual residues: {' ZN': 1, 'PCF': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 798 SG CYS A 104 66.417 45.251 46.373 1.00107.92 S ATOM 6825 SG CYS B 83 63.861 48.087 44.306 1.00103.76 S ATOM 3896 SG CYS C 104 49.470 68.990 46.280 1.00107.92 S ATOM 3902 SG CYS C 105 52.826 69.884 45.032 1.00105.62 S ATOM 9923 SG CYS D 83 52.151 66.104 44.334 1.00103.76 S ATOM 3727 SG CYS C 83 67.058 63.051 44.262 1.00103.76 S ATOM 6994 SG CYS B 104 69.820 65.671 46.295 1.00107.92 S ATOM 7000 SG CYS B 105 70.709 62.314 45.050 1.00105.62 S ATOM 629 SG CYS A 83 48.854 51.266 44.358 1.00103.76 S ATOM 10092 SG CYS D 104 46.102 48.552 46.344 1.00107.92 S ATOM 10098 SG CYS D 105 45.231 51.913 45.096 1.00105.62 S Time building chain proxies: 6.99, per 1000 atoms: 0.55 Number of scatterers: 12708 At special positions: 0 Unit cell: (115.92, 115.08, 124.32, 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 2188 8.00 N 2108 7.00 C 8328 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: 5.64 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A 603 " - pdb=" SG CYS B 83 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 104 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B 601 " - pdb=" SG CYS C 83 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 104 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 105 " pdb=" ZN C 602 " pdb="ZN ZN C 602 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 602 " - pdb=" SG CYS D 83 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 104 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 105 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 601 " - pdb=" SG CYS A 83 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 105 " Number of angles added : 9 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 8 sheets defined 64.6% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 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: 4.559A 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 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 103 through 119 removed outlier: 3.614A pdb=" N TRP A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N MET A 107 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR A 108 " --> pdb=" O CYS A 105 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG A 110 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN A 111 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS A 112 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG A 113 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 116 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 4.076A 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: 3.792A pdb=" N GLU A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 327 removed outlier: 3.766A pdb=" N ASP A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N PHE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 4.985A 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: 3.699A 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: 4.560A 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 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 103 through 119 removed outlier: 3.615A pdb=" N TRP C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N MET C 107 " --> pdb=" O CYS C 104 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR C 108 " --> pdb=" O CYS C 105 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG C 110 " --> pdb=" O MET C 107 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN C 111 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS C 112 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG C 113 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 116 " --> pdb=" O ARG C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 removed outlier: 4.075A 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: 3.793A pdb=" N GLU C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL C 293 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY C 294 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 327 removed outlier: 3.766A pdb=" N ASP C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL C 316 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE C 318 " --> pdb=" O ARG C 314 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 4.984A 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: 3.699A 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: 4.559A 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 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 103 through 119 removed outlier: 3.613A pdb=" N TRP B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N MET B 107 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR B 108 " --> pdb=" O CYS B 105 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG B 110 " --> pdb=" O MET B 107 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN B 111 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS B 112 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG B 113 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 116 " --> pdb=" O ARG B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 4.075A 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: 3.793A pdb=" N GLU B 292 " --> pdb=" O PRO B 288 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY B 294 " --> pdb=" O TYR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 327 removed outlier: 3.765A pdb=" N ASP B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL B 316 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 4.985A 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: 3.699A 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: 4.559A 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 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 103 through 119 removed outlier: 3.613A pdb=" N TRP D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N MET D 107 " --> pdb=" O CYS D 104 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR D 108 " --> pdb=" O CYS D 105 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG D 110 " --> pdb=" O MET D 107 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN D 111 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS D 112 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ARG D 113 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 116 " --> pdb=" O ARG D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 removed outlier: 4.076A 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: 3.793A pdb=" N GLU D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY D 294 " --> pdb=" O TYR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 327 removed outlier: 3.765A pdb=" N ASP D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL D 316 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE D 318 " --> pdb=" O ARG D 314 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE D 321 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N PHE D 322 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 4.984A 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: 3.699A 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 'A' and resid 218 through 221 removed outlier: 3.692A pdb=" N GLU A 238 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 17 through 22 Processing sheet with id= D, first strand: chain 'C' and resid 218 through 221 removed outlier: 3.692A pdb=" N GLU C 238 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 17 through 22 Processing sheet with id= F, first strand: chain 'B' and resid 218 through 221 removed outlier: 3.692A pdb=" N GLU B 238 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 17 through 22 Processing sheet with id= H, first strand: chain 'D' and resid 218 through 221 removed outlier: 3.692A pdb=" N GLU D 238 " --> pdb=" O VAL D 219 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1920 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: 3.40 Time building geometry restraints manager: 6.01 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: 1932 1.31 - 1.43: 3790 1.43 - 1.56: 7214 1.56 - 1.68: 20 1.68 - 1.81: 104 Bond restraints: 13060 Sorted by residual: bond pdb=" CG LEU C 401 " pdb=" CD1 LEU C 401 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.09e+00 bond pdb=" CG LEU D 401 " pdb=" CD1 LEU D 401 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.99e+00 bond pdb=" CG LEU B 401 " pdb=" CD1 LEU B 401 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.94e+00 bond pdb=" CG LEU A 401 " pdb=" CD1 LEU A 401 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.90e+00 bond pdb=" CB VAL C 101 " pdb=" CG2 VAL C 101 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.14e+00 ... (remaining 13055 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.65: 328 105.65 - 112.78: 7038 112.78 - 119.91: 4401 119.91 - 127.03: 5770 127.03 - 134.16: 231 Bond angle restraints: 17768 Sorted by residual: angle pdb=" CA LEU B 91 " pdb=" CB LEU B 91 " pdb=" CG LEU B 91 " ideal model delta sigma weight residual 116.30 125.41 -9.11 3.50e+00 8.16e-02 6.78e+00 angle pdb=" CA LEU D 91 " pdb=" CB LEU D 91 " pdb=" CG LEU D 91 " ideal model delta sigma weight residual 116.30 125.36 -9.06 3.50e+00 8.16e-02 6.71e+00 angle pdb=" CA LEU A 91 " pdb=" CB LEU A 91 " pdb=" CG LEU A 91 " ideal model delta sigma weight residual 116.30 125.35 -9.05 3.50e+00 8.16e-02 6.69e+00 angle pdb=" CA LEU C 91 " pdb=" CB LEU C 91 " pdb=" CG LEU C 91 " ideal model delta sigma weight residual 116.30 125.35 -9.05 3.50e+00 8.16e-02 6.68e+00 angle pdb=" N PHE A 207 " pdb=" CA PHE A 207 " pdb=" CB PHE A 207 " ideal model delta sigma weight residual 109.91 106.41 3.50 1.46e+00 4.69e-01 5.75e+00 ... (remaining 17763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 6964 17.63 - 35.25: 443 35.25 - 52.88: 123 52.88 - 70.50: 38 70.50 - 88.13: 16 Dihedral angle restraints: 7584 sinusoidal: 2996 harmonic: 4588 Sorted by residual: dihedral pdb=" CG ARG B 339 " pdb=" CD ARG B 339 " pdb=" NE ARG B 339 " pdb=" CZ ARG B 339 " ideal model delta sinusoidal sigma weight residual 180.00 135.24 44.76 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG D 339 " pdb=" CD ARG D 339 " pdb=" NE ARG D 339 " pdb=" CZ ARG D 339 " ideal model delta sinusoidal sigma weight residual 180.00 135.24 44.76 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG C 339 " pdb=" CD ARG C 339 " pdb=" NE ARG C 339 " pdb=" CZ ARG C 339 " ideal model delta sinusoidal sigma weight residual 180.00 135.28 44.72 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 7581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1036 0.036 - 0.072: 631 0.072 - 0.108: 208 0.108 - 0.143: 57 0.143 - 0.179: 20 Chirality restraints: 1952 Sorted by residual: chirality pdb=" CA GLU B 8 " pdb=" N GLU B 8 " pdb=" C GLU B 8 " pdb=" CB GLU B 8 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CA GLU A 8 " pdb=" N GLU A 8 " pdb=" C GLU A 8 " pdb=" CB GLU A 8 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA GLU D 8 " pdb=" N GLU D 8 " pdb=" C GLU D 8 " pdb=" CB GLU D 8 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1949 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 190 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ARG A 190 " 0.055 2.00e-02 2.50e+03 pdb=" O ARG A 190 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR A 191 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 190 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ARG D 190 " 0.055 2.00e-02 2.50e+03 pdb=" O ARG D 190 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR D 191 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 190 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ARG C 190 " -0.055 2.00e-02 2.50e+03 pdb=" O ARG C 190 " 0.021 2.00e-02 2.50e+03 pdb=" N TYR C 191 " 0.019 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 4130 2.84 - 3.41: 14329 3.41 - 3.99: 22659 3.99 - 4.56: 33027 4.56 - 5.14: 47388 Nonbonded interactions: 121533 Sorted by model distance: nonbonded pdb=" NH1 ARG D 113 " pdb=" OE1 GLU D 116 " model vdw 2.265 2.520 nonbonded pdb=" NH1 ARG A 113 " pdb=" OE1 GLU A 116 " model vdw 2.265 2.520 nonbonded pdb=" NH1 ARG C 113 " pdb=" OE1 GLU C 116 " model vdw 2.266 2.520 nonbonded pdb=" NH1 ARG B 113 " pdb=" OE1 GLU B 116 " model vdw 2.266 2.520 nonbonded pdb=" OG1 THR A 32 " pdb=" OH TYR A 71 " model vdw 2.282 2.440 ... (remaining 121528 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) selection = (chain 'B' and resid 7 through 464) selection = (chain 'C' and resid 7 through 464) selection = (chain 'D' and resid 7 through 464) } 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.180 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 39.090 Find NCS groups from input model: 1.270 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 13060 Z= 0.591 Angle : 0.753 9.111 17768 Z= 0.406 Chirality : 0.051 0.179 1952 Planarity : 0.006 0.054 2220 Dihedral : 14.163 88.126 4608 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % 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 (0.19), residues: 1540 helix: -0.49 (0.15), residues: 960 sheet: 0.42 (0.69), residues: 40 loop : -1.43 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 172 HIS 0.009 0.002 HIS B 212 PHE 0.025 0.002 PHE B 207 TYR 0.020 0.003 TYR C 70 ARG 0.008 0.001 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.453 Fit side-chains REVERT: A 54 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6467 (pt0) REVERT: A 116 GLU cc_start: 0.6569 (tt0) cc_final: 0.6333 (tt0) REVERT: A 339 ARG cc_start: 0.6898 (ttt180) cc_final: 0.6175 (mtt90) REVERT: A 458 LYS cc_start: 0.7267 (mmtp) cc_final: 0.6888 (tptp) REVERT: C 116 GLU cc_start: 0.6519 (tt0) cc_final: 0.6272 (tt0) REVERT: C 339 ARG cc_start: 0.6927 (ttt180) cc_final: 0.6162 (mtt90) REVERT: C 380 GLU cc_start: 0.6500 (tp30) cc_final: 0.6267 (mm-30) REVERT: B 54 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6130 (pt0) REVERT: B 116 GLU cc_start: 0.6415 (tt0) cc_final: 0.6209 (tt0) REVERT: B 339 ARG cc_start: 0.7277 (ttt180) cc_final: 0.6620 (mtt90) REVERT: D 54 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6422 (pt0) REVERT: D 89 GLU cc_start: 0.6422 (tm-30) cc_final: 0.6014 (tm-30) REVERT: D 339 ARG cc_start: 0.7021 (ttt180) cc_final: 0.6323 (mtt90) REVERT: D 380 GLU cc_start: 0.6465 (tp30) cc_final: 0.6166 (mm-30) REVERT: D 430 MET cc_start: 0.7126 (mmt) cc_final: 0.6887 (mmt) REVERT: D 458 LYS cc_start: 0.7387 (mmtp) cc_final: 0.6685 (tptp) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.3040 time to fit residues: 79.2233 Evaluate side-chains 144 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 30.0000 chunk 141 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 111 GLN A 112 HIS A 450 GLN C 20 GLN C 111 GLN C 112 HIS C 279 ASN B 20 GLN B 111 GLN B 279 ASN B 450 GLN D 20 GLN D 111 GLN D 112 HIS D 279 ASN D 450 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13060 Z= 0.182 Angle : 0.492 6.234 17768 Z= 0.247 Chirality : 0.039 0.149 1952 Planarity : 0.004 0.044 2220 Dihedral : 11.277 59.943 1900 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.27 % Allowed : 9.41 % Favored : 89.32 % 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: 0.53 (0.21), residues: 1540 helix: 0.90 (0.16), residues: 1000 sheet: 0.48 (1.04), residues: 32 loop : -0.63 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 177 HIS 0.003 0.001 HIS B 43 PHE 0.009 0.001 PHE A 244 TYR 0.009 0.001 TYR B 71 ARG 0.002 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.411 Fit side-chains REVERT: A 54 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6562 (pt0) REVERT: A 339 ARG cc_start: 0.6709 (ttt180) cc_final: 0.6064 (mtt90) REVERT: A 442 TYR cc_start: 0.7498 (m-80) cc_final: 0.7165 (m-80) REVERT: A 458 LYS cc_start: 0.7202 (mmtp) cc_final: 0.6800 (tptp) REVERT: C 54 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6367 (pt0) REVERT: C 339 ARG cc_start: 0.6721 (ttt180) cc_final: 0.6099 (mtt90) REVERT: C 442 TYR cc_start: 0.7488 (m-80) cc_final: 0.7058 (m-80) REVERT: C 450 GLN cc_start: 0.7169 (tt0) cc_final: 0.6923 (tt0) REVERT: B 27 ARG cc_start: 0.7190 (ttm170) cc_final: 0.6799 (mtm110) REVERT: B 54 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6344 (pt0) REVERT: B 339 ARG cc_start: 0.6924 (ttt180) cc_final: 0.6378 (mtt90) REVERT: B 380 GLU cc_start: 0.6609 (tp30) cc_final: 0.6373 (mm-30) REVERT: B 442 TYR cc_start: 0.7465 (m-80) cc_final: 0.6929 (m-80) REVERT: D 27 ARG cc_start: 0.7228 (ttm170) cc_final: 0.6843 (mtm110) REVERT: D 54 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6554 (pt0) REVERT: D 89 GLU cc_start: 0.6477 (tm-30) cc_final: 0.6056 (tm-30) REVERT: D 339 ARG cc_start: 0.6884 (ttt180) cc_final: 0.6241 (mtt90) REVERT: D 380 GLU cc_start: 0.6526 (tp30) cc_final: 0.6324 (mm-30) REVERT: D 442 TYR cc_start: 0.7396 (m-80) cc_final: 0.6952 (m-80) REVERT: D 445 LEU cc_start: 0.6843 (tp) cc_final: 0.6480 (tp) REVERT: D 458 LYS cc_start: 0.7406 (mmtp) cc_final: 0.6779 (tptp) outliers start: 16 outliers final: 9 residues processed: 172 average time/residue: 0.2803 time to fit residues: 67.2001 Evaluate side-chains 155 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN C 279 ASN B 112 HIS B 450 GLN D 279 ASN D 450 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13060 Z= 0.305 Angle : 0.534 7.945 17768 Z= 0.269 Chirality : 0.042 0.151 1952 Planarity : 0.005 0.046 2220 Dihedral : 10.668 59.939 1900 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.82 % Allowed : 9.57 % Favored : 88.61 % 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: 0.57 (0.21), residues: 1540 helix: 0.88 (0.17), residues: 1000 sheet: 0.52 (1.03), residues: 32 loop : -0.49 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 94 HIS 0.005 0.001 HIS C 77 PHE 0.012 0.001 PHE B 359 TYR 0.012 0.001 TYR B 70 ARG 0.003 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 1.457 Fit side-chains REVERT: A 54 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6404 (pt0) REVERT: A 339 ARG cc_start: 0.6717 (ttt180) cc_final: 0.6010 (mtt90) REVERT: A 442 TYR cc_start: 0.7556 (m-80) cc_final: 0.7176 (m-80) REVERT: A 458 LYS cc_start: 0.7235 (mmtp) cc_final: 0.6838 (tptp) REVERT: C 54 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6331 (pt0) REVERT: C 98 GLU cc_start: 0.7856 (pt0) cc_final: 0.6724 (mt-10) REVERT: C 339 ARG cc_start: 0.6709 (ttt180) cc_final: 0.6097 (mtt90) REVERT: C 442 TYR cc_start: 0.7588 (m-80) cc_final: 0.7126 (m-80) REVERT: B 54 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6314 (pt0) REVERT: B 259 GLU cc_start: 0.5711 (tt0) cc_final: 0.5509 (tt0) REVERT: B 339 ARG cc_start: 0.6739 (ttt180) cc_final: 0.6110 (mtt90) REVERT: B 406 MET cc_start: 0.8306 (ptp) cc_final: 0.8018 (ptm) REVERT: B 442 TYR cc_start: 0.7479 (m-80) cc_final: 0.7061 (m-80) REVERT: D 54 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6451 (pt0) REVERT: D 89 GLU cc_start: 0.6493 (tm-30) cc_final: 0.5991 (tm-30) REVERT: D 339 ARG cc_start: 0.6855 (ttt180) cc_final: 0.6180 (mtt90) REVERT: D 406 MET cc_start: 0.8308 (ptp) cc_final: 0.8059 (ptm) REVERT: D 442 TYR cc_start: 0.7482 (m-80) cc_final: 0.7117 (m-80) REVERT: D 451 LYS cc_start: 0.6887 (ttmm) cc_final: 0.6172 (tttt) REVERT: D 458 LYS cc_start: 0.7514 (mmtp) cc_final: 0.6955 (tptp) outliers start: 23 outliers final: 15 residues processed: 166 average time/residue: 0.3027 time to fit residues: 70.1063 Evaluate side-chains 149 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN B 450 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13060 Z= 0.267 Angle : 0.501 7.416 17768 Z= 0.252 Chirality : 0.041 0.184 1952 Planarity : 0.005 0.047 2220 Dihedral : 10.368 59.448 1900 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.42 % Allowed : 11.55 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1540 helix: 0.99 (0.17), residues: 1000 sheet: 0.63 (1.01), residues: 32 loop : -0.31 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 392 HIS 0.004 0.001 HIS C 77 PHE 0.010 0.001 PHE A 359 TYR 0.009 0.001 TYR D 70 ARG 0.003 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.284 Fit side-chains REVERT: A 54 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6374 (pt0) REVERT: A 339 ARG cc_start: 0.6706 (ttt180) cc_final: 0.5997 (mtt90) REVERT: A 442 TYR cc_start: 0.7529 (m-80) cc_final: 0.7145 (m-80) REVERT: A 458 LYS cc_start: 0.7462 (mmtp) cc_final: 0.7040 (tptp) REVERT: C 54 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6339 (pt0) REVERT: C 98 GLU cc_start: 0.7896 (pt0) cc_final: 0.6847 (mt-10) REVERT: C 339 ARG cc_start: 0.6694 (ttt180) cc_final: 0.6063 (mtt90) REVERT: C 442 TYR cc_start: 0.7586 (m-80) cc_final: 0.7198 (m-80) REVERT: B 54 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6476 (pt0) REVERT: B 339 ARG cc_start: 0.6731 (ttt180) cc_final: 0.6084 (mtt90) REVERT: B 406 MET cc_start: 0.8105 (ptp) cc_final: 0.7859 (ptm) REVERT: B 442 TYR cc_start: 0.7466 (m-80) cc_final: 0.7077 (m-80) REVERT: D 54 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6389 (pt0) REVERT: D 89 GLU cc_start: 0.6507 (tm-30) cc_final: 0.5993 (tm-30) REVERT: D 339 ARG cc_start: 0.6777 (ttt180) cc_final: 0.6111 (mtt90) REVERT: D 406 MET cc_start: 0.8110 (ptp) cc_final: 0.7876 (ptm) REVERT: D 442 TYR cc_start: 0.7450 (m-80) cc_final: 0.7112 (m-80) REVERT: D 458 LYS cc_start: 0.7509 (mmtp) cc_final: 0.6973 (tptp) outliers start: 18 outliers final: 12 residues processed: 152 average time/residue: 0.2863 time to fit residues: 60.6838 Evaluate side-chains 147 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS A 450 GLN C 22 HIS C 450 GLN B 22 HIS ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13060 Z= 0.353 Angle : 0.543 7.677 17768 Z= 0.273 Chirality : 0.043 0.218 1952 Planarity : 0.005 0.049 2220 Dihedral : 10.217 59.800 1900 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.14 % Allowed : 13.45 % Favored : 84.41 % 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: 0.84 (0.22), residues: 1540 helix: 0.96 (0.17), residues: 980 sheet: 0.75 (1.00), residues: 32 loop : -0.03 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 392 HIS 0.006 0.001 HIS D 77 PHE 0.015 0.001 PHE D 260 TYR 0.012 0.001 TYR D 70 ARG 0.003 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.747 Fit side-chains REVERT: A 54 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6301 (pt0) REVERT: A 113 ARG cc_start: 0.7723 (mpt90) cc_final: 0.7232 (mmm160) REVERT: A 339 ARG cc_start: 0.6733 (ttt180) cc_final: 0.6070 (mtt90) REVERT: A 442 TYR cc_start: 0.7581 (m-80) cc_final: 0.7180 (m-80) REVERT: A 458 LYS cc_start: 0.7492 (mmtp) cc_final: 0.7063 (tptp) REVERT: C 54 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6302 (pt0) REVERT: C 91 LEU cc_start: 0.6520 (pp) cc_final: 0.6314 (pt) REVERT: C 98 GLU cc_start: 0.7914 (pt0) cc_final: 0.6939 (mt-10) REVERT: C 339 ARG cc_start: 0.6724 (ttt180) cc_final: 0.6080 (mtt90) REVERT: C 442 TYR cc_start: 0.7591 (m-80) cc_final: 0.7191 (m-80) REVERT: B 54 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6407 (pt0) REVERT: B 339 ARG cc_start: 0.6752 (ttt180) cc_final: 0.6097 (mtt90) REVERT: B 406 MET cc_start: 0.8253 (ptp) cc_final: 0.7883 (ptm) REVERT: B 442 TYR cc_start: 0.7518 (m-80) cc_final: 0.7137 (m-80) REVERT: D 54 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6336 (pt0) REVERT: D 89 GLU cc_start: 0.6483 (tm-30) cc_final: 0.5909 (tm-30) REVERT: D 113 ARG cc_start: 0.7734 (mpt90) cc_final: 0.7320 (mmm160) REVERT: D 339 ARG cc_start: 0.6852 (ttt180) cc_final: 0.6219 (mtt90) REVERT: D 406 MET cc_start: 0.8247 (ptp) cc_final: 0.7844 (ptm) REVERT: D 442 TYR cc_start: 0.7472 (m-10) cc_final: 0.7097 (m-80) REVERT: D 458 LYS cc_start: 0.7566 (mmtp) cc_final: 0.6978 (tptp) outliers start: 27 outliers final: 18 residues processed: 163 average time/residue: 0.2832 time to fit residues: 64.4315 Evaluate side-chains 155 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13060 Z= 0.218 Angle : 0.490 12.365 17768 Z= 0.244 Chirality : 0.040 0.207 1952 Planarity : 0.005 0.048 2220 Dihedral : 9.904 59.990 1900 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.19 % Allowed : 14.32 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.22), residues: 1540 helix: 1.05 (0.17), residues: 1000 sheet: 0.82 (0.98), residues: 32 loop : -0.10 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 94 HIS 0.003 0.001 HIS B 77 PHE 0.009 0.001 PHE A 359 TYR 0.008 0.001 TYR A 365 ARG 0.002 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.452 Fit side-chains REVERT: A 54 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6345 (pt0) REVERT: A 339 ARG cc_start: 0.6676 (ttt180) cc_final: 0.6026 (mtt90) REVERT: A 442 TYR cc_start: 0.7510 (m-80) cc_final: 0.7138 (m-80) REVERT: A 458 LYS cc_start: 0.7477 (mmtp) cc_final: 0.7023 (tptp) REVERT: C 54 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6327 (pt0) REVERT: C 98 GLU cc_start: 0.7915 (pt0) cc_final: 0.6974 (mp0) REVERT: C 339 ARG cc_start: 0.6695 (ttt180) cc_final: 0.6046 (mtt90) REVERT: C 442 TYR cc_start: 0.7544 (m-80) cc_final: 0.7154 (m-80) REVERT: B 54 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6394 (pt0) REVERT: B 339 ARG cc_start: 0.6718 (ttt180) cc_final: 0.6060 (mtt90) REVERT: B 386 ASN cc_start: 0.8019 (p0) cc_final: 0.7807 (p0) REVERT: B 406 MET cc_start: 0.8186 (ptp) cc_final: 0.7942 (ptm) REVERT: B 442 TYR cc_start: 0.7392 (m-80) cc_final: 0.7059 (m-80) REVERT: D 54 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6330 (pt0) REVERT: D 89 GLU cc_start: 0.6500 (tm-30) cc_final: 0.5875 (mp0) REVERT: D 339 ARG cc_start: 0.6711 (ttt180) cc_final: 0.6043 (mtt90) REVERT: D 406 MET cc_start: 0.8172 (ptp) cc_final: 0.7930 (ptm) REVERT: D 442 TYR cc_start: 0.7392 (m-10) cc_final: 0.7093 (m-80) REVERT: D 458 LYS cc_start: 0.7571 (mmtp) cc_final: 0.6991 (tptp) outliers start: 15 outliers final: 11 residues processed: 144 average time/residue: 0.2860 time to fit residues: 57.5886 Evaluate side-chains 142 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 84 optimal weight: 0.4980 chunk 150 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 91 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 66 HIS D 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13060 Z= 0.159 Angle : 0.450 9.751 17768 Z= 0.224 Chirality : 0.038 0.192 1952 Planarity : 0.004 0.046 2220 Dihedral : 9.313 59.805 1900 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.19 % Allowed : 14.95 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.22), residues: 1540 helix: 1.28 (0.17), residues: 1000 sheet: 1.01 (0.97), residues: 32 loop : 0.14 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 177 HIS 0.002 0.000 HIS B 383 PHE 0.008 0.001 PHE D 93 TYR 0.006 0.001 TYR B 70 ARG 0.002 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 1.328 Fit side-chains REVERT: A 54 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6122 (pt0) REVERT: A 98 GLU cc_start: 0.7918 (pt0) cc_final: 0.7016 (mp0) REVERT: A 339 ARG cc_start: 0.6653 (ttt180) cc_final: 0.6009 (mtt90) REVERT: A 442 TYR cc_start: 0.7474 (m-80) cc_final: 0.7125 (m-80) REVERT: A 458 LYS cc_start: 0.7464 (mmtp) cc_final: 0.7026 (tptp) REVERT: C 54 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6369 (pt0) REVERT: C 98 GLU cc_start: 0.7893 (pt0) cc_final: 0.6966 (mp0) REVERT: C 339 ARG cc_start: 0.6649 (ttt180) cc_final: 0.6018 (mtt90) REVERT: C 386 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7543 (p0) REVERT: C 442 TYR cc_start: 0.7495 (m-80) cc_final: 0.7126 (m-80) REVERT: B 54 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6418 (pt0) REVERT: B 98 GLU cc_start: 0.7915 (pt0) cc_final: 0.7058 (mp0) REVERT: B 339 ARG cc_start: 0.6689 (ttt180) cc_final: 0.6012 (mtt90) REVERT: B 442 TYR cc_start: 0.7339 (m-80) cc_final: 0.7073 (m-80) REVERT: D 54 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6403 (pt0) REVERT: D 89 GLU cc_start: 0.6538 (tm-30) cc_final: 0.6085 (tm-30) REVERT: D 98 GLU cc_start: 0.7946 (pt0) cc_final: 0.7039 (mp0) REVERT: D 339 ARG cc_start: 0.6673 (ttt180) cc_final: 0.6015 (mtt90) REVERT: D 442 TYR cc_start: 0.7349 (m-10) cc_final: 0.7078 (m-80) REVERT: D 458 LYS cc_start: 0.7451 (mmtp) cc_final: 0.6887 (tptp) outliers start: 15 outliers final: 9 residues processed: 163 average time/residue: 0.2739 time to fit residues: 62.2239 Evaluate side-chains 153 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 0.1980 chunk 136 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 HIS C 66 HIS ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN D 173 GLN D 279 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13060 Z= 0.205 Angle : 0.478 10.189 17768 Z= 0.238 Chirality : 0.040 0.209 1952 Planarity : 0.005 0.047 2220 Dihedral : 9.145 59.882 1900 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.42 % Allowed : 14.79 % Favored : 83.78 % 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: 1.33 (0.22), residues: 1540 helix: 1.25 (0.17), residues: 1000 sheet: 1.01 (0.96), residues: 32 loop : 0.34 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 255 HIS 0.002 0.001 HIS A 212 PHE 0.012 0.001 PHE A 93 TYR 0.017 0.001 TYR B 70 ARG 0.004 0.000 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.438 Fit side-chains REVERT: A 54 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6227 (pt0) REVERT: A 98 GLU cc_start: 0.7912 (pt0) cc_final: 0.7016 (mp0) REVERT: A 339 ARG cc_start: 0.6740 (ttt180) cc_final: 0.6120 (mtt90) REVERT: A 442 TYR cc_start: 0.7450 (m-80) cc_final: 0.7117 (m-80) REVERT: A 458 LYS cc_start: 0.7464 (mmtp) cc_final: 0.7022 (tptp) REVERT: C 43 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.6778 (m90) REVERT: C 54 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6360 (pt0) REVERT: C 98 GLU cc_start: 0.7909 (pt0) cc_final: 0.7008 (mp0) REVERT: C 339 ARG cc_start: 0.6669 (ttt180) cc_final: 0.6032 (mtt90) REVERT: C 386 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7790 (p0) REVERT: C 442 TYR cc_start: 0.7505 (m-80) cc_final: 0.7153 (m-80) REVERT: B 54 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6381 (pt0) REVERT: B 98 GLU cc_start: 0.7899 (pt0) cc_final: 0.7038 (mp0) REVERT: B 339 ARG cc_start: 0.6705 (ttt180) cc_final: 0.6032 (mtt90) REVERT: B 442 TYR cc_start: 0.7372 (m-80) cc_final: 0.7089 (m-80) REVERT: B 458 LYS cc_start: 0.7328 (ttmt) cc_final: 0.6566 (tptp) REVERT: D 54 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6363 (pt0) REVERT: D 89 GLU cc_start: 0.6418 (tm-30) cc_final: 0.5897 (tm-30) REVERT: D 98 GLU cc_start: 0.7934 (pt0) cc_final: 0.7037 (mp0) REVERT: D 339 ARG cc_start: 0.6677 (ttt180) cc_final: 0.6027 (mtt90) REVERT: D 442 TYR cc_start: 0.7380 (m-10) cc_final: 0.7094 (m-80) REVERT: D 458 LYS cc_start: 0.7507 (mmtp) cc_final: 0.6949 (tptp) outliers start: 18 outliers final: 10 residues processed: 153 average time/residue: 0.2866 time to fit residues: 61.0512 Evaluate side-chains 152 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 139 optimal weight: 0.0870 chunk 92 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13060 Z= 0.172 Angle : 0.465 9.218 17768 Z= 0.233 Chirality : 0.039 0.203 1952 Planarity : 0.005 0.063 2220 Dihedral : 8.969 59.897 1900 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.11 % Allowed : 15.51 % Favored : 83.39 % 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: 1.46 (0.22), residues: 1540 helix: 1.33 (0.17), residues: 1000 sheet: 1.02 (0.95), residues: 32 loop : 0.43 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 255 HIS 0.004 0.001 HIS C 45 PHE 0.015 0.001 PHE A 93 TYR 0.014 0.001 TYR B 70 ARG 0.003 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 1.517 Fit side-chains REVERT: A 54 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6236 (pt0) REVERT: A 98 GLU cc_start: 0.7907 (pt0) cc_final: 0.7007 (mp0) REVERT: A 339 ARG cc_start: 0.6644 (ttt180) cc_final: 0.6011 (mtt90) REVERT: A 442 TYR cc_start: 0.7434 (m-80) cc_final: 0.7081 (m-80) REVERT: A 458 LYS cc_start: 0.7452 (mmtp) cc_final: 0.7016 (tptp) REVERT: C 54 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6090 (pt0) REVERT: C 58 ASP cc_start: 0.7800 (t0) cc_final: 0.7583 (t0) REVERT: C 98 GLU cc_start: 0.7878 (pt0) cc_final: 0.6965 (mp0) REVERT: C 339 ARG cc_start: 0.6660 (ttt180) cc_final: 0.6022 (mtt90) REVERT: C 386 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7652 (p0) REVERT: C 442 TYR cc_start: 0.7488 (m-80) cc_final: 0.7105 (m-80) REVERT: B 43 HIS cc_start: 0.7502 (OUTLIER) cc_final: 0.6834 (m90) REVERT: B 54 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6381 (pt0) REVERT: B 98 GLU cc_start: 0.7887 (pt0) cc_final: 0.7029 (mp0) REVERT: B 339 ARG cc_start: 0.6686 (ttt180) cc_final: 0.6014 (mtt90) REVERT: B 442 TYR cc_start: 0.7349 (m-10) cc_final: 0.7051 (m-80) REVERT: B 458 LYS cc_start: 0.7330 (ttmt) cc_final: 0.6585 (tptp) REVERT: D 54 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6322 (pt0) REVERT: D 89 GLU cc_start: 0.6433 (tm-30) cc_final: 0.5942 (tm-30) REVERT: D 98 GLU cc_start: 0.7900 (pt0) cc_final: 0.7017 (mp0) REVERT: D 339 ARG cc_start: 0.6676 (ttt180) cc_final: 0.6021 (mtt90) REVERT: D 442 TYR cc_start: 0.7335 (m-10) cc_final: 0.7088 (m-80) REVERT: D 458 LYS cc_start: 0.7445 (mmtp) cc_final: 0.6908 (tptp) outliers start: 14 outliers final: 9 residues processed: 151 average time/residue: 0.2813 time to fit residues: 59.4132 Evaluate side-chains 153 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 142 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 43 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13060 Z= 0.253 Angle : 0.508 9.521 17768 Z= 0.255 Chirality : 0.041 0.229 1952 Planarity : 0.005 0.054 2220 Dihedral : 8.950 59.449 1900 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.19 % Allowed : 15.59 % Favored : 83.23 % 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: 1.19 (0.22), residues: 1540 helix: 1.18 (0.17), residues: 1000 sheet: 0.99 (0.95), residues: 32 loop : 0.18 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 255 HIS 0.003 0.001 HIS C 77 PHE 0.015 0.001 PHE C 93 TYR 0.014 0.001 TYR B 70 ARG 0.003 0.000 ARG C 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.466 Fit side-chains REVERT: A 54 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6212 (pt0) REVERT: A 98 GLU cc_start: 0.7937 (pt0) cc_final: 0.7012 (mp0) REVERT: A 339 ARG cc_start: 0.6777 (ttt180) cc_final: 0.6150 (mtt90) REVERT: A 442 TYR cc_start: 0.7487 (m-80) cc_final: 0.7100 (m-80) REVERT: A 458 LYS cc_start: 0.7468 (mmtp) cc_final: 0.7020 (tptp) REVERT: C 54 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6421 (pt0) REVERT: C 98 GLU cc_start: 0.7904 (pt0) cc_final: 0.7010 (mp0) REVERT: C 339 ARG cc_start: 0.6722 (ttt180) cc_final: 0.6056 (mtt90) REVERT: C 386 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7958 (p0) REVERT: C 442 TYR cc_start: 0.7502 (m-80) cc_final: 0.7103 (m-80) REVERT: B 54 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6367 (pt0) REVERT: B 98 GLU cc_start: 0.7915 (pt0) cc_final: 0.7038 (mp0) REVERT: B 339 ARG cc_start: 0.6744 (ttt180) cc_final: 0.6071 (mtt90) REVERT: B 442 TYR cc_start: 0.7404 (m-10) cc_final: 0.7057 (m-80) REVERT: B 458 LYS cc_start: 0.7342 (ttmt) cc_final: 0.6594 (tptp) REVERT: D 54 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6331 (pt0) REVERT: D 89 GLU cc_start: 0.6426 (tm-30) cc_final: 0.5883 (tm-30) REVERT: D 98 GLU cc_start: 0.7929 (pt0) cc_final: 0.7025 (mp0) REVERT: D 339 ARG cc_start: 0.6838 (ttt180) cc_final: 0.6202 (mtt90) REVERT: D 442 TYR cc_start: 0.7366 (m-10) cc_final: 0.7078 (m-80) REVERT: D 458 LYS cc_start: 0.7481 (mmtp) cc_final: 0.6919 (tptp) outliers start: 15 outliers final: 11 residues processed: 143 average time/residue: 0.2963 time to fit residues: 58.9811 Evaluate side-chains 144 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.219901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.195062 restraints weight = 12892.711| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.66 r_work: 0.3835 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13060 Z= 0.174 Angle : 0.466 8.560 17768 Z= 0.234 Chirality : 0.039 0.199 1952 Planarity : 0.005 0.046 2220 Dihedral : 8.789 59.889 1900 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.19 % Allowed : 15.59 % Favored : 83.23 % 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: 1.38 (0.22), residues: 1540 helix: 1.33 (0.17), residues: 1000 sheet: 1.03 (0.94), residues: 32 loop : 0.26 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 255 HIS 0.002 0.000 HIS B 212 PHE 0.014 0.001 PHE D 93 TYR 0.014 0.001 TYR B 70 ARG 0.002 0.000 ARG A 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2595.73 seconds wall clock time: 47 minutes 28.42 seconds (2848.42 seconds total)