Starting phenix.real_space_refine on Mon Mar 18 08:52:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmz_30775/03_2024/7dmz_30775_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmz_30775/03_2024/7dmz_30775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmz_30775/03_2024/7dmz_30775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmz_30775/03_2024/7dmz_30775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmz_30775/03_2024/7dmz_30775_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dmz_30775/03_2024/7dmz_30775_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 2 5.21 5 S 138 5.16 5 C 12831 2.51 5 N 3462 2.21 5 O 3945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 3": "OE1" <-> "OE2" Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 220": "OE1" <-> "OE2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D GLU 429": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B GLU 434": "OE1" <-> "OE2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ASP 226": "OD1" <-> "OD2" Residue "E GLU 417": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 290": "OE1" <-> "OE2" Residue "C GLU 420": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F GLU 160": "OE1" <-> "OE2" Residue "F GLU 330": "OE1" <-> "OE2" Residue "F GLU 386": "OE1" <-> "OE2" Residue "F GLU 411": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20396 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3346 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3346 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3346 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "F" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'G2P': 1, 'TAJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'G2P': 1, 'TAJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'G2P': 1, 'TAJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.97, per 1000 atoms: 0.54 Number of scatterers: 20396 At special positions: 0 Unit cell: (129.6, 89.1, 167.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 138 16.00 P 18 15.00 Mg 2 11.99 O 3945 8.00 N 3462 7.00 C 12831 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.65 Conformation dependent library (CDL) restraints added in 3.4 seconds 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4746 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 16 sheets defined 43.4% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'D' and resid 11 through 27 Processing helix chain 'D' and resid 72 through 80 removed outlier: 3.746A pdb=" N ASP D 76 " --> pdb=" O PRO D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.594A pdb=" N TYR D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 115 through 126 Processing helix chain 'D' and resid 145 through 161 removed outlier: 4.532A pdb=" N THR D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 194 Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 224 through 243 removed outlier: 4.906A pdb=" N SER D 241 " --> pdb=" O SER D 237 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 removed outlier: 4.454A pdb=" N GLN D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 296 removed outlier: 3.849A pdb=" N PHE D 296 " --> pdb=" O THR D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 325 through 336 Processing helix chain 'D' and resid 383 through 399 Processing helix chain 'D' and resid 406 through 411 removed outlier: 4.019A pdb=" N GLU D 411 " --> pdb=" O TRP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 436 Processing helix chain 'A' and resid 10 through 27 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.758A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.941A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.253A pdb=" N LEU A 259 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.147A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 383 through 400 Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.897A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'B' and resid 11 through 27 Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 80 removed outlier: 3.817A pdb=" N ASP B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 80' Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 115 through 128 removed outlier: 4.786A pdb=" N GLN B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 removed outlier: 4.626A pdb=" N THR B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 224 through 243 removed outlier: 4.915A pdb=" N SER B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.960A pdb=" N PHE B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 326 through 336 Processing helix chain 'B' and resid 384 through 400 Processing helix chain 'B' and resid 405 through 411 removed outlier: 5.438A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 436 Processing helix chain 'E' and resid 12 through 27 Processing helix chain 'E' and resid 49 through 51 No H-bonds generated for 'chain 'E' and resid 49 through 51' Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 111 through 127 removed outlier: 5.434A pdb=" N ASP E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N SER E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 160 Processing helix chain 'E' and resid 183 through 197 removed outlier: 4.135A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 224 through 238 Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 288 through 295 Processing helix chain 'E' and resid 325 through 338 Processing helix chain 'E' and resid 383 through 401 removed outlier: 5.120A pdb=" N GLU E 393 " --> pdb=" O ARG E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 409 No H-bonds generated for 'chain 'E' and resid 406 through 409' Processing helix chain 'E' and resid 415 through 434 Processing helix chain 'C' and resid 11 through 27 Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 111 through 127 removed outlier: 5.179A pdb=" N ASP C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 160 Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 224 through 241 removed outlier: 5.783A pdb=" N CYS C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 338 Processing helix chain 'C' and resid 382 through 401 removed outlier: 5.120A pdb=" N GLU C 393 " --> pdb=" O ARG C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.201A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 434 Processing helix chain 'F' and resid 11 through 27 Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 111 through 127 removed outlier: 4.596A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.831A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 Processing helix chain 'F' and resid 224 through 241 removed outlier: 5.602A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 259 Processing helix chain 'F' and resid 288 through 295 Processing helix chain 'F' and resid 307 through 309 No H-bonds generated for 'chain 'F' and resid 307 through 309' Processing helix chain 'F' and resid 325 through 338 Processing helix chain 'F' and resid 382 through 400 removed outlier: 5.131A pdb=" N GLU F 393 " --> pdb=" O ARG F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 4.504A pdb=" N GLU F 411 " --> pdb=" O TRP F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 434 Processing sheet with id= A, first strand: chain 'D' and resid 65 through 68 removed outlier: 8.981A pdb=" N VAL D 66 " --> pdb=" O CYS D 4 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N SER D 6 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL D 68 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N HIS D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLY D 134 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ILE D 7 " --> pdb=" O GLY D 134 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU D 136 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL D 9 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N PHE D 138 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N SER D 165 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL D 137 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 167 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N HIS D 139 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N PHE D 169 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N CYS D 200 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N SER D 170 " --> pdb=" O CYS D 200 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE D 202 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR D 172 " --> pdb=" O PHE D 202 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL D 204 " --> pdb=" O TYR D 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.573A pdb=" N LYS D 60 " --> pdb=" O THR D 56 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 269 through 273 Processing sheet with id= D, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.338A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 138 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 9 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= F, first strand: chain 'A' and resid 269 through 273 Processing sheet with id= G, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.166A pdb=" N ILE B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE B 67 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N VAL B 66 " --> pdb=" O CYS B 4 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N SER B 6 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL B 68 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N HIS B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE B 135 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL B 9 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS B 139 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N SER B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N VAL B 137 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU B 167 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N HIS B 139 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= I, first strand: chain 'B' and resid 269 through 273 removed outlier: 3.559A pdb=" N ASN B 356 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 65 through 68 removed outlier: 9.020A pdb=" N ILE E 66 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS E 6 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL E 68 " --> pdb=" O HIS E 6 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLN E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N VAL E 5 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE E 135 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE E 7 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU E 137 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ALA E 9 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N HIS E 139 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU E 137 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN E 167 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS E 139 " --> pdb=" O ASN E 167 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= L, first strand: chain 'E' and resid 269 through 273 removed outlier: 6.611A pdb=" N LYS E 352 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N PHE E 319 " --> pdb=" O LYS E 352 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA E 354 " --> pdb=" O PHE E 319 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 351 through 356 removed outlier: 8.328A pdb=" N LYS C 352 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C 315 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA C 354 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA C 317 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N CYS C 356 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE C 319 " --> pdb=" O CYS C 356 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN C 380 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 315 " --> pdb=" O ILE C 378 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE C 378 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA C 317 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR C 376 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N PHE C 319 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER C 374 " --> pdb=" O PHE C 319 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER C 381 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE C 267 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR C 201 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N CYS C 203 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N PHE C 272 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 170 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS C 139 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 171 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 7 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR C 138 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER C 140 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP C 69 " --> pdb=" O VAL C 93 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 65 through 68 removed outlier: 9.394A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLY F 134 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ILE F 7 " --> pdb=" O GLY F 134 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLN F 136 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ALA F 9 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N THR F 138 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE F 165 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LEU F 137 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN F 167 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N HIS F 139 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE F 169 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TYR F 202 " --> pdb=" O SER F 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 53 through 56 Processing sheet with id= P, first strand: chain 'F' and resid 269 through 273 811 hydrogen bonds defined for protein. 2115 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: 6.38 Time building geometry restraints manager: 8.23 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: 3438 1.31 - 1.44: 5620 1.44 - 1.57: 11573 1.57 - 1.69: 27 1.69 - 1.82: 222 Bond restraints: 20880 Sorted by residual: bond pdb=" C ASP D 98 " pdb=" N ALA D 99 " ideal model delta sigma weight residual 1.334 1.524 -0.190 1.46e-02 4.69e+03 1.69e+02 bond pdb=" C1' GTP A 501 " pdb=" C2' GTP A 501 " ideal model delta sigma weight residual 1.524 1.286 0.238 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1' GTP B 501 " pdb=" C2' GTP B 501 " ideal model delta sigma weight residual 1.524 1.287 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1' GTP D 501 " pdb=" C2' GTP D 501 " ideal model delta sigma weight residual 1.524 1.289 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1' GTP B 501 " pdb=" O4' GTP B 501 " ideal model delta sigma weight residual 1.410 1.611 -0.201 2.00e-02 2.50e+03 1.01e+02 ... (remaining 20875 not shown) Histogram of bond angle deviations from ideal: 59.45 - 76.87: 9 76.87 - 94.29: 0 94.29 - 111.71: 9458 111.71 - 129.13: 18823 129.13 - 146.55: 150 Bond angle restraints: 28440 Sorted by residual: angle pdb=" C PRO E 173 " pdb=" N SER E 174 " pdb=" CA SER E 174 " ideal model delta sigma weight residual 120.68 146.55 -25.87 1.52e+00 4.33e-01 2.90e+02 angle pdb=" C ASP D 98 " pdb=" N ALA D 99 " pdb=" CA ALA D 99 " ideal model delta sigma weight residual 120.68 108.90 11.78 1.70e+00 3.46e-01 4.80e+01 angle pdb=" O ALA D 99 " pdb=" C ALA D 99 " pdb=" N ALA D 100 " ideal model delta sigma weight residual 122.33 130.97 -8.64 1.34e+00 5.57e-01 4.16e+01 angle pdb=" C THR F 287 " pdb=" N VAL F 288 " pdb=" CA VAL F 288 " ideal model delta sigma weight residual 120.24 124.15 -3.91 6.30e-01 2.52e+00 3.85e+01 angle pdb=" CA ALA D 99 " pdb=" C ALA D 99 " pdb=" N ALA D 100 " ideal model delta sigma weight residual 117.82 109.71 8.11 1.42e+00 4.96e-01 3.26e+01 ... (remaining 28435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 12412 35.84 - 71.68: 307 71.68 - 107.51: 46 107.51 - 143.35: 6 143.35 - 179.19: 6 Dihedral angle restraints: 12777 sinusoidal: 5376 harmonic: 7401 Sorted by residual: dihedral pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sinusoidal sigma weight residual 69.27 -111.54 -179.19 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -96.77 166.04 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C8 GTP D 501 " pdb=" C1' GTP D 501 " pdb=" N9 GTP D 501 " pdb=" O4' GTP D 501 " ideal model delta sinusoidal sigma weight residual 104.59 -55.07 159.67 1 2.00e+01 2.50e-03 4.65e+01 ... (remaining 12774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 3107 0.177 - 0.353: 24 0.353 - 0.530: 0 0.530 - 0.706: 3 0.706 - 0.883: 1 Chirality restraints: 3135 Sorted by residual: chirality pdb=" CAZ TAJ E 501 " pdb=" CAV TAJ E 501 " pdb=" CAY TAJ E 501 " pdb=" OAD TAJ E 501 " both_signs ideal model delta sigma weight residual False -2.52 -1.64 -0.88 2.00e-01 2.50e+01 1.95e+01 chirality pdb=" CBB TAJ E 501 " pdb=" CBA TAJ E 501 " pdb=" CBC TAJ E 501 " pdb=" CBD TAJ E 501 " both_signs ideal model delta sigma weight residual False 2.06 2.69 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CBB TAJ F 501 " pdb=" CBA TAJ F 501 " pdb=" CBC TAJ F 501 " pdb=" CBD TAJ F 501 " both_signs ideal model delta sigma weight residual False 2.06 2.61 -0.55 2.00e-01 2.50e+01 7.47e+00 ... (remaining 3132 not shown) Planarity restraints: 3681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 397 " 0.016 2.00e-02 2.50e+03 3.09e-02 9.56e+00 pdb=" C LEU A 397 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU A 397 " 0.020 2.00e-02 2.50e+03 pdb=" N MET A 398 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 324 " 0.049 5.00e-02 4.00e+02 7.36e-02 8.66e+00 pdb=" N PRO A 325 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 288 " 0.048 5.00e-02 4.00e+02 7.19e-02 8.28e+00 pdb=" N PRO C 289 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 289 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 289 " 0.040 5.00e-02 4.00e+02 ... (remaining 3678 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 285 2.63 - 3.20: 17121 3.20 - 3.77: 31297 3.77 - 4.33: 40079 4.33 - 4.90: 65921 Nonbonded interactions: 154703 Sorted by model distance: nonbonded pdb=" O1B GTP B 501 " pdb="MG MG B 502 " model vdw 2.063 2.170 nonbonded pdb=" O2G GTP B 501 " pdb="MG MG B 502 " model vdw 2.075 2.170 nonbonded pdb=" O ASN C 59 " pdb=" ND2 ASN C 59 " model vdw 2.078 2.520 nonbonded pdb=" O2G GTP A 501 " pdb="MG MG A 502 " model vdw 2.085 2.170 nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 2.125 2.170 ... (remaining 154698 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 1 through 437 or resid 501)) selection = (chain 'B' and (resid 1 through 437 or resid 501)) selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.010 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 52.090 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 0.238 20880 Z= 0.567 Angle : 1.015 25.867 28440 Z= 0.576 Chirality : 0.063 0.883 3135 Planarity : 0.008 0.074 3681 Dihedral : 17.323 179.189 8031 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.74 % Allowed : 9.46 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.14), residues: 2544 helix: -1.96 (0.12), residues: 1083 sheet: -0.93 (0.26), residues: 354 loop : -2.69 (0.15), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 346 HIS 0.007 0.002 HIS C 406 PHE 0.024 0.003 PHE C 418 TYR 0.024 0.002 TYR B 224 ARG 0.008 0.001 ARG F 390 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 571 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 ASP cc_start: 0.8411 (t70) cc_final: 0.7978 (t70) REVERT: D 70 LEU cc_start: 0.8759 (mt) cc_final: 0.8446 (mt) REVERT: D 85 GLN cc_start: 0.7832 (mp10) cc_final: 0.5567 (tp40) REVERT: D 327 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8447 (p0) REVERT: D 413 MET cc_start: 0.7682 (ttm) cc_final: 0.7266 (ttm) REVERT: A 128 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7420 (tm-30) REVERT: A 154 MET cc_start: 0.8545 (tpp) cc_final: 0.8266 (tpt) REVERT: A 161 TYR cc_start: 0.8658 (m-80) cc_final: 0.8453 (m-80) REVERT: A 280 LYS cc_start: 0.6198 (mttp) cc_final: 0.5891 (tptt) REVERT: A 284 GLU cc_start: 0.7563 (tp30) cc_final: 0.7102 (pm20) REVERT: A 372 GLN cc_start: 0.8570 (tp40) cc_final: 0.8312 (tp-100) REVERT: A 390 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7884 (mmp80) REVERT: B 35 GLN cc_start: 0.7512 (tt0) cc_final: 0.7307 (tt0) REVERT: B 102 ASN cc_start: 0.8479 (t0) cc_final: 0.8192 (t0) REVERT: B 192 HIS cc_start: 0.7844 (t70) cc_final: 0.7563 (t70) REVERT: B 221 ARG cc_start: 0.7256 (mtt180) cc_final: 0.5733 (ptt180) REVERT: B 290 GLU cc_start: 0.8266 (pt0) cc_final: 0.7930 (pt0) REVERT: B 302 MET cc_start: 0.8202 (mmm) cc_final: 0.7599 (mpp) REVERT: B 358 GLN cc_start: 0.9256 (tp40) cc_final: 0.8872 (tp-100) REVERT: B 398 MET cc_start: 0.7347 (mtt) cc_final: 0.7082 (mtm) REVERT: B 414 GLU cc_start: 0.6176 (mp0) cc_final: 0.5450 (mp0) REVERT: E 71 GLU cc_start: 0.7473 (mp0) cc_final: 0.7000 (pm20) REVERT: E 96 GLN cc_start: 0.7651 (mm110) cc_final: 0.7213 (mm-40) REVERT: E 102 ASN cc_start: 0.9066 (m-40) cc_final: 0.8699 (m110) REVERT: E 123 ARG cc_start: 0.6764 (ttm110) cc_final: 0.6561 (ttm170) REVERT: E 282 GLN cc_start: 0.7433 (mt0) cc_final: 0.7122 (pt0) REVERT: E 299 LYS cc_start: 0.8663 (ptmm) cc_final: 0.8263 (tttm) REVERT: E 308 ARG cc_start: 0.7655 (ptt-90) cc_final: 0.6820 (ptt-90) REVERT: E 320 ARG cc_start: 0.7753 (mtp180) cc_final: 0.6352 (mtm110) REVERT: E 325 MET cc_start: 0.8320 (mmm) cc_final: 0.8112 (mmm) REVERT: C 14 ASN cc_start: 0.8448 (t0) cc_final: 0.7853 (t0) REVERT: C 54 ASN cc_start: 0.8676 (t0) cc_final: 0.8376 (t0) REVERT: C 103 TRP cc_start: 0.7213 (t60) cc_final: 0.6492 (t60) REVERT: C 110 GLU cc_start: 0.8360 (mp0) cc_final: 0.8129 (mp0) REVERT: C 113 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8187 (mp0) REVERT: C 183 GLU cc_start: 0.8400 (tt0) cc_final: 0.8187 (tt0) REVERT: C 259 MET cc_start: 0.8377 (mmm) cc_final: 0.7997 (mmp) REVERT: C 299 LYS cc_start: 0.7722 (tttt) cc_final: 0.7276 (mmmt) REVERT: C 373 MET cc_start: 0.7901 (ptp) cc_final: 0.7579 (ptp) REVERT: C 407 TRP cc_start: 0.6911 (m100) cc_final: 0.6128 (m-90) REVERT: C 411 GLU cc_start: 0.6452 (mm-30) cc_final: 0.5627 (tm-30) REVERT: C 420 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7371 (mt-10) REVERT: F 37 HIS cc_start: 0.8134 (m-70) cc_final: 0.7672 (m90) REVERT: F 61 TYR cc_start: 0.7370 (m-80) cc_final: 0.5931 (m-80) REVERT: F 92 PHE cc_start: 0.8548 (m-80) cc_final: 0.8257 (m-10) REVERT: F 193 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7492 (tp-100) REVERT: F 228 ASN cc_start: 0.9227 (m-40) cc_final: 0.8782 (m-40) REVERT: F 235 MET cc_start: 0.7810 (mtp) cc_final: 0.7518 (mtp) REVERT: F 295 MET cc_start: 0.8421 (ttm) cc_final: 0.8197 (ttp) REVERT: F 425 MET cc_start: 0.7014 (tpp) cc_final: 0.6536 (mmm) REVERT: F 428 LEU cc_start: 0.8759 (tp) cc_final: 0.8537 (tp) outliers start: 16 outliers final: 10 residues processed: 583 average time/residue: 0.3232 time to fit residues: 282.6843 Evaluate side-chains 441 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 430 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 6.9990 chunk 191 optimal weight: 0.0980 chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 GLN D 15 GLN D 88 HIS D 107 HIS ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN D 358 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS A 216 ASN A 226 ASN A 406 HIS B 88 HIS B 107 HIS B 216 ASN B 300 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS E 281 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN C 96 GLN C 192 HIS ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS F 6 HIS F 8 GLN ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 ASN F 309 HIS F 331 GLN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20880 Z= 0.211 Angle : 0.617 11.628 28440 Z= 0.313 Chirality : 0.044 0.167 3135 Planarity : 0.006 0.065 3681 Dihedral : 11.657 172.826 3339 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.23 % Allowed : 4.62 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 2544 helix: -0.47 (0.15), residues: 1110 sheet: -0.68 (0.24), residues: 408 loop : -2.45 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 346 HIS 0.010 0.001 HIS C 309 PHE 0.026 0.002 PHE C 399 TYR 0.015 0.001 TYR E 36 ARG 0.007 0.000 ARG C 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 537 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 49 PHE cc_start: 0.7640 (p90) cc_final: 0.7171 (p90) REVERT: D 69 ASP cc_start: 0.8427 (t70) cc_final: 0.7985 (t70) REVERT: D 70 LEU cc_start: 0.8697 (mt) cc_final: 0.8435 (mt) REVERT: D 85 GLN cc_start: 0.8080 (mp10) cc_final: 0.5492 (tp-100) REVERT: D 88 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.7329 (t-90) REVERT: D 90 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6584 (tt0) REVERT: D 210 TYR cc_start: 0.8872 (m-10) cc_final: 0.8280 (m-80) REVERT: D 226 ASN cc_start: 0.8607 (m-40) cc_final: 0.8279 (m110) REVERT: D 358 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8248 (tp40) REVERT: D 413 MET cc_start: 0.7663 (ttm) cc_final: 0.7238 (ttm) REVERT: A 128 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7430 (tm-30) REVERT: A 154 MET cc_start: 0.8499 (tpp) cc_final: 0.8261 (tpt) REVERT: A 161 TYR cc_start: 0.8522 (m-80) cc_final: 0.8300 (m-80) REVERT: A 284 GLU cc_start: 0.7345 (tp30) cc_final: 0.6864 (pm20) REVERT: A 413 MET cc_start: 0.7928 (mmm) cc_final: 0.7226 (mmt) REVERT: B 22 GLU cc_start: 0.7954 (tt0) cc_final: 0.7661 (tm-30) REVERT: B 35 GLN cc_start: 0.7506 (tt0) cc_final: 0.7297 (tt0) REVERT: B 52 PHE cc_start: 0.7849 (m-10) cc_final: 0.7391 (m-80) REVERT: B 64 ARG cc_start: 0.8787 (mtt90) cc_final: 0.7485 (mtt-85) REVERT: B 90 GLU cc_start: 0.8544 (tp30) cc_final: 0.7894 (tp30) REVERT: B 102 ASN cc_start: 0.8532 (t0) cc_final: 0.8167 (t0) REVERT: B 192 HIS cc_start: 0.8010 (t70) cc_final: 0.7792 (t70) REVERT: B 221 ARG cc_start: 0.7223 (mtt180) cc_final: 0.5730 (ptt180) REVERT: B 301 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7996 (mm-40) REVERT: B 302 MET cc_start: 0.8221 (mmm) cc_final: 0.7831 (tpp) REVERT: B 358 GLN cc_start: 0.9170 (tp40) cc_final: 0.8844 (tp-100) REVERT: E 96 GLN cc_start: 0.7514 (mm110) cc_final: 0.7026 (mm-40) REVERT: E 202 TYR cc_start: 0.8926 (m-80) cc_final: 0.8625 (m-80) REVERT: E 308 ARG cc_start: 0.7197 (ptt-90) cc_final: 0.6838 (ptt-90) REVERT: E 320 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7401 (mtm180) REVERT: E 325 MET cc_start: 0.8258 (mmm) cc_final: 0.8030 (mmm) REVERT: C 14 ASN cc_start: 0.8442 (t0) cc_final: 0.7694 (t0) REVERT: C 54 ASN cc_start: 0.8690 (t0) cc_final: 0.8294 (t0) REVERT: C 75 MET cc_start: 0.8575 (mmt) cc_final: 0.7969 (mmt) REVERT: C 103 TRP cc_start: 0.6597 (t60) cc_final: 0.6174 (t60) REVERT: C 113 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8299 (mp0) REVERT: C 166 MET cc_start: 0.9191 (tpp) cc_final: 0.8911 (mmm) REVERT: C 278 ARG cc_start: 0.7859 (tpm170) cc_final: 0.7536 (tpm170) REVERT: C 373 MET cc_start: 0.7878 (ptp) cc_final: 0.7536 (ptp) REVERT: C 407 TRP cc_start: 0.6936 (m100) cc_final: 0.6086 (m-90) REVERT: C 411 GLU cc_start: 0.6381 (mm-30) cc_final: 0.5918 (tm-30) REVERT: F 6 HIS cc_start: 0.8034 (t70) cc_final: 0.7667 (t70) REVERT: F 37 HIS cc_start: 0.8031 (m-70) cc_final: 0.7432 (m90) REVERT: F 61 TYR cc_start: 0.6957 (m-80) cc_final: 0.6285 (m-80) REVERT: F 228 ASN cc_start: 0.9317 (m-40) cc_final: 0.8925 (m-40) REVERT: F 320 ARG cc_start: 0.8181 (mtp180) cc_final: 0.6903 (mtp-110) REVERT: F 323 MET cc_start: 0.7893 (mtt) cc_final: 0.7521 (mtt) REVERT: F 413 MET cc_start: 0.7072 (mtp) cc_final: 0.6768 (mtm) outliers start: 5 outliers final: 2 residues processed: 541 average time/residue: 0.3093 time to fit residues: 256.8739 Evaluate side-chains 403 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 400 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 10.0000 chunk 71 optimal weight: 0.0670 chunk 190 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 229 optimal weight: 8.9990 chunk 247 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN E 192 HIS ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN C 294 GLN ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 HIS ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20880 Z= 0.332 Angle : 0.684 10.465 28440 Z= 0.351 Chirality : 0.047 0.221 3135 Planarity : 0.006 0.065 3681 Dihedral : 11.384 176.072 3339 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2544 helix: -0.15 (0.15), residues: 1092 sheet: -0.94 (0.26), residues: 375 loop : -2.14 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 346 HIS 0.006 0.002 HIS E 28 PHE 0.027 0.002 PHE F 169 TYR 0.019 0.002 TYR B 432 ARG 0.005 0.001 ARG C 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 492 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 49 PHE cc_start: 0.7745 (p90) cc_final: 0.7530 (p90) REVERT: D 69 ASP cc_start: 0.8480 (t70) cc_final: 0.8157 (t70) REVERT: D 85 GLN cc_start: 0.7927 (mp10) cc_final: 0.5508 (tp-100) REVERT: D 210 TYR cc_start: 0.8856 (m-10) cc_final: 0.8321 (m-80) REVERT: D 220 GLU cc_start: 0.7229 (tp30) cc_final: 0.6980 (mm-30) REVERT: D 226 ASN cc_start: 0.8979 (m-40) cc_final: 0.8700 (m-40) REVERT: D 301 GLN cc_start: 0.8269 (mm110) cc_final: 0.8053 (mm110) REVERT: D 413 MET cc_start: 0.7881 (ttm) cc_final: 0.6892 (ttm) REVERT: A 123 ARG cc_start: 0.8234 (mmm-85) cc_final: 0.7646 (mmm-85) REVERT: A 128 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7415 (tm-30) REVERT: A 161 TYR cc_start: 0.8476 (m-80) cc_final: 0.7676 (m-80) REVERT: A 203 MET cc_start: 0.8674 (mmm) cc_final: 0.7779 (mmm) REVERT: A 284 GLU cc_start: 0.7591 (tp30) cc_final: 0.6986 (pm20) REVERT: A 302 MET cc_start: 0.8761 (mmm) cc_final: 0.8090 (mtt) REVERT: B 22 GLU cc_start: 0.7996 (tt0) cc_final: 0.7740 (tm-30) REVERT: B 35 GLN cc_start: 0.7721 (tt0) cc_final: 0.7409 (tt0) REVERT: B 102 ASN cc_start: 0.8771 (t0) cc_final: 0.8365 (t0) REVERT: B 221 ARG cc_start: 0.7223 (mtt90) cc_final: 0.5922 (ptt180) REVERT: B 301 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7856 (mm-40) REVERT: B 302 MET cc_start: 0.8320 (mmm) cc_final: 0.7808 (tpp) REVERT: B 358 GLN cc_start: 0.9166 (tp40) cc_final: 0.8817 (tp-100) REVERT: B 377 MET cc_start: 0.8011 (ttp) cc_final: 0.7526 (ttp) REVERT: E 96 GLN cc_start: 0.7558 (mm110) cc_final: 0.7249 (mm-40) REVERT: E 308 ARG cc_start: 0.7548 (ptt-90) cc_final: 0.6852 (ptt-90) REVERT: E 320 ARG cc_start: 0.7860 (mtp180) cc_final: 0.7388 (mtm180) REVERT: E 323 MET cc_start: 0.8432 (mtm) cc_final: 0.8128 (mtm) REVERT: C 14 ASN cc_start: 0.8280 (t0) cc_final: 0.7643 (t0) REVERT: C 31 ASP cc_start: 0.9083 (t0) cc_final: 0.8484 (t0) REVERT: C 54 ASN cc_start: 0.8789 (t0) cc_final: 0.8366 (t0) REVERT: C 75 MET cc_start: 0.8580 (mmt) cc_final: 0.7956 (mmt) REVERT: C 103 TRP cc_start: 0.6721 (t60) cc_final: 0.6250 (t60) REVERT: C 113 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8203 (mp0) REVERT: C 299 LYS cc_start: 0.8985 (pptt) cc_final: 0.8407 (tttt) REVERT: C 333 LEU cc_start: 0.8748 (tp) cc_final: 0.8482 (tp) REVERT: C 373 MET cc_start: 0.8062 (ptp) cc_final: 0.7646 (ptm) REVERT: C 407 TRP cc_start: 0.7041 (m100) cc_final: 0.6083 (m-90) REVERT: C 411 GLU cc_start: 0.6548 (mm-30) cc_final: 0.5968 (tm-30) REVERT: F 37 HIS cc_start: 0.8075 (m-70) cc_final: 0.7475 (m90) REVERT: F 154 ILE cc_start: 0.9302 (tt) cc_final: 0.9057 (tt) REVERT: F 228 ASN cc_start: 0.9387 (m-40) cc_final: 0.9000 (m-40) REVERT: F 323 MET cc_start: 0.8067 (mtt) cc_final: 0.7668 (mtt) REVERT: F 384 ILE cc_start: 0.8421 (pt) cc_final: 0.8116 (pt) REVERT: F 413 MET cc_start: 0.7536 (mtp) cc_final: 0.7199 (mtp) outliers start: 1 outliers final: 0 residues processed: 493 average time/residue: 0.3216 time to fit residues: 240.7144 Evaluate side-chains 384 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 243 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 218 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 HIS D 176 GLN D 192 HIS D 358 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS C 14 ASN C 59 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20880 Z= 0.312 Angle : 0.663 9.833 28440 Z= 0.340 Chirality : 0.047 0.162 3135 Planarity : 0.005 0.064 3681 Dihedral : 11.027 174.611 3339 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.14 % Allowed : 4.57 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2544 helix: -0.06 (0.15), residues: 1083 sheet: -0.91 (0.26), residues: 366 loop : -2.13 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 346 HIS 0.007 0.002 HIS F 309 PHE 0.022 0.002 PHE F 404 TYR 0.021 0.002 TYR D 432 ARG 0.007 0.001 ARG B 422 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 486 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 49 PHE cc_start: 0.7698 (p90) cc_final: 0.7441 (p90) REVERT: D 85 GLN cc_start: 0.7815 (mp10) cc_final: 0.5540 (tp40) REVERT: D 88 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.7308 (t-90) REVERT: D 210 TYR cc_start: 0.8850 (m-10) cc_final: 0.8321 (m-80) REVERT: D 220 GLU cc_start: 0.7252 (tp30) cc_final: 0.6831 (mm-30) REVERT: D 301 GLN cc_start: 0.8264 (mm110) cc_final: 0.7977 (mm110) REVERT: D 302 MET cc_start: 0.9034 (mmm) cc_final: 0.8532 (mmt) REVERT: D 413 MET cc_start: 0.7699 (ttm) cc_final: 0.6921 (ttm) REVERT: A 112 LYS cc_start: 0.8710 (ttmm) cc_final: 0.7489 (tptt) REVERT: A 123 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7639 (mmm-85) REVERT: A 128 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7307 (tm-30) REVERT: A 161 TYR cc_start: 0.8459 (m-80) cc_final: 0.7735 (m-80) REVERT: A 203 MET cc_start: 0.8541 (mmm) cc_final: 0.7625 (mmm) REVERT: A 211 ASP cc_start: 0.8149 (m-30) cc_final: 0.7869 (t0) REVERT: A 302 MET cc_start: 0.8685 (mmm) cc_final: 0.8115 (mtt) REVERT: B 22 GLU cc_start: 0.7991 (tt0) cc_final: 0.7644 (tm-30) REVERT: B 90 GLU cc_start: 0.8535 (tp30) cc_final: 0.8030 (tp30) REVERT: B 102 ASN cc_start: 0.8726 (t0) cc_final: 0.8331 (t0) REVERT: B 221 ARG cc_start: 0.7254 (mtt90) cc_final: 0.5736 (ptt180) REVERT: B 301 GLN cc_start: 0.8355 (mm-40) cc_final: 0.7869 (mm-40) REVERT: B 302 MET cc_start: 0.8390 (mmm) cc_final: 0.7858 (tpp) REVERT: B 358 GLN cc_start: 0.9070 (tp40) cc_final: 0.8762 (tp-100) REVERT: E 96 GLN cc_start: 0.7574 (mm110) cc_final: 0.6927 (mm-40) REVERT: E 132 LEU cc_start: 0.8755 (pp) cc_final: 0.8247 (pp) REVERT: E 308 ARG cc_start: 0.7832 (ptt-90) cc_final: 0.7020 (ptt-90) REVERT: E 320 ARG cc_start: 0.7780 (mtp180) cc_final: 0.6635 (mtm110) REVERT: E 323 MET cc_start: 0.8308 (mtm) cc_final: 0.8060 (mtm) REVERT: E 413 MET cc_start: 0.8315 (mtm) cc_final: 0.8042 (mtm) REVERT: C 54 ASN cc_start: 0.8764 (t0) cc_final: 0.8362 (t0) REVERT: C 103 TRP cc_start: 0.7046 (t60) cc_final: 0.6546 (t60) REVERT: C 110 GLU cc_start: 0.8089 (mp0) cc_final: 0.7718 (mp0) REVERT: C 113 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8196 (mp0) REVERT: C 259 MET cc_start: 0.8363 (mmm) cc_final: 0.7713 (mmm) REVERT: C 299 LYS cc_start: 0.8880 (pptt) cc_final: 0.8475 (pttt) REVERT: C 333 LEU cc_start: 0.8811 (tp) cc_final: 0.8602 (tp) REVERT: C 373 MET cc_start: 0.8007 (ptp) cc_final: 0.7594 (ptt) REVERT: C 407 TRP cc_start: 0.7072 (m100) cc_final: 0.6081 (m-90) REVERT: C 411 GLU cc_start: 0.6426 (mm-30) cc_final: 0.5854 (tm-30) REVERT: F 37 HIS cc_start: 0.7878 (m-70) cc_final: 0.7339 (m90) REVERT: F 76 ASP cc_start: 0.8627 (m-30) cc_final: 0.8398 (m-30) REVERT: F 154 ILE cc_start: 0.9293 (tt) cc_final: 0.9058 (tt) REVERT: F 228 ASN cc_start: 0.9158 (m-40) cc_final: 0.8779 (m-40) REVERT: F 320 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7374 (mtm110) REVERT: F 323 MET cc_start: 0.7888 (mtt) cc_final: 0.7462 (mtt) REVERT: F 413 MET cc_start: 0.7359 (mtp) cc_final: 0.6985 (mtp) outliers start: 3 outliers final: 1 residues processed: 489 average time/residue: 0.3091 time to fit residues: 231.8337 Evaluate side-chains 382 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 380 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.8980 chunk 138 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 0.0770 chunk 207 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 218 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS D 176 GLN D 293 ASN D 300 ASN D 358 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS E 167 ASN E 192 HIS ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS C 59 ASN C 101 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 ASN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20880 Z= 0.187 Angle : 0.579 10.443 28440 Z= 0.291 Chirality : 0.044 0.217 3135 Planarity : 0.005 0.075 3681 Dihedral : 10.466 176.512 3339 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.14 % Allowed : 2.26 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.16), residues: 2544 helix: 0.26 (0.15), residues: 1098 sheet: -0.73 (0.26), residues: 369 loop : -1.98 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 21 HIS 0.006 0.001 HIS E 6 PHE 0.025 0.001 PHE C 377 TYR 0.021 0.001 TYR E 36 ARG 0.005 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 516 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 49 PHE cc_start: 0.7639 (p90) cc_final: 0.7323 (p90) REVERT: D 210 TYR cc_start: 0.8809 (m-10) cc_final: 0.8204 (m-80) REVERT: D 220 GLU cc_start: 0.6960 (tp30) cc_final: 0.6613 (mm-30) REVERT: D 291 ILE cc_start: 0.7384 (pt) cc_final: 0.7108 (pt) REVERT: D 301 GLN cc_start: 0.8208 (mm110) cc_final: 0.7720 (mm110) REVERT: D 413 MET cc_start: 0.7239 (ttm) cc_final: 0.6655 (ttm) REVERT: A 123 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7619 (mmm-85) REVERT: A 128 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7329 (tm-30) REVERT: A 161 TYR cc_start: 0.8588 (m-80) cc_final: 0.7841 (m-10) REVERT: A 203 MET cc_start: 0.8501 (mmm) cc_final: 0.8059 (mmm) REVERT: A 233 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8345 (mm-40) REVERT: B 22 GLU cc_start: 0.7993 (tt0) cc_final: 0.7621 (tm-30) REVERT: B 52 PHE cc_start: 0.7932 (m-10) cc_final: 0.7390 (m-10) REVERT: B 64 ARG cc_start: 0.8831 (mtt90) cc_final: 0.7615 (mtt-85) REVERT: B 90 GLU cc_start: 0.8583 (tp30) cc_final: 0.8098 (tp30) REVERT: B 102 ASN cc_start: 0.8757 (t0) cc_final: 0.8304 (t0) REVERT: B 192 HIS cc_start: 0.7881 (t-90) cc_final: 0.7565 (t70) REVERT: B 221 ARG cc_start: 0.7275 (mtt90) cc_final: 0.5705 (ptt180) REVERT: B 301 GLN cc_start: 0.8341 (mm-40) cc_final: 0.7919 (mm-40) REVERT: B 302 MET cc_start: 0.8373 (mmm) cc_final: 0.7905 (tpp) REVERT: B 358 GLN cc_start: 0.9047 (tp40) cc_final: 0.8754 (tp-100) REVERT: E 132 LEU cc_start: 0.8734 (pp) cc_final: 0.8353 (pp) REVERT: E 308 ARG cc_start: 0.7239 (ptt-90) cc_final: 0.6920 (ptt-90) REVERT: E 320 ARG cc_start: 0.7947 (mtp180) cc_final: 0.7241 (mmm-85) REVERT: E 373 MET cc_start: 0.8067 (mmt) cc_final: 0.6744 (mtm) REVERT: E 413 MET cc_start: 0.8347 (mtm) cc_final: 0.8045 (mtm) REVERT: C 54 ASN cc_start: 0.8648 (t0) cc_final: 0.8274 (t0) REVERT: C 103 TRP cc_start: 0.7218 (t60) cc_final: 0.6664 (t60) REVERT: C 110 GLU cc_start: 0.7986 (mp0) cc_final: 0.7546 (mp0) REVERT: C 216 THR cc_start: 0.8185 (t) cc_final: 0.7788 (p) REVERT: C 259 MET cc_start: 0.8213 (mmm) cc_final: 0.7583 (mmm) REVERT: C 278 ARG cc_start: 0.8090 (tpt170) cc_final: 0.7659 (tpm170) REVERT: C 333 LEU cc_start: 0.8767 (tp) cc_final: 0.8542 (tp) REVERT: C 373 MET cc_start: 0.7958 (ptp) cc_final: 0.7605 (ptt) REVERT: C 407 TRP cc_start: 0.6920 (m100) cc_final: 0.5985 (m-90) REVERT: C 411 GLU cc_start: 0.6391 (mm-30) cc_final: 0.5874 (tm-30) REVERT: F 37 HIS cc_start: 0.7895 (m-70) cc_final: 0.7315 (m90) REVERT: F 76 ASP cc_start: 0.8563 (m-30) cc_final: 0.8352 (m-30) REVERT: F 86 ILE cc_start: 0.9067 (pt) cc_final: 0.8621 (tp) REVERT: F 154 ILE cc_start: 0.9260 (tt) cc_final: 0.9030 (tt) REVERT: F 156 LYS cc_start: 0.8585 (mmtm) cc_final: 0.8130 (mmtp) REVERT: F 228 ASN cc_start: 0.9231 (m-40) cc_final: 0.8858 (m-40) REVERT: F 235 MET cc_start: 0.7520 (mtp) cc_final: 0.7311 (mpp) REVERT: F 320 ARG cc_start: 0.7842 (mtp180) cc_final: 0.7191 (mtm110) REVERT: F 323 MET cc_start: 0.7728 (mtt) cc_final: 0.7518 (mpp) REVERT: F 413 MET cc_start: 0.7209 (mtp) cc_final: 0.6830 (mtp) outliers start: 3 outliers final: 2 residues processed: 519 average time/residue: 0.3133 time to fit residues: 248.7618 Evaluate side-chains 384 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 382 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 HIS D 139 HIS D 176 GLN D 300 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN B 139 HIS B 266 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20880 Z= 0.285 Angle : 0.634 11.937 28440 Z= 0.322 Chirality : 0.046 0.231 3135 Planarity : 0.005 0.072 3681 Dihedral : 10.400 176.876 3339 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.09 % Allowed : 2.63 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.16), residues: 2544 helix: 0.24 (0.15), residues: 1098 sheet: -0.78 (0.25), residues: 420 loop : -2.04 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 346 HIS 0.006 0.001 HIS E 37 PHE 0.023 0.002 PHE F 377 TYR 0.016 0.002 TYR E 36 ARG 0.007 0.000 ARG C 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 470 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 88 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7360 (t-90) REVERT: D 210 TYR cc_start: 0.8848 (m-10) cc_final: 0.8318 (m-80) REVERT: D 220 GLU cc_start: 0.7203 (tp30) cc_final: 0.6873 (mm-30) REVERT: D 300 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8346 (t0) REVERT: D 413 MET cc_start: 0.7812 (ttm) cc_final: 0.6822 (ttm) REVERT: A 112 LYS cc_start: 0.8662 (ttmm) cc_final: 0.7294 (tptt) REVERT: A 123 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.7642 (mmm-85) REVERT: A 128 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7323 (tm-30) REVERT: A 161 TYR cc_start: 0.8580 (m-80) cc_final: 0.7831 (m-10) REVERT: A 203 MET cc_start: 0.8540 (mmm) cc_final: 0.7919 (mmm) REVERT: A 302 MET cc_start: 0.8820 (mmm) cc_final: 0.8078 (mtt) REVERT: A 413 MET cc_start: 0.8226 (mmm) cc_final: 0.7835 (mmt) REVERT: B 22 GLU cc_start: 0.8083 (tt0) cc_final: 0.7641 (tm-30) REVERT: B 36 MET cc_start: 0.7087 (ptm) cc_final: 0.6808 (ptm) REVERT: B 90 GLU cc_start: 0.8630 (tp30) cc_final: 0.8168 (tp30) REVERT: B 102 ASN cc_start: 0.8818 (t0) cc_final: 0.8351 (t0) REVERT: B 203 MET cc_start: 0.8001 (tpp) cc_final: 0.7624 (tpp) REVERT: B 221 ARG cc_start: 0.7258 (mtt90) cc_final: 0.5764 (ptt180) REVERT: B 301 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7855 (mm-40) REVERT: B 302 MET cc_start: 0.8461 (mmm) cc_final: 0.7990 (tpp) REVERT: B 358 GLN cc_start: 0.9021 (tp40) cc_final: 0.8758 (tp-100) REVERT: E 295 MET cc_start: 0.7721 (mtp) cc_final: 0.7442 (mtp) REVERT: E 308 ARG cc_start: 0.7487 (ptt-90) cc_final: 0.6976 (ptt-90) REVERT: E 320 ARG cc_start: 0.7909 (mtp180) cc_final: 0.6807 (mtm110) REVERT: E 373 MET cc_start: 0.8115 (mmt) cc_final: 0.6825 (mtm) REVERT: E 413 MET cc_start: 0.8357 (mtm) cc_final: 0.7999 (mtm) REVERT: C 6 HIS cc_start: 0.8581 (t-90) cc_final: 0.8375 (t70) REVERT: C 54 ASN cc_start: 0.8712 (t0) cc_final: 0.8275 (t0) REVERT: C 103 TRP cc_start: 0.7252 (t60) cc_final: 0.6707 (t60) REVERT: C 110 GLU cc_start: 0.8119 (mp0) cc_final: 0.7608 (mp0) REVERT: C 216 THR cc_start: 0.8253 (t) cc_final: 0.7838 (p) REVERT: C 259 MET cc_start: 0.8262 (mmm) cc_final: 0.7606 (mmm) REVERT: C 333 LEU cc_start: 0.8861 (tp) cc_final: 0.8651 (tp) REVERT: C 373 MET cc_start: 0.8054 (ptp) cc_final: 0.7599 (ptt) REVERT: C 407 TRP cc_start: 0.6895 (m100) cc_final: 0.6066 (m-90) REVERT: C 411 GLU cc_start: 0.6390 (mm-30) cc_final: 0.5790 (tm-30) REVERT: F 37 HIS cc_start: 0.7930 (m-70) cc_final: 0.7364 (m90) REVERT: F 76 ASP cc_start: 0.8600 (m-30) cc_final: 0.8347 (m-30) REVERT: F 86 ILE cc_start: 0.9030 (pt) cc_final: 0.8572 (tp) REVERT: F 154 ILE cc_start: 0.9276 (tt) cc_final: 0.9064 (tt) REVERT: F 228 ASN cc_start: 0.9263 (m-40) cc_final: 0.8849 (m-40) REVERT: F 320 ARG cc_start: 0.7939 (mtp180) cc_final: 0.7295 (mtm110) REVERT: F 323 MET cc_start: 0.7917 (mtt) cc_final: 0.7672 (mpp) outliers start: 2 outliers final: 0 residues processed: 472 average time/residue: 0.3020 time to fit residues: 221.2745 Evaluate side-chains 371 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 369 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 138 optimal weight: 0.0980 chunk 178 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 HIS D 176 GLN D 293 ASN D 406 HIS ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 139 HIS B 216 ASN E 167 ASN E 192 HIS ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20880 Z= 0.232 Angle : 0.603 13.002 28440 Z= 0.306 Chirality : 0.045 0.201 3135 Planarity : 0.005 0.068 3681 Dihedral : 10.125 175.290 3339 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.09 % Allowed : 1.71 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.16), residues: 2544 helix: 0.32 (0.15), residues: 1095 sheet: -0.83 (0.25), residues: 420 loop : -1.94 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 346 HIS 0.004 0.001 HIS E 139 PHE 0.019 0.002 PHE C 377 TYR 0.023 0.001 TYR A 432 ARG 0.004 0.000 ARG B 422 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 473 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 210 TYR cc_start: 0.8822 (m-10) cc_final: 0.8293 (m-80) REVERT: D 220 GLU cc_start: 0.7458 (tp30) cc_final: 0.6740 (mm-30) REVERT: D 291 ILE cc_start: 0.7374 (pt) cc_final: 0.7160 (pt) REVERT: D 413 MET cc_start: 0.7380 (ttm) cc_final: 0.6613 (ttm) REVERT: D 414 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6358 (mt-10) REVERT: A 112 LYS cc_start: 0.8602 (ttmm) cc_final: 0.7257 (tptt) REVERT: A 123 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7619 (mmm-85) REVERT: A 128 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7312 (tm-30) REVERT: A 161 TYR cc_start: 0.8602 (m-80) cc_final: 0.7898 (m-10) REVERT: A 203 MET cc_start: 0.8499 (mmm) cc_final: 0.7899 (mmm) REVERT: A 302 MET cc_start: 0.8803 (mmm) cc_final: 0.8326 (mtt) REVERT: A 413 MET cc_start: 0.8208 (mmm) cc_final: 0.7536 (mmt) REVERT: A 425 MET cc_start: 0.8753 (mmm) cc_final: 0.8291 (mmm) REVERT: B 22 GLU cc_start: 0.8077 (tt0) cc_final: 0.7606 (tm-30) REVERT: B 36 MET cc_start: 0.7068 (ptm) cc_final: 0.6821 (ptm) REVERT: B 60 LYS cc_start: 0.7497 (mmtm) cc_final: 0.6681 (tppt) REVERT: B 90 GLU cc_start: 0.8608 (tp30) cc_final: 0.8238 (tp30) REVERT: B 102 ASN cc_start: 0.8720 (t0) cc_final: 0.8283 (t0) REVERT: B 192 HIS cc_start: 0.7729 (t-90) cc_final: 0.7375 (t70) REVERT: B 203 MET cc_start: 0.7927 (tpp) cc_final: 0.7593 (tpp) REVERT: B 221 ARG cc_start: 0.7253 (mtt90) cc_final: 0.5809 (ptt180) REVERT: B 301 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7793 (mm-40) REVERT: B 302 MET cc_start: 0.8445 (mmm) cc_final: 0.7702 (mtt) REVERT: B 358 GLN cc_start: 0.8986 (tp40) cc_final: 0.8730 (tp-100) REVERT: B 417 GLU cc_start: 0.7588 (pm20) cc_final: 0.7381 (pm20) REVERT: E 215 ARG cc_start: 0.8479 (mmm160) cc_final: 0.8028 (tmm160) REVERT: E 308 ARG cc_start: 0.7539 (ptt-90) cc_final: 0.6871 (ptt-90) REVERT: E 320 ARG cc_start: 0.7882 (mtp180) cc_final: 0.6672 (mtm110) REVERT: E 413 MET cc_start: 0.8274 (mtm) cc_final: 0.7977 (mtm) REVERT: C 6 HIS cc_start: 0.8538 (t-90) cc_final: 0.8285 (t70) REVERT: C 54 ASN cc_start: 0.8641 (t0) cc_final: 0.8227 (t0) REVERT: C 76 ASP cc_start: 0.8382 (m-30) cc_final: 0.7894 (m-30) REVERT: C 103 TRP cc_start: 0.7187 (t60) cc_final: 0.6692 (t60) REVERT: C 110 GLU cc_start: 0.8165 (mp0) cc_final: 0.7561 (mp0) REVERT: C 216 THR cc_start: 0.7983 (t) cc_final: 0.7558 (p) REVERT: C 235 MET cc_start: 0.8528 (mtp) cc_final: 0.8171 (mtp) REVERT: C 333 LEU cc_start: 0.8851 (tp) cc_final: 0.8628 (tp) REVERT: C 373 MET cc_start: 0.7977 (ptp) cc_final: 0.7588 (ptp) REVERT: C 407 TRP cc_start: 0.6762 (m100) cc_final: 0.5760 (m-10) REVERT: C 411 GLU cc_start: 0.6399 (mm-30) cc_final: 0.5809 (tm-30) REVERT: F 37 HIS cc_start: 0.7922 (m-70) cc_final: 0.7303 (m90) REVERT: F 86 ILE cc_start: 0.9085 (pt) cc_final: 0.8602 (tp) REVERT: F 228 ASN cc_start: 0.9232 (m-40) cc_final: 0.8823 (m-40) REVERT: F 301 MET cc_start: 0.8819 (mmt) cc_final: 0.8565 (mpp) REVERT: F 320 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7189 (mtm110) REVERT: F 384 ILE cc_start: 0.8651 (pt) cc_final: 0.8438 (pt) REVERT: F 399 PHE cc_start: 0.8235 (t80) cc_final: 0.7846 (t80) outliers start: 2 outliers final: 1 residues processed: 475 average time/residue: 0.3001 time to fit residues: 219.5375 Evaluate side-chains 374 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 373 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 HIS D 139 HIS D 176 GLN D 293 ASN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN B 216 ASN B 266 HIS B 300 ASN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN E 192 HIS ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20880 Z= 0.241 Angle : 0.620 13.005 28440 Z= 0.314 Chirality : 0.046 0.235 3135 Planarity : 0.005 0.068 3681 Dihedral : 10.061 174.125 3339 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.09 % Allowed : 1.80 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.16), residues: 2544 helix: 0.31 (0.15), residues: 1095 sheet: -0.79 (0.25), residues: 417 loop : -1.94 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 407 HIS 0.004 0.001 HIS B 406 PHE 0.025 0.002 PHE F 83 TYR 0.026 0.001 TYR E 36 ARG 0.003 0.000 ARG B 422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 459 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 88 HIS cc_start: 0.8293 (OUTLIER) cc_final: 0.7454 (t-90) REVERT: D 210 TYR cc_start: 0.8816 (m-10) cc_final: 0.8297 (m-80) REVERT: D 220 GLU cc_start: 0.7504 (tp30) cc_final: 0.6726 (mm-30) REVERT: D 413 MET cc_start: 0.7576 (ttm) cc_final: 0.6715 (ttm) REVERT: D 414 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6617 (mt-10) REVERT: A 112 LYS cc_start: 0.8610 (ttmm) cc_final: 0.7256 (tptt) REVERT: A 123 ARG cc_start: 0.8077 (mmm-85) cc_final: 0.7646 (mmm-85) REVERT: A 128 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7311 (tm-30) REVERT: A 161 TYR cc_start: 0.8587 (m-80) cc_final: 0.7869 (m-10) REVERT: A 203 MET cc_start: 0.8542 (mmm) cc_final: 0.7958 (mmm) REVERT: A 302 MET cc_start: 0.8779 (mmm) cc_final: 0.8319 (mtt) REVERT: A 413 MET cc_start: 0.8218 (mmm) cc_final: 0.7570 (mmt) REVERT: B 22 GLU cc_start: 0.7972 (tt0) cc_final: 0.7582 (tm-30) REVERT: B 90 GLU cc_start: 0.8577 (tp30) cc_final: 0.8124 (tp30) REVERT: B 102 ASN cc_start: 0.8743 (t0) cc_final: 0.8315 (t0) REVERT: B 203 MET cc_start: 0.7975 (tpp) cc_final: 0.7595 (tpp) REVERT: B 221 ARG cc_start: 0.7176 (mtt90) cc_final: 0.5755 (ptt180) REVERT: B 301 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7717 (mm-40) REVERT: B 302 MET cc_start: 0.8474 (mmm) cc_final: 0.7696 (mtt) REVERT: B 358 GLN cc_start: 0.8972 (tp40) cc_final: 0.8765 (tp-100) REVERT: B 407 TRP cc_start: 0.6579 (m100) cc_final: 0.6216 (m-10) REVERT: E 215 ARG cc_start: 0.8501 (mmm160) cc_final: 0.8100 (tmm160) REVERT: E 308 ARG cc_start: 0.7618 (ptt-90) cc_final: 0.6839 (ptt-90) REVERT: E 320 ARG cc_start: 0.7820 (mtp180) cc_final: 0.7225 (mmm-85) REVERT: E 373 MET cc_start: 0.7814 (mmt) cc_final: 0.6520 (mtm) REVERT: E 413 MET cc_start: 0.8195 (mtm) cc_final: 0.7933 (mtm) REVERT: E 416 MET cc_start: 0.7013 (tpt) cc_final: 0.6689 (tpt) REVERT: C 54 ASN cc_start: 0.8675 (t0) cc_final: 0.8237 (t0) REVERT: C 76 ASP cc_start: 0.8346 (m-30) cc_final: 0.7833 (m-30) REVERT: C 103 TRP cc_start: 0.7150 (t60) cc_final: 0.6746 (t60) REVERT: C 110 GLU cc_start: 0.7972 (mp0) cc_final: 0.7455 (mp0) REVERT: C 216 THR cc_start: 0.7965 (t) cc_final: 0.7559 (p) REVERT: C 333 LEU cc_start: 0.8856 (tp) cc_final: 0.8626 (tp) REVERT: C 373 MET cc_start: 0.8038 (ptp) cc_final: 0.7699 (ptm) REVERT: C 407 TRP cc_start: 0.6770 (m100) cc_final: 0.5743 (m-10) REVERT: C 411 GLU cc_start: 0.6426 (mm-30) cc_final: 0.5814 (tm-30) REVERT: F 6 HIS cc_start: 0.8241 (t-90) cc_final: 0.8028 (t-90) REVERT: F 37 HIS cc_start: 0.7794 (m-70) cc_final: 0.7205 (m90) REVERT: F 76 ASP cc_start: 0.8581 (m-30) cc_final: 0.8273 (m-30) REVERT: F 86 ILE cc_start: 0.9101 (pt) cc_final: 0.8623 (tp) REVERT: F 154 ILE cc_start: 0.9231 (tt) cc_final: 0.8963 (tt) REVERT: F 228 ASN cc_start: 0.9209 (m-40) cc_final: 0.8858 (m-40) REVERT: F 301 MET cc_start: 0.8851 (mmt) cc_final: 0.8534 (mpp) REVERT: F 320 ARG cc_start: 0.7822 (mtp180) cc_final: 0.6703 (mtp-110) REVERT: F 413 MET cc_start: 0.7276 (mtp) cc_final: 0.6936 (mtm) outliers start: 2 outliers final: 0 residues processed: 461 average time/residue: 0.3055 time to fit residues: 218.2709 Evaluate side-chains 368 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 367 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 226 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 HIS D 176 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 ASN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20880 Z= 0.226 Angle : 0.610 11.865 28440 Z= 0.308 Chirality : 0.045 0.228 3135 Planarity : 0.005 0.067 3681 Dihedral : 9.951 173.131 3339 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.05 % Allowed : 0.42 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.16), residues: 2544 helix: 0.38 (0.16), residues: 1086 sheet: -0.69 (0.25), residues: 423 loop : -1.88 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 346 HIS 0.005 0.001 HIS B 406 PHE 0.024 0.002 PHE C 377 TYR 0.026 0.001 TYR F 432 ARG 0.006 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 464 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 210 TYR cc_start: 0.8811 (m-10) cc_final: 0.8276 (m-80) REVERT: D 220 GLU cc_start: 0.7469 (tp30) cc_final: 0.6721 (mm-30) REVERT: D 256 GLN cc_start: 0.8044 (mp10) cc_final: 0.7836 (mp10) REVERT: D 291 ILE cc_start: 0.7500 (pt) cc_final: 0.7200 (pt) REVERT: D 293 ASN cc_start: 0.8777 (p0) cc_final: 0.8534 (p0) REVERT: D 413 MET cc_start: 0.7582 (ttm) cc_final: 0.6676 (ttm) REVERT: D 414 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6667 (mt-10) REVERT: A 112 LYS cc_start: 0.8599 (ttmm) cc_final: 0.7323 (tptt) REVERT: A 123 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.7654 (mmm-85) REVERT: A 128 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7309 (tm-30) REVERT: A 161 TYR cc_start: 0.8595 (m-80) cc_final: 0.7921 (m-10) REVERT: A 203 MET cc_start: 0.8516 (mmm) cc_final: 0.7990 (mmm) REVERT: A 302 MET cc_start: 0.8735 (mmm) cc_final: 0.8213 (mtt) REVERT: A 413 MET cc_start: 0.8238 (mmm) cc_final: 0.7651 (mmt) REVERT: B 22 GLU cc_start: 0.7958 (tt0) cc_final: 0.7566 (tm-30) REVERT: B 90 GLU cc_start: 0.8572 (tp30) cc_final: 0.8103 (tp30) REVERT: B 102 ASN cc_start: 0.8726 (t0) cc_final: 0.8269 (t0) REVERT: B 203 MET cc_start: 0.7936 (tpp) cc_final: 0.7642 (tpp) REVERT: B 221 ARG cc_start: 0.7149 (mtt90) cc_final: 0.5764 (ptt180) REVERT: B 301 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7799 (mm-40) REVERT: B 302 MET cc_start: 0.8428 (mmm) cc_final: 0.7916 (tpp) REVERT: B 358 GLN cc_start: 0.8986 (tp40) cc_final: 0.8758 (tp-100) REVERT: B 417 GLU cc_start: 0.7660 (pm20) cc_final: 0.7455 (pm20) REVERT: E 61 TYR cc_start: 0.5431 (m-80) cc_final: 0.5201 (m-80) REVERT: E 215 ARG cc_start: 0.8483 (mmm160) cc_final: 0.8118 (tmm160) REVERT: E 295 MET cc_start: 0.7676 (ttt) cc_final: 0.7237 (ttm) REVERT: E 308 ARG cc_start: 0.7592 (ptt-90) cc_final: 0.6816 (ptt-90) REVERT: E 320 ARG cc_start: 0.7853 (mtp180) cc_final: 0.7231 (mmm-85) REVERT: E 373 MET cc_start: 0.7761 (mmt) cc_final: 0.6567 (mtm) REVERT: E 413 MET cc_start: 0.8196 (mtm) cc_final: 0.7864 (mtm) REVERT: E 416 MET cc_start: 0.7051 (tpt) cc_final: 0.6726 (tpt) REVERT: C 54 ASN cc_start: 0.8670 (t0) cc_final: 0.8225 (t0) REVERT: C 75 MET cc_start: 0.8446 (mmt) cc_final: 0.8020 (mmm) REVERT: C 76 ASP cc_start: 0.8250 (m-30) cc_final: 0.7792 (m-30) REVERT: C 103 TRP cc_start: 0.7117 (t60) cc_final: 0.6803 (t60) REVERT: C 110 GLU cc_start: 0.7636 (mp0) cc_final: 0.7185 (mp0) REVERT: C 216 THR cc_start: 0.7874 (t) cc_final: 0.7442 (p) REVERT: C 295 MET cc_start: 0.8508 (tpp) cc_final: 0.8044 (tpp) REVERT: C 333 LEU cc_start: 0.8827 (tp) cc_final: 0.8577 (tp) REVERT: C 373 MET cc_start: 0.8099 (ptp) cc_final: 0.7727 (ptp) REVERT: C 407 TRP cc_start: 0.6727 (m100) cc_final: 0.5739 (m-10) REVERT: C 411 GLU cc_start: 0.6432 (mm-30) cc_final: 0.5807 (tm-30) REVERT: F 6 HIS cc_start: 0.8176 (t-90) cc_final: 0.7964 (t-90) REVERT: F 37 HIS cc_start: 0.7742 (m-70) cc_final: 0.7106 (m90) REVERT: F 76 ASP cc_start: 0.8629 (m-30) cc_final: 0.8281 (m-30) REVERT: F 154 ILE cc_start: 0.9220 (tt) cc_final: 0.8944 (tt) REVERT: F 228 ASN cc_start: 0.9195 (m-40) cc_final: 0.8822 (m-40) REVERT: F 259 MET cc_start: 0.8031 (mpp) cc_final: 0.7589 (mtt) REVERT: F 301 MET cc_start: 0.8796 (mmt) cc_final: 0.8506 (mpp) REVERT: F 369 ARG cc_start: 0.7935 (ttp-170) cc_final: 0.7484 (ttm-80) outliers start: 1 outliers final: 1 residues processed: 465 average time/residue: 0.3018 time to fit residues: 216.9891 Evaluate side-chains 372 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 371 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 HIS D 139 HIS D 176 GLN ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN B 266 HIS E 192 HIS ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN F 258 ASN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20880 Z= 0.187 Angle : 0.582 11.841 28440 Z= 0.292 Chirality : 0.044 0.212 3135 Planarity : 0.005 0.065 3681 Dihedral : 9.744 174.101 3339 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.05 % Allowed : 0.51 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.16), residues: 2544 helix: 0.51 (0.16), residues: 1095 sheet: -0.55 (0.26), residues: 411 loop : -1.84 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 407 HIS 0.005 0.001 HIS E 309 PHE 0.024 0.001 PHE C 377 TYR 0.023 0.001 TYR E 36 ARG 0.007 0.000 ARG B 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 463 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 88 HIS cc_start: 0.8259 (OUTLIER) cc_final: 0.7440 (t-90) REVERT: D 220 GLU cc_start: 0.7395 (tp30) cc_final: 0.6703 (mm-30) REVERT: D 256 GLN cc_start: 0.7890 (mp10) cc_final: 0.7671 (mp10) REVERT: D 293 ASN cc_start: 0.8670 (p0) cc_final: 0.8384 (p0) REVERT: D 413 MET cc_start: 0.7652 (ttm) cc_final: 0.6771 (ttm) REVERT: D 414 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6673 (mt-10) REVERT: A 123 ARG cc_start: 0.8084 (mmm-85) cc_final: 0.7664 (mmm-85) REVERT: A 128 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7299 (tm-30) REVERT: A 161 TYR cc_start: 0.8624 (m-80) cc_final: 0.7925 (m-10) REVERT: A 203 MET cc_start: 0.8503 (mmm) cc_final: 0.7957 (mmm) REVERT: A 302 MET cc_start: 0.8746 (mmm) cc_final: 0.8176 (mtt) REVERT: A 425 MET cc_start: 0.8809 (mmm) cc_final: 0.8218 (mmm) REVERT: B 22 GLU cc_start: 0.7936 (tt0) cc_final: 0.7563 (tm-30) REVERT: B 90 GLU cc_start: 0.8561 (tp30) cc_final: 0.8111 (tp30) REVERT: B 102 ASN cc_start: 0.8667 (t0) cc_final: 0.8229 (t0) REVERT: B 192 HIS cc_start: 0.7630 (t-90) cc_final: 0.7314 (t70) REVERT: B 221 ARG cc_start: 0.7097 (mtt90) cc_final: 0.5739 (ptt180) REVERT: B 301 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7744 (mm-40) REVERT: B 302 MET cc_start: 0.8419 (mmm) cc_final: 0.7914 (tpp) REVERT: B 312 TYR cc_start: 0.7793 (m-80) cc_final: 0.7545 (m-80) REVERT: B 358 GLN cc_start: 0.8987 (tp40) cc_final: 0.8721 (tp-100) REVERT: B 373 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7573 (mtm-85) REVERT: E 61 TYR cc_start: 0.5384 (m-80) cc_final: 0.5162 (m-80) REVERT: E 74 THR cc_start: 0.8653 (p) cc_final: 0.8281 (p) REVERT: E 215 ARG cc_start: 0.8415 (mmm160) cc_final: 0.8075 (tmm160) REVERT: E 295 MET cc_start: 0.7679 (ttt) cc_final: 0.7266 (ttm) REVERT: E 320 ARG cc_start: 0.7854 (mtp180) cc_final: 0.7138 (mmm-85) REVERT: E 373 MET cc_start: 0.7634 (mmt) cc_final: 0.6452 (mtm) REVERT: E 413 MET cc_start: 0.8111 (mtm) cc_final: 0.7906 (mtm) REVERT: E 416 MET cc_start: 0.6908 (tpt) cc_final: 0.6564 (tpt) REVERT: C 54 ASN cc_start: 0.8613 (t0) cc_final: 0.8212 (t0) REVERT: C 75 MET cc_start: 0.8428 (mmt) cc_final: 0.8008 (mmm) REVERT: C 76 ASP cc_start: 0.8244 (m-30) cc_final: 0.7768 (m-30) REVERT: C 103 TRP cc_start: 0.7084 (t60) cc_final: 0.6761 (t60) REVERT: C 110 GLU cc_start: 0.7918 (mp0) cc_final: 0.7083 (mp0) REVERT: C 216 THR cc_start: 0.7990 (t) cc_final: 0.7505 (p) REVERT: C 295 MET cc_start: 0.8417 (tpp) cc_final: 0.7970 (tpp) REVERT: C 333 LEU cc_start: 0.8807 (tp) cc_final: 0.8568 (tp) REVERT: C 373 MET cc_start: 0.8049 (ptp) cc_final: 0.7757 (ptm) REVERT: C 392 SER cc_start: 0.8979 (t) cc_final: 0.8732 (t) REVERT: C 407 TRP cc_start: 0.6699 (m100) cc_final: 0.6419 (m100) REVERT: C 411 GLU cc_start: 0.6448 (mm-30) cc_final: 0.5965 (tm-30) REVERT: F 37 HIS cc_start: 0.7854 (m-70) cc_final: 0.7224 (m90) REVERT: F 228 ASN cc_start: 0.9124 (m-40) cc_final: 0.8801 (m-40) REVERT: F 259 MET cc_start: 0.7986 (mpp) cc_final: 0.7567 (mtt) REVERT: F 301 MET cc_start: 0.8821 (mmt) cc_final: 0.8537 (mpp) REVERT: F 399 PHE cc_start: 0.8254 (t80) cc_final: 0.7804 (t80) outliers start: 1 outliers final: 0 residues processed: 464 average time/residue: 0.3088 time to fit residues: 221.2318 Evaluate side-chains 380 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 379 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 chunk 25 optimal weight: 0.1980 chunk 36 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 HIS D 176 GLN ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 HIS ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.129027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.113757 restraints weight = 38975.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.116335 restraints weight = 23510.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118180 restraints weight = 16089.810| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20880 Z= 0.269 Angle : 0.640 11.793 28440 Z= 0.324 Chirality : 0.046 0.226 3135 Planarity : 0.005 0.069 3681 Dihedral : 9.920 172.262 3339 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.05 % Allowed : 0.60 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2544 helix: 0.28 (0.15), residues: 1119 sheet: -0.69 (0.27), residues: 360 loop : -1.92 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 407 HIS 0.006 0.001 HIS A 139 PHE 0.037 0.002 PHE F 169 TYR 0.025 0.002 TYR F 432 ARG 0.007 0.001 ARG A 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4359.44 seconds wall clock time: 80 minutes 52.73 seconds (4852.73 seconds total)