Starting phenix.real_space_refine on Thu Feb 22 05:42:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa0_15289/02_2024/8aa0_15289_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa0_15289/02_2024/8aa0_15289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa0_15289/02_2024/8aa0_15289.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa0_15289/02_2024/8aa0_15289.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa0_15289/02_2024/8aa0_15289_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa0_15289/02_2024/8aa0_15289_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians Mg 4 5.21 5 S 128 5.16 5 C 20892 2.51 5 N 5520 2.21 5 O 6514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33058 Number of models: 1 Model: "" Number of chains: 16 Chain: "E" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3979 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 18, 'TRANS': 478} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "T" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 733 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3979 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 18, 'TRANS': 478} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 733 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4432 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 7260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7260 Classifications: {'peptide': 924} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 891} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4432 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 7260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7260 Classifications: {'peptide': 924} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 891} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FRU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'FRU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FRU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'FRU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.32, per 1000 atoms: 0.49 Number of scatterers: 33058 At special positions: 0 Unit cell: (197.025, 161.88, 138.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 128 16.00 Mg 4 11.99 O 6514 8.00 N 5520 7.00 C 20892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 389 " distance=2.04 Simple disulfide: pdb=" SG CYS J 387 " - pdb=" SG CYS J 389 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA2-1 " FRU C 3 " - " FRU C 7 " ~> Even though FRU is a beta isomer, an alpha linkage is required... " FRU K 3 " - " FRU K 7 " ALPHA2-6 " FRU C 1 " - " FRU C 2 " " FRU C 2 " - " FRU C 3 " " FRU C 3 " - " FRU C 4 " " FRU C 4 " - " FRU C 5 " " FRU C 5 " - " FRU C 6 " " FRU D 1 " - " FRU D 2 " " FRU D 2 " - " FRU D 3 " " FRU D 3 " - " FRU D 4 " " FRU K 1 " - " FRU K 2 " " FRU K 2 " - " FRU K 3 " " FRU K 3 " - " FRU K 4 " " FRU K 4 " - " FRU K 5 " " FRU K 5 " - " FRU K 6 " " FRU L 1 " - " FRU L 2 " " FRU L 2 " - " FRU L 3 " " FRU L 3 " - " FRU L 4 " Time building additional restraints: 12.81 Conformation dependent library (CDL) restraints added in 5.8 seconds 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 42 sheets defined 17.9% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.57 Creating SS restraints... Processing helix chain 'E' and resid 158 through 161 Processing helix chain 'E' and resid 255 through 260 Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 341 through 346 Processing helix chain 'M' and resid 158 through 161 Processing helix chain 'M' and resid 255 through 260 Processing helix chain 'M' and resid 304 through 306 No H-bonds generated for 'chain 'M' and resid 304 through 306' Processing helix chain 'M' and resid 341 through 346 Processing helix chain 'B' and resid 3 through 5 No H-bonds generated for 'chain 'B' and resid 3 through 5' Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 22 through 38 removed outlier: 3.683A pdb=" N VAL B 25 " --> pdb=" O PRO B 22 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASP B 26 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE B 35 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 38 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 85 through 110 removed outlier: 3.979A pdb=" N GLN B 110 " --> pdb=" O GLN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 140 removed outlier: 4.404A pdb=" N ASN B 120 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.720A pdb=" N ASN B 158 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 184 removed outlier: 3.916A pdb=" N ASP B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 227 through 236 Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 286 through 291 removed outlier: 4.579A pdb=" N LEU B 290 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 339 through 344 Processing helix chain 'B' and resid 407 through 421 Processing helix chain 'B' and resid 426 through 442 Processing helix chain 'B' and resid 448 through 454 removed outlier: 3.642A pdb=" N LYS B 451 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR B 454 " --> pdb=" O LYS B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 Processing helix chain 'B' and resid 491 through 498 Processing helix chain 'B' and resid 501 through 512 Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'A' and resid 106 through 112 removed outlier: 4.354A pdb=" N LYS A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 185 through 191 removed outlier: 4.788A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 248 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 377 through 383 Processing helix chain 'A' and resid 410 through 419 removed outlier: 4.935A pdb=" N ASP A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 605 through 607 No H-bonds generated for 'chain 'A' and resid 605 through 607' Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 962 through 967 Processing helix chain 'A' and resid 995 through 997 No H-bonds generated for 'chain 'A' and resid 995 through 997' Processing helix chain 'J' and resid 3 through 5 No H-bonds generated for 'chain 'J' and resid 3 through 5' Processing helix chain 'J' and resid 16 through 20 removed outlier: 3.911A pdb=" N ALA J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 16 through 20' Processing helix chain 'J' and resid 22 through 38 removed outlier: 3.683A pdb=" N VAL J 25 " --> pdb=" O PRO J 22 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASP J 26 " --> pdb=" O GLU J 23 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE J 35 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR J 38 " --> pdb=" O ILE J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 54 No H-bonds generated for 'chain 'J' and resid 52 through 54' Processing helix chain 'J' and resid 69 through 76 Processing helix chain 'J' and resid 85 through 110 removed outlier: 3.979A pdb=" N GLN J 110 " --> pdb=" O GLN J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 140 removed outlier: 4.404A pdb=" N ASN J 120 " --> pdb=" O PRO J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 159 removed outlier: 3.720A pdb=" N ASN J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 184 removed outlier: 3.915A pdb=" N ASP J 177 " --> pdb=" O LYS J 173 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE J 178 " --> pdb=" O ILE J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 212 Processing helix chain 'J' and resid 227 through 236 Processing helix chain 'J' and resid 239 through 245 Processing helix chain 'J' and resid 254 through 256 No H-bonds generated for 'chain 'J' and resid 254 through 256' Processing helix chain 'J' and resid 259 through 261 No H-bonds generated for 'chain 'J' and resid 259 through 261' Processing helix chain 'J' and resid 286 through 291 removed outlier: 4.578A pdb=" N LEU J 290 " --> pdb=" O GLY J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 296 No H-bonds generated for 'chain 'J' and resid 294 through 296' Processing helix chain 'J' and resid 306 through 312 Processing helix chain 'J' and resid 339 through 344 Processing helix chain 'J' and resid 407 through 421 Processing helix chain 'J' and resid 426 through 442 Processing helix chain 'J' and resid 448 through 454 removed outlier: 3.642A pdb=" N LYS J 451 " --> pdb=" O PHE J 448 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR J 454 " --> pdb=" O LYS J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 470 through 484 Processing helix chain 'J' and resid 491 through 498 Processing helix chain 'J' and resid 501 through 512 Processing helix chain 'J' and resid 517 through 519 No H-bonds generated for 'chain 'J' and resid 517 through 519' Processing helix chain 'J' and resid 536 through 541 Processing helix chain 'I' and resid 106 through 112 removed outlier: 4.354A pdb=" N LYS I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 No H-bonds generated for 'chain 'I' and resid 117 through 120' Processing helix chain 'I' and resid 168 through 170 No H-bonds generated for 'chain 'I' and resid 168 through 170' Processing helix chain 'I' and resid 185 through 191 removed outlier: 4.788A pdb=" N ILE I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR I 191 " --> pdb=" O SER I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 248 Processing helix chain 'I' and resid 252 through 255 Processing helix chain 'I' and resid 295 through 299 Processing helix chain 'I' and resid 377 through 383 Processing helix chain 'I' and resid 410 through 419 removed outlier: 4.936A pdb=" N ASP I 419 " --> pdb=" O GLU I 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 601 through 603 No H-bonds generated for 'chain 'I' and resid 601 through 603' Processing helix chain 'I' and resid 605 through 607 No H-bonds generated for 'chain 'I' and resid 605 through 607' Processing helix chain 'I' and resid 780 through 785 Processing helix chain 'I' and resid 816 through 821 Processing helix chain 'I' and resid 890 through 894 Processing helix chain 'I' and resid 909 through 913 Processing helix chain 'I' and resid 962 through 967 Processing helix chain 'I' and resid 995 through 997 No H-bonds generated for 'chain 'I' and resid 995 through 997' Processing sheet with id= A, first strand: chain 'E' and resid 55 through 60 removed outlier: 3.644A pdb=" N ILE E 91 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY E 75 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU E 89 " --> pdb=" O GLY E 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.019A pdb=" N THR E 122 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 107 through 111 Processing sheet with id= D, first strand: chain 'E' and resid 172 through 175 removed outlier: 6.035A pdb=" N GLU E 197 " --> pdb=" O THR E 211 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR E 211 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 225 through 229 Processing sheet with id= F, first strand: chain 'E' and resid 286 through 289 removed outlier: 5.317A pdb=" N ARG E 294 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 349 through 351 removed outlier: 4.107A pdb=" N VAL E 500 " --> pdb=" O GLN E 351 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 363 through 365 Processing sheet with id= I, first strand: chain 'E' and resid 436 through 442 removed outlier: 6.941A pdb=" N PHE E 428 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP E 440 " --> pdb=" O ALA E 426 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA E 426 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE E 401 " --> pdb=" O VAL E 419 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE E 378 " --> pdb=" O ALA E 357 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA E 357 " --> pdb=" O ILE E 378 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 27 through 30 removed outlier: 8.339A pdb=" N ILE T 36 " --> pdb=" O SER T 88 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR T 90 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL T 38 " --> pdb=" O THR T 90 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR T 92 " --> pdb=" O VAL T 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'T' and resid 19 through 22 removed outlier: 3.748A pdb=" N SER T 19 " --> pdb=" O ASN T 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU T 53 " --> pdb=" O ARG T 21 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'M' and resid 55 through 60 removed outlier: 3.643A pdb=" N ILE M 91 " --> pdb=" O ILE M 73 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY M 75 " --> pdb=" O GLU M 89 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU M 89 " --> pdb=" O GLY M 75 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 102 through 104 removed outlier: 4.018A pdb=" N THR M 122 " --> pdb=" O GLY M 104 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'M' and resid 107 through 111 Processing sheet with id= O, first strand: chain 'M' and resid 172 through 175 removed outlier: 6.035A pdb=" N GLU M 197 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N THR M 211 " --> pdb=" O GLU M 197 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'M' and resid 225 through 229 Processing sheet with id= Q, first strand: chain 'M' and resid 286 through 289 removed outlier: 5.317A pdb=" N ARG M 294 " --> pdb=" O LEU M 327 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'M' and resid 349 through 351 removed outlier: 4.107A pdb=" N VAL M 500 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'M' and resid 363 through 365 Processing sheet with id= T, first strand: chain 'M' and resid 436 through 442 removed outlier: 6.942A pdb=" N PHE M 428 " --> pdb=" O LEU M 438 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP M 440 " --> pdb=" O ALA M 426 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA M 426 " --> pdb=" O ASP M 440 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE M 401 " --> pdb=" O VAL M 419 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE M 378 " --> pdb=" O ALA M 357 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA M 357 " --> pdb=" O ILE M 378 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 27 through 30 removed outlier: 8.340A pdb=" N ILE G 36 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR G 90 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL G 38 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR G 92 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 19 through 22 removed outlier: 3.748A pdb=" N SER G 19 " --> pdb=" O ASN G 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU G 53 " --> pdb=" O ARG G 21 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 390 through 392 Processing sheet with id= X, first strand: chain 'A' and resid 101 through 104 removed outlier: 4.099A pdb=" N ILE A 179 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 203 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE A 179 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 201 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL A 181 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A 199 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 156 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE A 202 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 158 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR A 204 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 128 through 132 Processing sheet with id= Z, first strand: chain 'A' and resid 303 through 315 removed outlier: 6.640A pdb=" N PHE A 877 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE A 954 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 875 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU A 956 " --> pdb=" O ASP A 873 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP A 873 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA A 740 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY A 626 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N THR A 591 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG A 457 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG A 421 " --> pdb=" O ARG A 457 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 719 through 722 Processing sheet with id= AB, first strand: chain 'A' and resid 885 through 887 Processing sheet with id= AC, first strand: chain 'A' and resid 948 through 951 removed outlier: 4.312A pdb=" N LEU A 983 " --> pdb=" O LEU A 951 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 259 through 265 removed outlier: 6.798A pdb=" N GLY A 264 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU A 273 " --> pdb=" O GLY A 264 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 638 through 640 removed outlier: 3.879A pdb=" N GLN A 677 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA A 640 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ARG A 675 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 804 through 806 removed outlier: 3.514A pdb=" N GLN A 804 " --> pdb=" O TYR A 853 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY A 806 " --> pdb=" O TRP A 851 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TRP A 851 " --> pdb=" O GLY A 806 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 390 through 392 Processing sheet with id= AH, first strand: chain 'I' and resid 101 through 104 removed outlier: 4.101A pdb=" N ILE I 179 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR I 203 " --> pdb=" O GLU I 177 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE I 179 " --> pdb=" O ILE I 201 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE I 201 " --> pdb=" O ILE I 179 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL I 181 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL I 199 " --> pdb=" O VAL I 181 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU I 156 " --> pdb=" O ILE I 200 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE I 202 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE I 158 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR I 204 " --> pdb=" O ILE I 158 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 128 through 132 Processing sheet with id= AJ, first strand: chain 'I' and resid 303 through 315 removed outlier: 6.638A pdb=" N PHE I 877 " --> pdb=" O ARG I 952 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE I 954 " --> pdb=" O THR I 875 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR I 875 " --> pdb=" O ILE I 954 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU I 956 " --> pdb=" O ASP I 873 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP I 873 " --> pdb=" O LEU I 956 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA I 740 " --> pdb=" O LEU I 776 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY I 626 " --> pdb=" O THR I 591 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N THR I 591 " --> pdb=" O GLY I 626 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG I 457 " --> pdb=" O ARG I 421 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG I 421 " --> pdb=" O ARG I 457 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'I' and resid 719 through 722 Processing sheet with id= AL, first strand: chain 'I' and resid 885 through 887 Processing sheet with id= AM, first strand: chain 'I' and resid 948 through 951 removed outlier: 4.312A pdb=" N LEU I 983 " --> pdb=" O LEU I 951 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'I' and resid 259 through 265 removed outlier: 6.797A pdb=" N GLY I 264 " --> pdb=" O LEU I 273 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU I 273 " --> pdb=" O GLY I 264 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 638 through 640 removed outlier: 3.878A pdb=" N GLN I 677 " --> pdb=" O ILE I 638 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA I 640 " --> pdb=" O ARG I 675 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ARG I 675 " --> pdb=" O ALA I 640 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 804 through 806 removed outlier: 3.513A pdb=" N GLN I 804 " --> pdb=" O TYR I 853 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY I 806 " --> pdb=" O TRP I 851 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TRP I 851 " --> pdb=" O GLY I 806 " (cutoff:3.500A) 1266 hydrogen bonds defined for protein. 3282 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: 13.21 Time building geometry restraints manager: 13.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10830 1.34 - 1.46: 6949 1.46 - 1.57: 15777 1.57 - 1.69: 66 1.69 - 1.81: 228 Bond restraints: 33850 Sorted by residual: bond pdb=" C2 FRU D 4 " pdb=" O5 FRU D 4 " ideal model delta sigma weight residual 1.412 1.641 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C2 FRU L 4 " pdb=" O5 FRU L 4 " ideal model delta sigma weight residual 1.412 1.641 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C2 FRU C 7 " pdb=" O5 FRU C 7 " ideal model delta sigma weight residual 1.412 1.638 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C2 FRU K 7 " pdb=" O5 FRU K 7 " ideal model delta sigma weight residual 1.412 1.637 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C2 FRU D 1 " pdb=" O5 FRU D 1 " ideal model delta sigma weight residual 1.412 1.637 -0.225 2.00e-02 2.50e+03 1.26e+02 ... (remaining 33845 not shown) Histogram of bond angle deviations from ideal: 94.99 - 102.82: 179 102.82 - 110.65: 10558 110.65 - 118.47: 15004 118.47 - 126.30: 19630 126.30 - 134.12: 543 Bond angle restraints: 45914 Sorted by residual: angle pdb=" C CYS J 298 " pdb=" N CYS J 299 " pdb=" CA CYS J 299 " ideal model delta sigma weight residual 121.54 130.18 -8.64 1.91e+00 2.74e-01 2.05e+01 angle pdb=" C CYS B 298 " pdb=" N CYS B 299 " pdb=" CA CYS B 299 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" CA LYS A 318 " pdb=" CB LYS A 318 " pdb=" CG LYS A 318 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA LYS I 318 " pdb=" CB LYS I 318 " pdb=" CG LYS I 318 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" N CYS J 299 " pdb=" CA CYS J 299 " pdb=" C CYS J 299 " ideal model delta sigma weight residual 110.80 117.11 -6.31 2.13e+00 2.20e-01 8.77e+00 ... (remaining 45909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 18756 17.96 - 35.91: 1042 35.91 - 53.87: 201 53.87 - 71.82: 106 71.82 - 89.78: 19 Dihedral angle restraints: 20124 sinusoidal: 8202 harmonic: 11922 Sorted by residual: dihedral pdb=" CB CYS B 387 " pdb=" SG CYS B 387 " pdb=" SG CYS B 389 " pdb=" CB CYS B 389 " ideal model delta sinusoidal sigma weight residual -86.00 -149.13 63.13 1 1.00e+01 1.00e-02 5.26e+01 dihedral pdb=" CB CYS J 387 " pdb=" SG CYS J 387 " pdb=" SG CYS J 389 " pdb=" CB CYS J 389 " ideal model delta sinusoidal sigma weight residual -86.00 -149.12 63.12 1 1.00e+01 1.00e-02 5.26e+01 dihedral pdb=" CA CYS J 389 " pdb=" C CYS J 389 " pdb=" N LEU J 390 " pdb=" CA LEU J 390 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 20121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2754 0.031 - 0.063: 1336 0.063 - 0.094: 458 0.094 - 0.125: 255 0.125 - 0.157: 45 Chirality restraints: 4848 Sorted by residual: chirality pdb=" C2 FRU C 7 " pdb=" O1 FRU C 3 " pdb=" C1 FRU C 7 " pdb=" O5 FRU C 7 " both_signs ideal model delta sigma weight residual False 2.60 2.76 -0.16 2.00e-02 2.50e+03 6.14e+01 chirality pdb=" C2 FRU K 7 " pdb=" O1 FRU K 3 " pdb=" C1 FRU K 7 " pdb=" O5 FRU K 7 " both_signs ideal model delta sigma weight residual False 2.60 2.75 -0.15 2.00e-02 2.50e+03 5.98e+01 chirality pdb=" C2 FRU D 4 " pdb=" O6 FRU D 3 " pdb=" C1 FRU D 4 " pdb=" O5 FRU D 4 " both_signs ideal model delta sigma weight residual False 2.60 2.68 -0.08 2.00e-02 2.50e+03 1.48e+01 ... (remaining 4845 not shown) Planarity restraints: 5976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL T 40 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO T 41 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO T 41 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO T 41 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 40 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO G 41 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO G 41 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 41 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 127 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO E 128 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 128 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 128 " -0.018 5.00e-02 4.00e+02 ... (remaining 5973 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 354 2.56 - 3.15: 27107 3.15 - 3.73: 51719 3.73 - 4.32: 76579 4.32 - 4.90: 129197 Nonbonded interactions: 284956 Sorted by model distance: nonbonded pdb=" OD1 ASN J 401 " pdb="MG MG J 601 " model vdw 1.978 2.170 nonbonded pdb=" OD1 ASN B 401 " pdb="MG MG B 601 " model vdw 1.978 2.170 nonbonded pdb=" OD2 ASP I 848 " pdb="MG MG I1101 " model vdw 2.057 2.170 nonbonded pdb=" OD2 ASP A 848 " pdb="MG MG A1101 " model vdw 2.058 2.170 nonbonded pdb=" ND2 ASN I 664 " pdb="MG MG J 601 " model vdw 2.059 2.250 ... (remaining 284951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.480 Check model and map are aligned: 0.450 Set scattering table: 0.260 Process input model: 87.380 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.229 33850 Z= 0.650 Angle : 0.616 8.644 45914 Z= 0.314 Chirality : 0.045 0.157 4848 Planarity : 0.003 0.039 5976 Dihedral : 12.833 89.780 12582 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.44 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.13), residues: 4118 helix: 1.59 (0.20), residues: 732 sheet: 0.42 (0.15), residues: 1256 loop : -0.37 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 851 HIS 0.008 0.001 HIS M 71 PHE 0.018 0.001 PHE A1016 TYR 0.017 0.001 TYR I 225 ARG 0.004 0.001 ARG I 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 3.932 Fit side-chains revert: symmetry clash REVERT: E 276 MET cc_start: 0.8066 (mmm) cc_final: 0.7750 (mmt) REVERT: G 30 ASP cc_start: 0.8229 (t0) cc_final: 0.7996 (t0) REVERT: B 465 LEU cc_start: 0.9199 (mt) cc_final: 0.8994 (mm) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.4553 time to fit residues: 149.8551 Evaluate side-chains 152 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 3.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 0.9980 chunk 310 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 209 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 321 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 372 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 GLN B 43 ASN B 336 ASN A 153 ASN A 243 GLN A 247 ASN A 468 GLN A 632 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 ASN I 247 ASN I 361 GLN I 372 GLN I 468 GLN ** I 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 744 GLN I 816 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33850 Z= 0.169 Angle : 0.489 7.715 45914 Z= 0.258 Chirality : 0.043 0.152 4848 Planarity : 0.003 0.035 5976 Dihedral : 7.627 52.002 5014 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.30 % Favored : 96.50 % Rotamer: Outliers : 0.40 % Allowed : 3.80 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.13), residues: 4118 helix: 1.37 (0.20), residues: 704 sheet: 0.57 (0.15), residues: 1244 loop : -0.35 (0.14), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 91 HIS 0.003 0.001 HIS M 71 PHE 0.011 0.001 PHE B 301 TYR 0.014 0.001 TYR A 225 ARG 0.005 0.000 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 4.098 Fit side-chains revert: symmetry clash REVERT: E 215 MET cc_start: 0.7865 (mtt) cc_final: 0.7587 (mtt) REVERT: E 276 MET cc_start: 0.8071 (mmm) cc_final: 0.7696 (mmt) REVERT: M 356 MET cc_start: 0.9202 (mmm) cc_final: 0.8956 (mmm) outliers start: 14 outliers final: 6 residues processed: 176 average time/residue: 0.4450 time to fit residues: 131.6032 Evaluate side-chains 161 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 4.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 977 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 206 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 chunk 253 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 372 optimal weight: 0.0170 chunk 402 optimal weight: 2.9990 chunk 332 optimal weight: 5.9990 chunk 369 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 299 optimal weight: 6.9990 overall best weight: 2.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN A 247 ASN I 243 GLN I 361 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 33850 Z= 0.261 Angle : 0.508 12.995 45914 Z= 0.268 Chirality : 0.043 0.254 4848 Planarity : 0.003 0.034 5976 Dihedral : 5.955 50.115 5014 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.03 % Favored : 95.77 % Rotamer: Outliers : 0.63 % Allowed : 5.61 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.13), residues: 4118 helix: 0.98 (0.20), residues: 718 sheet: 0.62 (0.15), residues: 1240 loop : -0.41 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.003 0.001 HIS M 71 PHE 0.015 0.001 PHE J 342 TYR 0.021 0.001 TYR G 42 ARG 0.006 0.000 ARG T 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 3.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 276 MET cc_start: 0.8106 (mmm) cc_final: 0.7702 (mmt) REVERT: T 21 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7944 (ttm-80) REVERT: T 49 MET cc_start: 0.8272 (mpp) cc_final: 0.7984 (mpp) REVERT: M 356 MET cc_start: 0.9204 (mmm) cc_final: 0.8932 (mmm) REVERT: G 19 SER cc_start: 0.9115 (m) cc_final: 0.8885 (m) REVERT: G 49 MET cc_start: 0.8418 (mpp) cc_final: 0.7990 (mpp) REVERT: A 736 ILE cc_start: 0.9243 (tt) cc_final: 0.9016 (tt) REVERT: I 968 MET cc_start: 0.8275 (ttm) cc_final: 0.7908 (ttm) outliers start: 22 outliers final: 14 residues processed: 168 average time/residue: 0.4730 time to fit residues: 133.4543 Evaluate side-chains 166 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain I residue 509 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 368 optimal weight: 8.9990 chunk 280 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 374 optimal weight: 0.9980 chunk 396 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 354 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN I 632 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 33850 Z= 0.413 Angle : 0.561 8.480 45914 Z= 0.298 Chirality : 0.045 0.195 4848 Planarity : 0.004 0.045 5976 Dihedral : 5.720 59.991 5014 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.44 % Favored : 95.36 % Rotamer: Outliers : 0.95 % Allowed : 6.76 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.13), residues: 4118 helix: 0.69 (0.19), residues: 728 sheet: 0.50 (0.15), residues: 1242 loop : -0.50 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 36 HIS 0.005 0.001 HIS M 71 PHE 0.019 0.001 PHE B 342 TYR 0.017 0.002 TYR J 203 ARG 0.005 0.001 ARG J 515 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 150 time to evaluate : 3.804 Fit side-chains REVERT: E 44 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8266 (mpp) REVERT: E 215 MET cc_start: 0.8226 (mtt) cc_final: 0.7881 (mtt) REVERT: E 216 MET cc_start: 0.6536 (mmm) cc_final: 0.6324 (mmm) REVERT: E 276 MET cc_start: 0.8188 (mmm) cc_final: 0.7747 (mmt) REVERT: T 49 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7936 (mpp) REVERT: T 56 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7771 (mt) REVERT: G 19 SER cc_start: 0.9118 (m) cc_final: 0.8904 (m) REVERT: G 49 MET cc_start: 0.8419 (mpp) cc_final: 0.7977 (mpp) REVERT: G 56 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8071 (mt) REVERT: A 736 ILE cc_start: 0.9217 (tt) cc_final: 0.8941 (tt) REVERT: I 427 MET cc_start: 0.8321 (mtm) cc_final: 0.8053 (mtt) REVERT: I 477 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8477 (tp30) REVERT: I 968 MET cc_start: 0.8259 (ttm) cc_final: 0.7967 (ttm) outliers start: 33 outliers final: 22 residues processed: 172 average time/residue: 0.4429 time to fit residues: 128.7095 Evaluate side-chains 172 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain J residue 347 MET Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 477 GLU Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 330 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 295 optimal weight: 6.9990 chunk 163 optimal weight: 0.0870 chunk 338 optimal weight: 4.9990 chunk 273 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 355 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 632 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33850 Z= 0.196 Angle : 0.467 7.893 45914 Z= 0.251 Chirality : 0.042 0.210 4848 Planarity : 0.003 0.037 5976 Dihedral : 5.103 58.159 5014 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.55 % Favored : 96.26 % Rotamer: Outliers : 0.89 % Allowed : 7.33 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.13), residues: 4118 helix: 0.71 (0.19), residues: 726 sheet: 0.52 (0.15), residues: 1238 loop : -0.46 (0.14), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 486 HIS 0.003 0.001 HIS A 482 PHE 0.010 0.001 PHE B 301 TYR 0.021 0.001 TYR G 42 ARG 0.005 0.000 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 3.702 Fit side-chains REVERT: E 215 MET cc_start: 0.8107 (mtt) cc_final: 0.7800 (mtt) REVERT: E 244 MET cc_start: 0.8778 (tpp) cc_final: 0.8445 (tpp) REVERT: E 276 MET cc_start: 0.8124 (mmm) cc_final: 0.7858 (mmt) REVERT: T 49 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8001 (mpp) REVERT: T 56 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7693 (mt) REVERT: M 44 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8192 (mmm) REVERT: M 356 MET cc_start: 0.9232 (mmm) cc_final: 0.9006 (mmm) REVERT: G 19 SER cc_start: 0.9043 (m) cc_final: 0.8829 (m) REVERT: G 49 MET cc_start: 0.8309 (mpp) cc_final: 0.7862 (mpp) REVERT: G 56 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7775 (mt) REVERT: A 477 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8449 (tp30) REVERT: A 736 ILE cc_start: 0.9207 (tt) cc_final: 0.8984 (tp) REVERT: I 968 MET cc_start: 0.8275 (ttm) cc_final: 0.7973 (ttm) outliers start: 31 outliers final: 18 residues processed: 173 average time/residue: 0.4437 time to fit residues: 129.4243 Evaluate side-chains 172 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 3.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 133 optimal weight: 2.9990 chunk 356 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 396 optimal weight: 8.9990 chunk 329 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 33850 Z= 0.452 Angle : 0.577 10.904 45914 Z= 0.305 Chirality : 0.046 0.195 4848 Planarity : 0.004 0.047 5976 Dihedral : 5.414 58.604 5014 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.69 % Favored : 95.14 % Rotamer: Outliers : 1.18 % Allowed : 7.82 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.16 (0.13), residues: 4118 helix: 0.53 (0.19), residues: 730 sheet: 0.39 (0.14), residues: 1252 loop : -0.58 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 36 HIS 0.005 0.001 HIS M 71 PHE 0.017 0.001 PHE J 342 TYR 0.021 0.002 TYR B 203 ARG 0.006 0.001 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 148 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8333 (mpp) REVERT: T 49 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7933 (mpp) REVERT: T 56 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7726 (mt) REVERT: M 44 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8074 (mtm) REVERT: M 356 MET cc_start: 0.9225 (mmm) cc_final: 0.8971 (mmm) REVERT: G 19 SER cc_start: 0.9081 (m) cc_final: 0.8866 (m) REVERT: G 46 ILE cc_start: 0.9189 (pt) cc_final: 0.8943 (pt) REVERT: G 49 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7909 (mpp) REVERT: G 56 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 736 ILE cc_start: 0.9208 (tt) cc_final: 0.8969 (tp) REVERT: I 477 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8485 (tp30) outliers start: 41 outliers final: 26 residues processed: 176 average time/residue: 0.4477 time to fit residues: 132.8335 Evaluate side-chains 180 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 3.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 55 ASN Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 477 GLU Chi-restraints excluded: chain I residue 496 LEU Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 382 optimal weight: 0.3980 chunk 44 optimal weight: 9.9990 chunk 226 optimal weight: 1.9990 chunk 289 optimal weight: 0.9990 chunk 224 optimal weight: 0.9980 chunk 333 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 395 optimal weight: 10.0000 chunk 247 optimal weight: 0.6980 chunk 240 optimal weight: 0.0980 chunk 182 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 33850 Z= 0.123 Angle : 0.469 8.741 45914 Z= 0.252 Chirality : 0.042 0.199 4848 Planarity : 0.003 0.039 5976 Dihedral : 4.913 58.582 5014 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.35 % Favored : 96.48 % Rotamer: Outliers : 0.98 % Allowed : 8.19 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.13), residues: 4118 helix: 0.62 (0.19), residues: 726 sheet: 0.51 (0.15), residues: 1242 loop : -0.48 (0.14), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 486 HIS 0.003 0.001 HIS E 71 PHE 0.017 0.001 PHE I 758 TYR 0.013 0.001 TYR B 203 ARG 0.006 0.000 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 4.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 216 MET cc_start: 0.6570 (mmm) cc_final: 0.5748 (mmm) REVERT: E 276 MET cc_start: 0.8098 (mmm) cc_final: 0.7537 (mmt) REVERT: T 49 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7994 (mpp) REVERT: T 56 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7897 (mt) REVERT: M 44 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8130 (mmm) REVERT: M 356 MET cc_start: 0.9229 (mmm) cc_final: 0.8972 (mmm) REVERT: G 49 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8118 (mpp) REVERT: G 56 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7801 (mt) REVERT: G 94 LYS cc_start: 0.9029 (ptpp) cc_final: 0.8810 (ptpp) REVERT: A 427 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8265 (mpp) REVERT: I 477 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8428 (tp30) outliers start: 34 outliers final: 20 residues processed: 170 average time/residue: 0.4311 time to fit residues: 124.7748 Evaluate side-chains 171 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 3.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 84 ASP Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 477 GLU Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 977 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 244 optimal weight: 0.0670 chunk 157 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 chunk 269 optimal weight: 9.9990 chunk 195 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 310 optimal weight: 7.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 33850 Z= 0.255 Angle : 0.491 8.346 45914 Z= 0.262 Chirality : 0.043 0.208 4848 Planarity : 0.003 0.038 5976 Dihedral : 4.871 59.469 5014 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 0.98 % Allowed : 8.57 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.13), residues: 4118 helix: 0.61 (0.19), residues: 728 sheet: 0.49 (0.15), residues: 1256 loop : -0.48 (0.14), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 486 HIS 0.005 0.001 HIS E 71 PHE 0.013 0.001 PHE I 758 TYR 0.024 0.001 TYR G 42 ARG 0.006 0.000 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 4.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8256 (mpp) REVERT: E 216 MET cc_start: 0.6617 (mmm) cc_final: 0.6328 (mmm) REVERT: E 276 MET cc_start: 0.8232 (mmm) cc_final: 0.7836 (mmt) REVERT: T 49 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7925 (mpp) REVERT: T 56 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7871 (mt) REVERT: M 44 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8255 (mmm) REVERT: M 276 MET cc_start: 0.8193 (mmm) cc_final: 0.7513 (mmt) REVERT: M 356 MET cc_start: 0.9232 (mmm) cc_final: 0.8963 (mmm) REVERT: G 49 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7954 (mpp) REVERT: G 56 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7801 (mt) REVERT: A 427 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8300 (mpp) REVERT: I 477 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8418 (tp30) outliers start: 34 outliers final: 23 residues processed: 166 average time/residue: 0.4467 time to fit residues: 125.0512 Evaluate side-chains 176 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 477 GLU Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 359 optimal weight: 8.9990 chunk 378 optimal weight: 9.9990 chunk 345 optimal weight: 4.9990 chunk 368 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 289 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 332 optimal weight: 6.9990 chunk 348 optimal weight: 0.0770 chunk 366 optimal weight: 0.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 372 GLN ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 33850 Z= 0.331 Angle : 0.520 8.356 45914 Z= 0.277 Chirality : 0.044 0.226 4848 Planarity : 0.003 0.038 5976 Dihedral : 5.003 52.662 5014 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.40 % Favored : 95.43 % Rotamer: Outliers : 1.04 % Allowed : 8.51 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 4118 helix: 0.52 (0.19), residues: 730 sheet: 0.42 (0.14), residues: 1254 loop : -0.52 (0.14), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 217 HIS 0.006 0.001 HIS E 71 PHE 0.014 0.001 PHE J 342 TYR 0.021 0.001 TYR G 42 ARG 0.007 0.000 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8285 (mpp) REVERT: E 276 MET cc_start: 0.8261 (mmm) cc_final: 0.7899 (mmt) REVERT: T 49 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7926 (mpp) REVERT: T 56 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7681 (mt) REVERT: M 244 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8551 (tpp) REVERT: G 49 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7999 (mpp) REVERT: G 56 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8038 (mt) REVERT: A 427 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8334 (mpp) REVERT: I 427 MET cc_start: 0.8287 (mtm) cc_final: 0.8008 (mtt) REVERT: I 477 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8434 (tp30) outliers start: 36 outliers final: 24 residues processed: 171 average time/residue: 0.4422 time to fit residues: 127.7219 Evaluate side-chains 180 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 244 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 477 GLU Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 977 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 241 optimal weight: 0.0470 chunk 389 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 408 optimal weight: 1.9990 chunk 375 optimal weight: 0.0370 chunk 325 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 overall best weight: 0.6174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 33850 Z= 0.127 Angle : 0.455 7.533 45914 Z= 0.244 Chirality : 0.042 0.194 4848 Planarity : 0.003 0.039 5976 Dihedral : 4.537 56.279 5014 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.38 % Favored : 96.45 % Rotamer: Outliers : 0.86 % Allowed : 8.83 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.13), residues: 4118 helix: 0.61 (0.19), residues: 726 sheet: 0.54 (0.15), residues: 1244 loop : -0.45 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 486 HIS 0.003 0.001 HIS I 362 PHE 0.015 0.001 PHE A 758 TYR 0.023 0.001 TYR G 42 ARG 0.006 0.000 ARG G 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8236 Ramachandran restraints generated. 4118 Oldfield, 0 Emsley, 4118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 215 MET cc_start: 0.8298 (mtt) cc_final: 0.8068 (mtt) REVERT: E 276 MET cc_start: 0.8083 (mmm) cc_final: 0.7410 (mmt) REVERT: T 49 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7942 (mpp) REVERT: T 56 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7699 (mt) REVERT: M 244 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8337 (tpp) REVERT: M 276 MET cc_start: 0.8149 (mmm) cc_final: 0.7698 (mmt) REVERT: G 49 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7991 (mpp) REVERT: G 56 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7738 (mt) REVERT: I 477 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8377 (tp30) outliers start: 30 outliers final: 20 residues processed: 167 average time/residue: 0.4431 time to fit residues: 125.5521 Evaluate side-chains 172 residues out of total 3488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 4.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 49 MET Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 HIS Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 244 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 977 CYS Chi-restraints excluded: chain J residue 445 MET Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 477 GLU Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 977 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 258 optimal weight: 0.0070 chunk 346 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 299 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 325 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 334 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 60 optimal weight: 0.0870 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 GLN ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.070414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.053344 restraints weight = 83077.705| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.19 r_work: 0.2706 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33850 Z= 0.128 Angle : 0.450 7.928 45914 Z= 0.240 Chirality : 0.042 0.206 4848 Planarity : 0.003 0.038 5976 Dihedral : 4.368 55.426 5014 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.57 % Favored : 96.28 % Rotamer: Outliers : 0.86 % Allowed : 8.97 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 4118 helix: 0.76 (0.20), residues: 714 sheet: 0.65 (0.15), residues: 1224 loop : -0.39 (0.14), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 486 HIS 0.003 0.001 HIS M 71 PHE 0.014 0.001 PHE A 758 TYR 0.021 0.001 TYR G 42 ARG 0.008 0.000 ARG T 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5553.53 seconds wall clock time: 103 minutes 58.30 seconds (6238.30 seconds total)