Starting phenix.real_space_refine on Mon Feb 19 03:16:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa1_15290/02_2024/8aa1_15290_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa1_15290/02_2024/8aa1_15290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa1_15290/02_2024/8aa1_15290.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa1_15290/02_2024/8aa1_15290.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa1_15290/02_2024/8aa1_15290_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa1_15290/02_2024/8aa1_15290_updated.pdb" } resolution = 2.9 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 82 5.16 5 C 14914 2.51 5 N 3968 2.21 5 O 4666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B ASP 464": "OD1" <-> "OD2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A ASP 515": "OD1" <-> "OD2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A ASP 763": "OD1" <-> "OD2" Residue "A TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 187": "OE1" <-> "OE2" Residue "J GLU 328": "OE1" <-> "OE2" Residue "J GLU 356": "OE1" <-> "OE2" Residue "J GLU 435": "OE1" <-> "OE2" Residue "J ASP 464": "OD1" <-> "OD2" Residue "I GLU 170": "OE1" <-> "OE2" Residue "I GLU 177": "OE1" <-> "OE2" Residue "I ASP 338": "OD1" <-> "OD2" Residue "I ASP 340": "OD1" <-> "OD2" Residue "I GLU 379": "OE1" <-> "OE2" Residue "I TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 477": "OE1" <-> "OE2" Residue "I ASP 515": "OD1" <-> "OD2" Residue "I ASP 614": "OD1" <-> "OD2" Residue "I GLU 709": "OE1" <-> "OE2" Residue "I ASP 763": "OD1" <-> "OD2" Residue "I TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23634 Number of models: 1 Model: "" Number of chains: 12 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: "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: "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: "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: 11.96, per 1000 atoms: 0.51 Number of scatterers: 23634 At special positions: 0 Unit cell: (148.035, 96.915, 135.255, 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 82 16.00 Mg 4 11.99 O 4666 8.00 N 3968 7.00 C 14914 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: 9.49 Conformation dependent library (CDL) restraints added in 4.1 seconds 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5360 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 20 sheets defined 22.3% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.53 Creating SS restraints... Processing helix chain 'B' and resid 25 through 38 removed outlier: 4.427A pdb=" N TRP B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 85 through 110 removed outlier: 3.849A pdb=" N GLN B 110 " --> pdb=" O GLN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 140 removed outlier: 4.505A pdb=" N ASN B 120 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.583A pdb=" N ASN B 158 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 184 removed outlier: 3.968A pdb=" N ASP B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 3.862A 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 244 Processing helix chain 'B' and resid 254 through 257 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: 4.614A pdb=" N LEU B 290 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 407 through 421 Processing helix chain 'B' and resid 426 through 441 Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.738A pdb=" N LYS B 451 " --> pdb=" O PHE B 448 " (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 520 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.642A pdb=" N LYS A 111 " --> pdb=" O ASP A 107 " (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: 4.690A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.022A 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 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' 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 417 Processing helix chain 'A' and resid 536 through 538 No H-bonds generated for 'chain 'A' and resid 536 through 538' 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 889 through 892 No H-bonds generated for 'chain 'A' and resid 889 through 892' 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 25 through 38 removed outlier: 4.427A pdb=" N TRP J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA J 37 " --> pdb=" O TYR J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 76 Processing helix chain 'J' and resid 85 through 110 removed outlier: 3.848A pdb=" N GLN J 110 " --> pdb=" O GLN J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 140 removed outlier: 4.505A pdb=" N ASN J 120 " --> pdb=" O PRO J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 159 removed outlier: 3.583A pdb=" N ASN J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 184 removed outlier: 3.968A pdb=" N ASP J 177 " --> pdb=" O LYS J 173 " (cutoff:3.500A) removed outlier: 3.862A 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 244 Processing helix chain 'J' and resid 254 through 257 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: 4.614A pdb=" N LEU J 290 " --> pdb=" O GLY J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 312 Processing helix chain 'J' and resid 339 through 341 No H-bonds generated for 'chain 'J' and resid 339 through 341' Processing helix chain 'J' and resid 407 through 421 Processing helix chain 'J' and resid 426 through 441 Processing helix chain 'J' and resid 448 through 452 removed outlier: 3.737A pdb=" N LYS J 451 " --> pdb=" O PHE J 448 " (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 520 Processing helix chain 'J' and resid 536 through 541 Processing helix chain 'I' and resid 106 through 111 removed outlier: 3.642A pdb=" N LYS I 111 " --> pdb=" O ASP I 107 " (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: 4.691A pdb=" N ILE I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) removed outlier: 5.022A 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 254 No H-bonds generated for 'chain 'I' and resid 252 through 254' 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 417 Processing helix chain 'I' and resid 536 through 538 No H-bonds generated for 'chain 'I' and resid 536 through 538' 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 889 through 892 No H-bonds generated for 'chain 'I' and resid 889 through 892' 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 'B' and resid 390 through 392 Processing sheet with id= B, first strand: chain 'A' and resid 101 through 104 removed outlier: 4.071A pdb=" N ILE A 179 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 203 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A 179 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE A 201 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL A 181 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 199 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 156 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE A 202 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE A 158 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR A 204 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 128 through 131 Processing sheet with id= D, first strand: chain 'A' and resid 303 through 314 removed outlier: 6.879A pdb=" N PHE A 877 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A 954 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR A 875 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A 956 " --> pdb=" O ASP A 873 " (cutoff:3.500A) removed outlier: 6.747A 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: 7.278A pdb=" N GLY A 626 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N THR A 591 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG A 457 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG A 421 " --> pdb=" O ARG A 457 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 719 through 722 Processing sheet with id= F, first strand: chain 'A' and resid 885 through 887 Processing sheet with id= G, first strand: chain 'A' and resid 948 through 951 removed outlier: 4.425A pdb=" N LEU A 983 " --> pdb=" O LEU A 951 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 259 through 265 removed outlier: 6.638A pdb=" N GLY A 264 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU A 273 " --> pdb=" O GLY A 264 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 638 through 640 removed outlier: 3.769A pdb=" N GLN A 677 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA A 640 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ARG A 675 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 804 through 806 removed outlier: 5.985A pdb=" N GLY A 806 " --> pdb=" O TRP A 851 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TRP A 851 " --> pdb=" O GLY A 806 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 390 through 392 Processing sheet with id= L, first strand: chain 'I' and resid 101 through 104 removed outlier: 4.071A pdb=" N ILE I 179 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR I 203 " --> pdb=" O GLU I 177 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE I 179 " --> pdb=" O ILE I 201 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE I 201 " --> pdb=" O ILE I 179 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL I 181 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL I 199 " --> pdb=" O VAL I 181 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU I 156 " --> pdb=" O ILE I 200 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE I 202 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE I 158 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR I 204 " --> pdb=" O ILE I 158 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 128 through 131 Processing sheet with id= N, first strand: chain 'I' and resid 303 through 314 removed outlier: 6.878A pdb=" N PHE I 877 " --> pdb=" O ARG I 952 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE I 954 " --> pdb=" O THR I 875 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR I 875 " --> pdb=" O ILE I 954 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU I 956 " --> pdb=" O ASP I 873 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP I 873 " --> pdb=" O LEU I 956 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA I 740 " --> pdb=" O LEU I 776 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY I 626 " --> pdb=" O THR I 591 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N THR I 591 " --> pdb=" O GLY I 626 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG I 457 " --> pdb=" O ARG I 421 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG I 421 " --> pdb=" O ARG I 457 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 719 through 722 Processing sheet with id= P, first strand: chain 'I' and resid 885 through 887 Processing sheet with id= Q, first strand: chain 'I' and resid 948 through 951 removed outlier: 4.425A pdb=" N LEU I 983 " --> pdb=" O LEU I 951 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 259 through 265 removed outlier: 6.637A pdb=" N GLY I 264 " --> pdb=" O LEU I 273 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU I 273 " --> pdb=" O GLY I 264 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 638 through 640 removed outlier: 3.769A pdb=" N GLN I 677 " --> pdb=" O ILE I 638 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA I 640 " --> pdb=" O ARG I 675 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ARG I 675 " --> pdb=" O ALA I 640 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 804 through 806 removed outlier: 5.985A pdb=" N GLY I 806 " --> pdb=" O TRP I 851 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TRP I 851 " --> pdb=" O GLY I 806 " (cutoff:3.500A) 958 hydrogen bonds defined for protein. 2592 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: 7.83 Time building geometry restraints manager: 10.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7774 1.34 - 1.46: 6037 1.46 - 1.58: 10163 1.58 - 1.70: 66 1.70 - 1.81: 148 Bond restraints: 24188 Sorted by residual: bond pdb=" C2 FRU C 7 " pdb=" O5 FRU C 7 " ideal model delta sigma weight residual 1.412 1.643 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C2 FRU L 4 " pdb=" O5 FRU L 4 " ideal model delta sigma weight residual 1.412 1.642 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 FRU K 3 " pdb=" O5 FRU K 3 " ideal model delta sigma weight residual 1.412 1.642 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 FRU L 3 " pdb=" O5 FRU L 3 " ideal model delta sigma weight residual 1.412 1.641 -0.229 2.00e-02 2.50e+03 1.32e+02 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 1.32e+02 ... (remaining 24183 not shown) Histogram of bond angle deviations from ideal: 96.21 - 103.76: 288 103.76 - 111.32: 9735 111.32 - 118.88: 9171 118.88 - 126.43: 13234 126.43 - 133.99: 382 Bond angle restraints: 32810 Sorted by residual: angle pdb=" C CYS B 298 " pdb=" N CYS B 299 " pdb=" CA CYS B 299 " ideal model delta sigma weight residual 121.54 129.62 -8.08 1.91e+00 2.74e-01 1.79e+01 angle pdb=" C CYS J 298 " pdb=" N CYS J 299 " pdb=" CA CYS J 299 " ideal model delta sigma weight residual 121.54 129.58 -8.04 1.91e+00 2.74e-01 1.77e+01 angle pdb=" CA LYS A 318 " pdb=" CB LYS A 318 " pdb=" CG LYS A 318 " ideal model delta sigma weight residual 114.10 120.88 -6.78 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA LYS I 318 " pdb=" CB LYS I 318 " pdb=" CG LYS I 318 " ideal model delta sigma weight residual 114.10 120.88 -6.78 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CB MET I 427 " pdb=" CG MET I 427 " pdb=" SD MET I 427 " ideal model delta sigma weight residual 112.70 102.72 9.98 3.00e+00 1.11e-01 1.11e+01 ... (remaining 32805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 13441 17.05 - 34.10: 727 34.10 - 51.15: 232 51.15 - 68.20: 74 68.20 - 85.25: 8 Dihedral angle restraints: 14482 sinusoidal: 5990 harmonic: 8492 Sorted by residual: dihedral pdb=" CA ARG J 7 " pdb=" C ARG J 7 " pdb=" N GLN J 8 " pdb=" CA GLN J 8 " ideal model delta harmonic sigma weight residual 180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ARG B 7 " pdb=" C ARG B 7 " pdb=" N GLN B 8 " pdb=" CA GLN B 8 " ideal model delta harmonic sigma weight residual -180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA CYS B 387 " pdb=" C CYS B 387 " pdb=" N ASP B 388 " pdb=" CA ASP B 388 " ideal model delta harmonic sigma weight residual 180.00 -161.83 -18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 14479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2380 0.038 - 0.077: 793 0.077 - 0.115: 244 0.115 - 0.153: 53 0.153 - 0.192: 4 Chirality restraints: 3474 Sorted by residual: 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 2.79 -0.19 2.00e-02 2.50e+03 9.19e+01 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 2.79 -0.19 2.00e-02 2.50e+03 9.04e+01 chirality pdb=" C2 FRU L 4 " pdb=" O6 FRU L 3 " pdb=" C1 FRU L 4 " pdb=" O5 FRU L 4 " both_signs ideal model delta sigma weight residual False 2.60 2.68 -0.08 2.00e-02 2.50e+03 1.41e+01 ... (remaining 3471 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 592 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO A 593 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 593 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 593 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE I 592 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO I 593 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO I 593 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 593 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 530 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO I 531 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO I 531 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 531 " 0.016 5.00e-02 4.00e+02 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 343 2.63 - 3.20: 20650 3.20 - 3.76: 37555 3.76 - 4.33: 55234 4.33 - 4.90: 90868 Nonbonded interactions: 204650 Sorted by model distance: nonbonded pdb=" OD1 ASN J 401 " pdb="MG MG J 601 " model vdw 2.061 2.170 nonbonded pdb=" OD1 ASN B 401 " pdb="MG MG B 601 " model vdw 2.062 2.170 nonbonded pdb=" OD1 ASN A 841 " pdb="MG MG A1101 " model vdw 2.107 2.170 nonbonded pdb=" OD1 ASN I 841 " pdb="MG MG I1101 " model vdw 2.107 2.170 nonbonded pdb=" OD2 ASP A 848 " pdb="MG MG A1101 " model vdw 2.108 2.170 ... (remaining 204645 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' } 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.740 Check model and map are aligned: 0.390 Set scattering table: 0.220 Process input model: 61.670 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 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 : 0.011 0.231 24188 Z= 0.697 Angle : 0.549 9.977 32810 Z= 0.267 Chirality : 0.043 0.192 3474 Planarity : 0.003 0.034 4272 Dihedral : 12.372 85.254 9116 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.56 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.16), residues: 2942 helix: 1.65 (0.21), residues: 670 sheet: 0.97 (0.18), residues: 794 loop : 0.39 (0.17), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 91 HIS 0.002 0.000 HIS J 302 PHE 0.010 0.001 PHE J 301 TYR 0.011 0.001 TYR I 225 ARG 0.004 0.000 ARG J 7 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.808 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 109 average time/residue: 1.4661 time to fit residues: 185.2006 Evaluate side-chains 101 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 1016 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 123 optimal weight: 0.0000 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 140 optimal weight: 0.3980 chunk 171 optimal weight: 6.9990 chunk 266 optimal weight: 0.8980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 302 HIS ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 ASN J 302 HIS ** I 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.0283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24188 Z= 0.120 Angle : 0.436 7.770 32810 Z= 0.229 Chirality : 0.041 0.144 3474 Planarity : 0.003 0.032 4272 Dihedral : 7.273 55.809 3716 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.60 % Favored : 98.33 % Rotamer: Outliers : 0.61 % Allowed : 6.63 % Favored : 92.76 % 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: 1.07 (0.16), residues: 2942 helix: 1.38 (0.20), residues: 684 sheet: 0.95 (0.18), residues: 798 loop : 0.37 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 91 HIS 0.003 0.001 HIS J 134 PHE 0.007 0.001 PHE I 438 TYR 0.012 0.001 TYR J 33 ARG 0.003 0.000 ARG I 513 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 2.700 Fit side-chains REVERT: A 427 MET cc_start: 0.8348 (ttm) cc_final: 0.8055 (mtt) REVERT: A 487 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8833 (ppp) REVERT: I 487 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8837 (ppp) outliers start: 15 outliers final: 6 residues processed: 118 average time/residue: 1.4657 time to fit residues: 200.1205 Evaluate side-chains 110 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 1016 PHE Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 516 CYS Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 1016 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 73 optimal weight: 0.0970 chunk 267 optimal weight: 7.9990 chunk 288 optimal weight: 6.9990 chunk 238 optimal weight: 4.9990 chunk 265 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 361 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 GLN I 153 ASN I 361 GLN I 955 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 24188 Z= 0.353 Angle : 0.530 9.388 32810 Z= 0.282 Chirality : 0.044 0.168 3474 Planarity : 0.004 0.045 4272 Dihedral : 5.884 49.749 3716 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.01 % Rotamer: Outliers : 1.33 % Allowed : 6.47 % Favored : 92.20 % 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: 0.79 (0.15), residues: 2942 helix: 1.02 (0.20), residues: 690 sheet: 0.79 (0.18), residues: 806 loop : 0.25 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 851 HIS 0.006 0.001 HIS J 302 PHE 0.014 0.002 PHE A 813 TYR 0.018 0.002 TYR A 422 ARG 0.007 0.001 ARG I 513 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 2.676 Fit side-chains REVERT: A 229 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8311 (mtt) REVERT: A 427 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8366 (mtt) REVERT: I 229 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8310 (mtt) outliers start: 33 outliers final: 12 residues processed: 119 average time/residue: 1.4726 time to fit residues: 201.8490 Evaluate side-chains 107 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 873 ASP Chi-restraints excluded: chain A residue 1016 PHE Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 873 ASP Chi-restraints excluded: chain I residue 1016 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 4.9990 chunk 201 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 268 optimal weight: 0.3980 chunk 284 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN A 361 GLN A 744 GLN I 309 ASN I 361 GLN I 744 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 24188 Z= 0.362 Angle : 0.523 9.153 32810 Z= 0.279 Chirality : 0.044 0.173 3474 Planarity : 0.004 0.036 4272 Dihedral : 5.755 55.127 3716 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.65 % Favored : 97.28 % Rotamer: Outliers : 1.33 % Allowed : 7.48 % Favored : 91.19 % 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: 0.58 (0.15), residues: 2942 helix: 0.83 (0.20), residues: 688 sheet: 0.66 (0.17), residues: 808 loop : 0.13 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 91 HIS 0.004 0.001 HIS J 302 PHE 0.012 0.001 PHE B 493 TYR 0.018 0.002 TYR I 422 ARG 0.004 0.001 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 95 time to evaluate : 2.510 Fit side-chains REVERT: A 229 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8184 (mtt) REVERT: A 427 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8341 (mtt) REVERT: A 534 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.9139 (mtt) REVERT: I 229 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8186 (mtt) REVERT: I 534 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.9141 (mtt) REVERT: I 1016 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.6863 (t80) outliers start: 33 outliers final: 17 residues processed: 115 average time/residue: 1.5944 time to fit residues: 210.2998 Evaluate side-chains 109 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 873 ASP Chi-restraints excluded: chain A residue 1016 PHE Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 534 MET Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 873 ASP Chi-restraints excluded: chain I residue 1016 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 211 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 242 optimal weight: 0.0970 chunk 196 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 GLN ** I 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24188 Z= 0.279 Angle : 0.490 8.609 32810 Z= 0.262 Chirality : 0.043 0.144 3474 Planarity : 0.003 0.035 4272 Dihedral : 5.576 57.034 3716 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.65 % Favored : 97.28 % Rotamer: Outliers : 1.50 % Allowed : 7.92 % Favored : 90.58 % 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: 0.54 (0.15), residues: 2942 helix: 0.77 (0.20), residues: 686 sheet: 0.63 (0.17), residues: 808 loop : 0.12 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 91 HIS 0.003 0.001 HIS B 132 PHE 0.014 0.001 PHE I 758 TYR 0.015 0.001 TYR I 422 ARG 0.005 0.000 ARG J 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 98 time to evaluate : 2.697 Fit side-chains REVERT: A 229 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8165 (mtt) REVERT: A 427 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8328 (mtt) outliers start: 37 outliers final: 17 residues processed: 122 average time/residue: 1.5014 time to fit residues: 210.8715 Evaluate side-chains 107 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 873 ASP Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 506 MET Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 873 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 166 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 284 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 GLN ** I 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 24188 Z= 0.351 Angle : 0.522 8.972 32810 Z= 0.278 Chirality : 0.044 0.180 3474 Planarity : 0.004 0.036 4272 Dihedral : 5.618 59.097 3714 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 1.29 % Allowed : 8.45 % Favored : 90.26 % 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: 0.44 (0.15), residues: 2942 helix: 0.69 (0.20), residues: 688 sheet: 0.57 (0.17), residues: 808 loop : 0.05 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 91 HIS 0.003 0.001 HIS B 302 PHE 0.013 0.001 PHE I 758 TYR 0.016 0.001 TYR I 422 ARG 0.007 0.001 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 2.645 Fit side-chains REVERT: A 229 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8148 (mtt) REVERT: A 427 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8377 (mtt) REVERT: I 229 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8148 (mtt) REVERT: I 1016 PHE cc_start: 0.7935 (m-80) cc_final: 0.6905 (t80) outliers start: 32 outliers final: 24 residues processed: 113 average time/residue: 1.5672 time to fit residues: 203.3386 Evaluate side-chains 115 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 873 ASP Chi-restraints excluded: chain A residue 1016 PHE Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 504 ASP Chi-restraints excluded: chain I residue 506 MET Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 873 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 160 optimal weight: 0.6980 chunk 239 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 283 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 361 GLN ** 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: 0.8903 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24188 Z= 0.157 Angle : 0.457 8.205 32810 Z= 0.245 Chirality : 0.041 0.161 3474 Planarity : 0.003 0.035 4272 Dihedral : 5.242 59.813 3714 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.90 % Favored : 98.03 % Rotamer: Outliers : 0.77 % Allowed : 9.46 % Favored : 89.77 % 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: 0.59 (0.15), residues: 2942 helix: 0.86 (0.20), residues: 676 sheet: 0.64 (0.17), residues: 804 loop : 0.15 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 91 HIS 0.002 0.001 HIS J 302 PHE 0.014 0.001 PHE I 758 TYR 0.011 0.001 TYR A 422 ARG 0.007 0.000 ARG J 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 2.710 Fit side-chains REVERT: B 114 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8380 (mmpt) REVERT: A 427 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8230 (mtt) REVERT: A 1016 PHE cc_start: 0.7856 (m-80) cc_final: 0.6923 (t80) REVERT: J 114 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8379 (mmpt) REVERT: I 1016 PHE cc_start: 0.7876 (m-80) cc_final: 0.6947 (t80) outliers start: 19 outliers final: 11 residues processed: 105 average time/residue: 1.5844 time to fit residues: 191.7107 Evaluate side-chains 108 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain J residue 114 LYS Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 506 MET Chi-restraints excluded: chain I residue 767 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 85 optimal weight: 0.1980 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 0.0770 chunk 180 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 overall best weight: 2.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 GLN ** I 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 24188 Z= 0.317 Angle : 0.505 10.125 32810 Z= 0.268 Chirality : 0.043 0.184 3474 Planarity : 0.003 0.036 4272 Dihedral : 5.380 58.682 3714 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.11 % Rotamer: Outliers : 1.05 % Allowed : 9.50 % Favored : 89.45 % 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: 0.49 (0.15), residues: 2942 helix: 0.82 (0.20), residues: 676 sheet: 0.55 (0.17), residues: 808 loop : 0.08 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 91 HIS 0.003 0.001 HIS J 302 PHE 0.012 0.001 PHE I 758 TYR 0.015 0.001 TYR I 422 ARG 0.004 0.000 ARG I 513 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 2.521 Fit side-chains REVERT: B 7 ARG cc_start: 0.8210 (ptm-80) cc_final: 0.7942 (ttt180) REVERT: A 427 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8362 (mtt) REVERT: A 574 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8863 (t) REVERT: A 1016 PHE cc_start: 0.7908 (m-80) cc_final: 0.6920 (t80) REVERT: J 7 ARG cc_start: 0.8208 (ptm-80) cc_final: 0.7942 (ttt180) REVERT: I 229 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8136 (mtt) REVERT: I 574 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8865 (t) REVERT: I 1016 PHE cc_start: 0.7929 (m-80) cc_final: 0.7053 (t80) outliers start: 26 outliers final: 18 residues processed: 112 average time/residue: 1.5541 time to fit residues: 200.0968 Evaluate side-chains 111 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 276 MET 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 506 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 873 ASP Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 506 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 873 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 264 optimal weight: 0.7980 chunk 158 optimal weight: 0.0570 chunk 115 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 361 GLN ** 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: 0.8919 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24188 Z= 0.227 Angle : 0.477 9.498 32810 Z= 0.255 Chirality : 0.042 0.199 3474 Planarity : 0.003 0.034 4272 Dihedral : 5.267 58.777 3714 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 1.01 % Allowed : 9.74 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 2942 helix: 0.83 (0.20), residues: 676 sheet: 0.61 (0.17), residues: 804 loop : 0.10 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 91 HIS 0.003 0.001 HIS J 302 PHE 0.013 0.001 PHE I 758 TYR 0.013 0.001 TYR I 422 ARG 0.003 0.000 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 2.812 Fit side-chains REVERT: B 7 ARG cc_start: 0.8248 (ptm-80) cc_final: 0.7979 (ttt180) REVERT: A 427 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8309 (mtt) REVERT: A 574 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8870 (t) REVERT: A 1016 PHE cc_start: 0.7886 (m-80) cc_final: 0.7011 (t80) REVERT: J 7 ARG cc_start: 0.8247 (ptm-80) cc_final: 0.7979 (ttt180) REVERT: I 229 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8151 (mtt) REVERT: I 574 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8870 (t) REVERT: I 1016 PHE cc_start: 0.7905 (m-80) cc_final: 0.7037 (t80) outliers start: 25 outliers final: 15 residues processed: 111 average time/residue: 1.5060 time to fit residues: 193.3458 Evaluate side-chains 113 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain A residue 109 ILE 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 506 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 873 ASP Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 506 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 873 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 132 optimal weight: 0.4980 chunk 194 optimal weight: 4.9990 chunk 292 optimal weight: 0.0370 chunk 269 optimal weight: 4.9990 chunk 233 optimal weight: 0.0980 chunk 24 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 overall best weight: 0.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 361 GLN ** 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: 0.8881 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24188 Z= 0.124 Angle : 0.443 8.898 32810 Z= 0.237 Chirality : 0.041 0.177 3474 Planarity : 0.003 0.034 4272 Dihedral : 4.875 57.814 3714 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.11 % Favored : 97.82 % Rotamer: Outliers : 0.65 % Allowed : 10.15 % Favored : 89.21 % 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: 0.62 (0.15), residues: 2942 helix: 0.88 (0.20), residues: 678 sheet: 0.67 (0.18), residues: 802 loop : 0.16 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 91 HIS 0.002 0.001 HIS J 302 PHE 0.014 0.001 PHE A 758 TYR 0.010 0.001 TYR A 422 ARG 0.002 0.000 ARG A 513 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 2.732 Fit side-chains REVERT: B 7 ARG cc_start: 0.8158 (ptm-80) cc_final: 0.7855 (ttt180) REVERT: A 427 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8163 (mtt) REVERT: A 574 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8866 (t) REVERT: A 1016 PHE cc_start: 0.7848 (m-80) cc_final: 0.7050 (t80) REVERT: J 7 ARG cc_start: 0.8157 (ptm-80) cc_final: 0.7857 (ttt180) REVERT: I 574 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8868 (t) REVERT: I 1016 PHE cc_start: 0.7852 (m-80) cc_final: 0.7051 (t80) outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 1.4775 time to fit residues: 200.0012 Evaluate side-chains 113 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 506 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 873 ASP Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 506 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 767 ASN Chi-restraints excluded: chain I residue 873 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.6980 chunk 248 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 239 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.073349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.058902 restraints weight = 44475.337| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.11 r_work: 0.2620 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 24188 Z= 0.379 Angle : 0.573 18.499 32810 Z= 0.306 Chirality : 0.044 0.167 3474 Planarity : 0.004 0.047 4272 Dihedral : 5.269 58.814 3714 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.11 % Rotamer: Outliers : 0.85 % Allowed : 9.70 % Favored : 89.45 % Cbeta Deviations : 0.07 % 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: 0.50 (0.15), residues: 2942 helix: 0.85 (0.20), residues: 676 sheet: 0.54 (0.17), residues: 808 loop : 0.09 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 851 HIS 0.004 0.001 HIS J 302 PHE 0.012 0.001 PHE I 758 TYR 0.017 0.001 TYR J 95 ARG 0.003 0.000 ARG J 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5322.97 seconds wall clock time: 98 minutes 45.91 seconds (5925.91 seconds total)