Starting phenix.real_space_refine on Mon Feb 19 03:16:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa3_15292/02_2024/8aa3_15292_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa3_15292/02_2024/8aa3_15292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa3_15292/02_2024/8aa3_15292.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa3_15292/02_2024/8aa3_15292.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa3_15292/02_2024/8aa3_15292_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aa3_15292/02_2024/8aa3_15292_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s 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: 12.37, per 1000 atoms: 0.52 Number of scatterers: 23634 At special positions: 0 Unit cell: (109.695, 156.555, 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=2.03 Simple disulfide: pdb=" SG CYS J 387 " - pdb=" SG CYS J 389 " distance=2.03 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 2 " - " FRU C 7 " ~> Even though FRU is a beta isomer, an alpha linkage is required... " FRU K 2 " - " 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: 9.93 Conformation dependent library (CDL) restraints added in 4.4 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: 86 helices and 20 sheets defined 23.3% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.87 Creating SS restraints... Processing helix chain 'B' and resid 25 through 38 removed outlier: 4.722A pdb=" N TRP B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 54 removed outlier: 3.897A pdb=" N ARG B 54 " --> pdb=" O TYR B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 54' Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 85 through 110 removed outlier: 3.868A pdb=" N GLN B 110 " --> pdb=" O GLN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 140 removed outlier: 4.491A pdb=" N ASN B 120 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 167 through 184 removed outlier: 3.886A pdb=" N ASP B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 3.894A 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 237 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: 4.737A 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 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 453 removed outlier: 3.620A pdb=" N LYS B 451 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B 453 " --> pdb=" O TYR B 450 " (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 513 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: 3.717A 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: 4.643A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.942A 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 removed outlier: 3.543A pdb=" N ASN A 255 " --> pdb=" O PRO A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 295 through 298 No H-bonds generated for 'chain 'A' and resid 295 through 298' Processing helix chain 'A' and resid 377 through 383 Processing helix chain 'A' and resid 410 through 419 removed outlier: 4.978A pdb=" N ASP A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) 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 893 removed outlier: 3.927A pdb=" N LYS A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 889 through 893' Processing helix chain 'A' and resid 909 through 912 Processing helix chain 'A' and resid 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' 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: 4.722A pdb=" N TRP J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA J 37 " --> pdb=" O TYR J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 54 removed outlier: 3.897A pdb=" N ARG J 54 " --> pdb=" O TYR J 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 51 through 54' Processing helix chain 'J' and resid 69 through 76 Processing helix chain 'J' and resid 85 through 110 removed outlier: 3.869A pdb=" N GLN J 110 " --> pdb=" O GLN J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 140 removed outlier: 4.491A pdb=" N ASN J 120 " --> pdb=" O PRO J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 159 Processing helix chain 'J' and resid 167 through 184 removed outlier: 3.886A pdb=" N ASP J 177 " --> pdb=" O LYS J 173 " (cutoff:3.500A) removed outlier: 3.894A 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 237 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: 4.737A 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 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 453 removed outlier: 3.620A pdb=" N LYS J 451 " --> pdb=" O PHE J 448 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP J 453 " --> pdb=" O TYR J 450 " (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 513 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: 3.717A 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: 4.643A pdb=" N ILE I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) removed outlier: 4.942A 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 removed outlier: 3.543A pdb=" N ASN I 255 " --> pdb=" O PRO I 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 252 through 255' Processing helix chain 'I' and resid 295 through 298 No H-bonds generated for 'chain 'I' and resid 295 through 298' Processing helix chain 'I' and resid 377 through 383 Processing helix chain 'I' and resid 410 through 419 removed outlier: 4.977A pdb=" N ASP I 419 " --> pdb=" O GLU I 415 " (cutoff:3.500A) 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 893 removed outlier: 3.928A pdb=" N LYS I 893 " --> pdb=" O ASP I 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 889 through 893' Processing helix chain 'I' and resid 909 through 912 Processing helix chain 'I' and resid 940 through 942 No H-bonds generated for 'chain 'I' and resid 940 through 942' 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: 4.014A pdb=" N ILE A 179 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR A 203 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE A 179 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 201 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL A 181 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 199 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 156 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE A 202 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE A 158 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.481A 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: 6.945A pdb=" N PHE A 877 " --> pdb=" O ARG A 952 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE A 954 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR A 875 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU A 956 " --> pdb=" O ASP A 873 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP A 873 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA A 740 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLY A 626 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N THR A 591 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 457 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 4.440A 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: 4.522A 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: 6.637A pdb=" N GLY A 264 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 5.146A 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: 3.705A pdb=" N GLN A 677 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA A 640 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 5.562A 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: 6.114A pdb=" N GLY A 806 " --> pdb=" O TRP A 851 " (cutoff:3.500A) removed outlier: 5.129A 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: 4.014A pdb=" N ILE I 179 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR I 203 " --> pdb=" O GLU I 177 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE I 179 " --> pdb=" O ILE I 201 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE I 201 " --> pdb=" O ILE I 179 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL I 181 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL I 199 " --> pdb=" O VAL I 181 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU I 156 " --> pdb=" O ILE I 200 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE I 202 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE I 158 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.482A 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: 6.945A pdb=" N PHE I 877 " --> pdb=" O ARG I 952 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE I 954 " --> pdb=" O THR I 875 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR I 875 " --> pdb=" O ILE I 954 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU I 956 " --> pdb=" O ASP I 873 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP I 873 " --> pdb=" O LEU I 956 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA I 740 " --> pdb=" O LEU I 776 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLY I 626 " --> pdb=" O THR I 591 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N THR I 591 " --> pdb=" O GLY I 626 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG I 457 " --> pdb=" O ARG I 421 " (cutoff:3.500A) removed outlier: 4.440A 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: 4.522A 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: 6.636A pdb=" N GLY I 264 " --> pdb=" O LEU I 273 " (cutoff:3.500A) removed outlier: 5.147A 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: 3.705A pdb=" N GLN I 677 " --> pdb=" O ILE I 638 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA I 640 " --> pdb=" O ARG I 675 " (cutoff:3.500A) removed outlier: 5.562A 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: 6.114A pdb=" N GLY I 806 " --> pdb=" O TRP I 851 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TRP I 851 " --> pdb=" O GLY I 806 " (cutoff:3.500A) 964 hydrogen bonds defined for protein. 2622 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: 9.01 Time building geometry restraints manager: 10.59 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: 6061 1.46 - 1.58: 10139 1.58 - 1.70: 66 1.70 - 1.82: 148 Bond restraints: 24188 Sorted by residual: bond pdb=" C2 FRU K 5 " pdb=" O5 FRU K 5 " 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 C 4 " pdb=" O5 FRU C 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 C 2 " pdb=" O5 FRU C 2 " 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 4 " pdb=" O5 FRU K 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 2 " pdb=" O5 FRU K 2 " ideal model delta sigma weight residual 1.412 1.642 -0.230 2.00e-02 2.50e+03 1.32e+02 ... (remaining 24183 not shown) Histogram of bond angle deviations from ideal: 97.96 - 105.17: 373 105.17 - 112.37: 11638 112.37 - 119.58: 8041 119.58 - 126.79: 12399 126.79 - 134.00: 359 Bond angle restraints: 32810 Sorted by residual: angle pdb=" C GLY B 393 " pdb=" N SER B 394 " pdb=" CA SER B 394 " ideal model delta sigma weight residual 121.54 127.55 -6.01 1.91e+00 2.74e-01 9.90e+00 angle pdb=" C GLY J 393 " pdb=" N SER J 394 " pdb=" CA SER J 394 " ideal model delta sigma weight residual 121.54 127.54 -6.00 1.91e+00 2.74e-01 9.88e+00 angle pdb=" C ILE I 353 " pdb=" N ASP I 354 " pdb=" CA ASP I 354 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.66e+00 angle pdb=" C ILE A 353 " pdb=" N ASP A 354 " pdb=" CA ASP A 354 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.50e+00 angle pdb=" CA LEU A 121 " pdb=" CB LEU A 121 " pdb=" CG LEU A 121 " ideal model delta sigma weight residual 116.30 124.97 -8.67 3.50e+00 8.16e-02 6.14e+00 ... (remaining 32805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 13088 17.71 - 35.42: 1074 35.42 - 53.13: 230 53.13 - 70.84: 70 70.84 - 88.56: 20 Dihedral angle restraints: 14482 sinusoidal: 5990 harmonic: 8492 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 93.00 124.13 -31.13 1 1.00e+01 1.00e-02 1.38e+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 93.00 124.11 -31.11 1 1.00e+01 1.00e-02 1.38e+01 dihedral pdb=" CG ARG A 444 " pdb=" CD ARG A 444 " pdb=" NE ARG A 444 " pdb=" CZ ARG A 444 " ideal model delta sinusoidal sigma weight residual -180.00 -136.01 -43.99 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 14479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2095 0.030 - 0.060: 950 0.060 - 0.091: 230 0.091 - 0.121: 162 0.121 - 0.151: 37 Chirality restraints: 3474 Sorted by residual: chirality pdb=" C2 FRU K 7 " pdb=" O1 FRU K 2 " 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 5.43e+01 chirality pdb=" C2 FRU C 7 " pdb=" O1 FRU C 2 " pdb=" C1 FRU C 7 " pdb=" O5 FRU C 7 " both_signs ideal model delta sigma weight residual False 2.60 2.74 -0.14 2.00e-02 2.50e+03 5.21e+01 chirality pdb=" C2 FRU K 3 " pdb=" O6 FRU K 2 " pdb=" C1 FRU K 3 " pdb=" O5 FRU K 3 " both_signs ideal model delta sigma weight residual False 2.60 2.68 -0.08 2.00e-02 2.50e+03 1.57e+01 ... (remaining 3471 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 530 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO I 531 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO I 531 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 531 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 530 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 531 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 531 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 531 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 353 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C ILE A 353 " -0.020 2.00e-02 2.50e+03 pdb=" O ILE A 353 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP A 354 " 0.007 2.00e-02 2.50e+03 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 336 2.65 - 3.21: 21057 3.21 - 3.77: 38058 3.77 - 4.34: 54623 4.34 - 4.90: 90091 Nonbonded interactions: 204165 Sorted by model distance: nonbonded pdb=" OD1 ASN J 401 " pdb="MG MG J 601 " model vdw 2.085 2.170 nonbonded pdb=" OD1 ASN B 401 " pdb="MG MG B 601 " model vdw 2.086 2.170 nonbonded pdb=" OD1 ASN I 841 " pdb="MG MG I1101 " model vdw 2.131 2.170 nonbonded pdb=" OD1 ASN A 841 " pdb="MG MG A1101 " model vdw 2.132 2.170 nonbonded pdb=" O TYR B 273 " pdb="MG MG B 601 " model vdw 2.144 2.170 ... (remaining 204160 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: 1.370 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: 6.960 Check model and map are aligned: 0.350 Set scattering table: 0.240 Process input model: 65.070 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.190 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 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 0.230 24188 Z= 0.716 Angle : 0.504 8.671 32810 Z= 0.238 Chirality : 0.042 0.151 3474 Planarity : 0.003 0.032 4272 Dihedral : 14.247 88.556 9116 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % 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: 1.42 (0.16), residues: 2942 helix: 1.72 (0.20), residues: 690 sheet: 1.05 (0.17), residues: 820 loop : 0.62 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 91 HIS 0.002 0.000 HIS A 799 PHE 0.008 0.001 PHE A 758 TYR 0.011 0.001 TYR B 95 ARG 0.003 0.000 ARG I 408 *********************** 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 197 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 2.711 Fit side-chains REVERT: B 18 GLN cc_start: 0.8670 (mt0) cc_final: 0.8327 (mt0) REVERT: J 18 GLN cc_start: 0.8664 (mt0) cc_final: 0.8318 (mt0) REVERT: I 988 LYS cc_start: 0.8490 (mppt) cc_final: 0.8186 (mppt) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 1.4872 time to fit residues: 334.7257 Evaluate side-chains 116 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 123 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 171 optimal weight: 6.9990 chunk 266 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 307 ASN A 153 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN A 816 GLN J 43 ASN J 96 GLN ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 ASN J 307 ASN I 153 ASN I 211 GLN ** I 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 749 ASN I 767 ASN I 816 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24188 Z= 0.300 Angle : 0.534 6.788 32810 Z= 0.281 Chirality : 0.044 0.152 3474 Planarity : 0.004 0.055 4272 Dihedral : 7.626 59.765 3714 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.94 % Allowed : 5.05 % Favored : 93.01 % 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: 0.99 (0.15), residues: 2942 helix: 1.02 (0.20), residues: 660 sheet: 1.04 (0.17), residues: 808 loop : 0.39 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 851 HIS 0.007 0.002 HIS B 134 PHE 0.012 0.002 PHE B 301 TYR 0.015 0.001 TYR I 422 ARG 0.014 0.001 ARG J 100 *********************** 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 170 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 122 time to evaluate : 2.718 Fit side-chains REVERT: B 18 GLN cc_start: 0.8813 (mt0) cc_final: 0.8332 (mt0) REVERT: B 40 ASP cc_start: 0.8216 (p0) cc_final: 0.7892 (p0) REVERT: B 203 TYR cc_start: 0.9457 (OUTLIER) cc_final: 0.8774 (t80) REVERT: A 502 ARG cc_start: 0.7698 (ttm110) cc_final: 0.7488 (mtp-110) REVERT: A 561 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7463 (tmt) REVERT: A 988 LYS cc_start: 0.8539 (mppt) cc_final: 0.8244 (mppt) REVERT: J 18 GLN cc_start: 0.8814 (mt0) cc_final: 0.8344 (mt0) REVERT: J 40 ASP cc_start: 0.8244 (p0) cc_final: 0.7923 (p0) REVERT: J 203 TYR cc_start: 0.9463 (OUTLIER) cc_final: 0.8790 (t80) REVERT: J 347 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8676 (mtm) REVERT: I 561 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7487 (tmt) REVERT: I 988 LYS cc_start: 0.8536 (mppt) cc_final: 0.8234 (mppt) outliers start: 48 outliers final: 16 residues processed: 149 average time/residue: 1.4540 time to fit residues: 249.4322 Evaluate side-chains 132 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 664 ASN Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 347 MET Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 504 ASP Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 594 SER Chi-restraints excluded: chain I residue 664 ASN Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 769 SER Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 909 THR Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 0.0030 chunk 82 optimal weight: 0.8980 chunk 222 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 288 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN A 362 HIS A 489 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 ASN I 362 HIS I 489 ASN ** I 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 749 ASN I 767 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24188 Z= 0.238 Angle : 0.468 12.298 32810 Z= 0.251 Chirality : 0.042 0.149 3474 Planarity : 0.003 0.032 4272 Dihedral : 6.293 50.552 3714 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.62 % Allowed : 6.75 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 2942 helix: 0.92 (0.20), residues: 672 sheet: 1.09 (0.17), residues: 804 loop : 0.32 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 91 HIS 0.004 0.001 HIS B 132 PHE 0.009 0.001 PHE B 342 TYR 0.012 0.001 TYR I 422 ARG 0.010 0.000 ARG J 100 *********************** 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 154 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 114 time to evaluate : 2.921 Fit side-chains REVERT: B 18 GLN cc_start: 0.8791 (mt0) cc_final: 0.8304 (mt0) REVERT: A 502 ARG cc_start: 0.7759 (ttm110) cc_final: 0.7521 (mtp-110) REVERT: A 561 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7527 (tmt) REVERT: A 988 LYS cc_start: 0.8543 (mppt) cc_final: 0.8250 (mppt) REVERT: J 18 GLN cc_start: 0.8791 (mt0) cc_final: 0.8297 (mt0) REVERT: I 502 ARG cc_start: 0.7957 (mtp-110) cc_final: 0.7620 (mtp-110) REVERT: I 561 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7581 (tmt) REVERT: I 763 ASP cc_start: 0.7750 (t70) cc_final: 0.7536 (t0) REVERT: I 988 LYS cc_start: 0.8543 (mppt) cc_final: 0.8245 (mppt) outliers start: 40 outliers final: 15 residues processed: 139 average time/residue: 1.4455 time to fit residues: 231.4636 Evaluate side-chains 128 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 594 SER Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 769 SER Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 909 THR Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 284 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 254 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN A 489 ASN A 749 ASN A 767 ASN J 167 ASN ** I 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 489 ASN I 749 ASN I 767 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 24188 Z= 0.535 Angle : 0.600 12.339 32810 Z= 0.320 Chirality : 0.048 0.160 3474 Planarity : 0.004 0.064 4272 Dihedral : 6.530 56.250 3714 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.74 % Allowed : 8.00 % 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: 0.58 (0.15), residues: 2942 helix: 0.49 (0.20), residues: 664 sheet: 1.09 (0.18), residues: 790 loop : 0.04 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 91 HIS 0.006 0.001 HIS A 362 PHE 0.013 0.002 PHE B 71 TYR 0.019 0.002 TYR I1002 ARG 0.011 0.001 ARG B 100 *********************** 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 155 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 112 time to evaluate : 3.201 Fit side-chains REVERT: B 203 TYR cc_start: 0.9544 (OUTLIER) cc_final: 0.8964 (t80) REVERT: A 561 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7604 (tmt) REVERT: A 968 MET cc_start: 0.7997 (tpp) cc_final: 0.7742 (tpt) REVERT: A 988 LYS cc_start: 0.8607 (mppt) cc_final: 0.8279 (mppt) REVERT: J 203 TYR cc_start: 0.9544 (OUTLIER) cc_final: 0.8963 (t80) REVERT: I 502 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7631 (mtp-110) REVERT: I 561 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7636 (tmt) REVERT: I 763 ASP cc_start: 0.7855 (t70) cc_final: 0.7617 (t0) REVERT: I 988 LYS cc_start: 0.8605 (mppt) cc_final: 0.8274 (mppt) outliers start: 43 outliers final: 17 residues processed: 138 average time/residue: 1.5184 time to fit residues: 239.6703 Evaluate side-chains 132 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 504 ASP Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 594 SER Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 769 SER Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 909 THR Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 242 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 chunk 255 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN I 767 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24188 Z= 0.210 Angle : 0.473 10.870 32810 Z= 0.257 Chirality : 0.042 0.146 3474 Planarity : 0.003 0.030 4272 Dihedral : 5.839 55.338 3714 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.62 % Allowed : 8.57 % Favored : 89.81 % 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: 0.60 (0.15), residues: 2942 helix: 0.54 (0.20), residues: 668 sheet: 1.03 (0.18), residues: 804 loop : 0.07 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 91 HIS 0.003 0.001 HIS I 362 PHE 0.009 0.001 PHE I 438 TYR 0.012 0.001 TYR B 95 ARG 0.005 0.000 ARG I 502 *********************** 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 154 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 114 time to evaluate : 2.892 Fit side-chains REVERT: B 7 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7412 (ttm170) REVERT: B 18 GLN cc_start: 0.8752 (mt0) cc_final: 0.8258 (mt0) REVERT: B 203 TYR cc_start: 0.9494 (OUTLIER) cc_final: 0.8929 (t80) REVERT: A 561 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7527 (tmt) REVERT: A 988 LYS cc_start: 0.8613 (mppt) cc_final: 0.8286 (mppt) REVERT: J 7 ARG cc_start: 0.7870 (ttp-170) cc_final: 0.7460 (ttm170) REVERT: J 18 GLN cc_start: 0.8753 (mt0) cc_final: 0.8256 (mt0) REVERT: J 203 TYR cc_start: 0.9496 (OUTLIER) cc_final: 0.8929 (t80) REVERT: I 502 ARG cc_start: 0.7968 (mtp-110) cc_final: 0.7678 (mtm-85) REVERT: I 561 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7643 (tmt) REVERT: I 763 ASP cc_start: 0.7761 (t70) cc_final: 0.7526 (t0) REVERT: I 988 LYS cc_start: 0.8615 (mppt) cc_final: 0.8295 (mppt) outliers start: 40 outliers final: 11 residues processed: 140 average time/residue: 1.4809 time to fit residues: 238.8072 Evaluate side-chains 128 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 504 ASP Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 594 SER Chi-restraints excluded: chain I residue 769 SER Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 909 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 284 optimal weight: 0.0020 chunk 236 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 ASN A 767 ASN I 767 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24188 Z= 0.245 Angle : 0.482 11.285 32810 Z= 0.260 Chirality : 0.042 0.145 3474 Planarity : 0.003 0.037 4272 Dihedral : 5.652 56.006 3714 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.25 % Allowed : 9.01 % Favored : 89.73 % 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: 0.63 (0.15), residues: 2942 helix: 0.52 (0.20), residues: 678 sheet: 1.09 (0.18), residues: 788 loop : 0.10 (0.16), residues: 1476 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 0.015 0.001 PHE A 758 TYR 0.013 0.001 TYR B 95 ARG 0.004 0.000 ARG I 502 *********************** 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 146 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 3.022 Fit side-chains REVERT: B 7 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7414 (ttm170) REVERT: B 18 GLN cc_start: 0.8753 (mt0) cc_final: 0.8241 (mt0) REVERT: B 203 TYR cc_start: 0.9498 (OUTLIER) cc_final: 0.8919 (t80) REVERT: A 561 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7604 (tmt) REVERT: A 741 MET cc_start: 0.9416 (ttp) cc_final: 0.9214 (ttm) REVERT: A 968 MET cc_start: 0.8012 (tpp) cc_final: 0.7735 (tpt) REVERT: A 988 LYS cc_start: 0.8616 (mppt) cc_final: 0.8405 (mppt) REVERT: J 7 ARG cc_start: 0.7879 (ttp-170) cc_final: 0.7449 (ttm170) REVERT: J 18 GLN cc_start: 0.8752 (mt0) cc_final: 0.8241 (mt0) REVERT: J 203 TYR cc_start: 0.9499 (OUTLIER) cc_final: 0.8919 (t80) REVERT: I 502 ARG cc_start: 0.7941 (mtp-110) cc_final: 0.7651 (mtm-85) REVERT: I 561 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7641 (tmt) REVERT: I 763 ASP cc_start: 0.7770 (t70) cc_final: 0.7534 (t0) REVERT: I 968 MET cc_start: 0.7996 (tpp) cc_final: 0.7700 (tpt) REVERT: I 988 LYS cc_start: 0.8616 (mppt) cc_final: 0.8404 (mppt) outliers start: 31 outliers final: 14 residues processed: 135 average time/residue: 1.5666 time to fit residues: 242.1536 Evaluate side-chains 130 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 504 ASP Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 594 SER Chi-restraints excluded: chain I residue 769 SER Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 909 THR Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 207 optimal weight: 0.5980 chunk 160 optimal weight: 0.5980 chunk 239 optimal weight: 3.9990 chunk 158 optimal weight: 0.0870 chunk 283 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 ASN A 767 ASN ** I 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 767 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24188 Z= 0.206 Angle : 0.464 12.170 32810 Z= 0.251 Chirality : 0.042 0.143 3474 Planarity : 0.003 0.031 4272 Dihedral : 5.415 56.521 3714 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.29 % Allowed : 9.18 % Favored : 89.53 % 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: 0.63 (0.15), residues: 2942 helix: 0.52 (0.20), residues: 678 sheet: 1.12 (0.18), residues: 784 loop : 0.09 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 91 HIS 0.003 0.001 HIS B 132 PHE 0.017 0.001 PHE A 758 TYR 0.012 0.001 TYR B 95 ARG 0.003 0.000 ARG B 100 *********************** 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 147 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 2.894 Fit side-chains REVERT: B 7 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7436 (ttm170) REVERT: B 18 GLN cc_start: 0.8746 (mt0) cc_final: 0.8454 (mt0) REVERT: B 203 TYR cc_start: 0.9484 (OUTLIER) cc_final: 0.8882 (t80) REVERT: A 208 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8101 (mmtm) REVERT: A 561 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7604 (tmt) REVERT: A 741 MET cc_start: 0.9420 (ttp) cc_final: 0.9161 (mtm) REVERT: A 968 MET cc_start: 0.8089 (tpp) cc_final: 0.7789 (tpt) REVERT: A 988 LYS cc_start: 0.8637 (mppt) cc_final: 0.8416 (mppt) REVERT: J 7 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7432 (ttm170) REVERT: J 18 GLN cc_start: 0.8746 (mt0) cc_final: 0.8453 (mt0) REVERT: J 203 TYR cc_start: 0.9484 (OUTLIER) cc_final: 0.8882 (t80) REVERT: I 502 ARG cc_start: 0.7932 (mtp-110) cc_final: 0.7655 (ttm170) REVERT: I 561 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7639 (tmt) REVERT: I 968 MET cc_start: 0.8115 (tpp) cc_final: 0.7807 (tpt) REVERT: I 988 LYS cc_start: 0.8637 (mppt) cc_final: 0.8416 (mppt) outliers start: 32 outliers final: 14 residues processed: 137 average time/residue: 1.5145 time to fit residues: 237.8494 Evaluate side-chains 135 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 504 ASP Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 594 SER Chi-restraints excluded: chain I residue 769 SER Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 909 THR Chi-restraints excluded: chain I residue 918 THR 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: 0.0070 chunk 169 optimal weight: 7.9990 chunk 85 optimal weight: 0.4980 chunk 55 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 180 optimal weight: 0.8980 chunk 193 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 overall best weight: 2.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 749 ASN I 489 ASN I 749 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24188 Z= 0.338 Angle : 0.521 15.405 32810 Z= 0.279 Chirality : 0.044 0.145 3474 Planarity : 0.004 0.047 4272 Dihedral : 5.695 59.853 3714 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.54 % Allowed : 9.14 % Favored : 89.33 % 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: 0.46 (0.20), residues: 680 sheet: 1.02 (0.18), residues: 790 loop : 0.03 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.004 0.001 HIS I 362 PHE 0.017 0.002 PHE I 758 TYR 0.015 0.001 TYR B 95 ARG 0.004 0.000 ARG B 100 *********************** 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 151 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 113 time to evaluate : 3.168 Fit side-chains REVERT: B 7 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7406 (ttm170) REVERT: B 18 GLN cc_start: 0.8786 (mt0) cc_final: 0.8282 (mt0) REVERT: B 203 TYR cc_start: 0.9515 (OUTLIER) cc_final: 0.8818 (t80) REVERT: A 561 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7608 (tmt) REVERT: A 741 MET cc_start: 0.9435 (ttp) cc_final: 0.9231 (ttm) REVERT: A 824 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.9243 (p) REVERT: A 968 MET cc_start: 0.8147 (tpp) cc_final: 0.7860 (tpt) REVERT: A 988 LYS cc_start: 0.8641 (mppt) cc_final: 0.8424 (mppt) REVERT: J 7 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7399 (ttm170) REVERT: J 18 GLN cc_start: 0.8785 (mt0) cc_final: 0.8280 (mt0) REVERT: J 203 TYR cc_start: 0.9517 (OUTLIER) cc_final: 0.8818 (t80) REVERT: I 502 ARG cc_start: 0.7937 (mtp-110) cc_final: 0.7676 (ttm170) REVERT: I 561 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7636 (tmt) REVERT: I 763 ASP cc_start: 0.7819 (t0) cc_final: 0.7607 (t0) REVERT: I 824 THR cc_start: 0.9446 (OUTLIER) cc_final: 0.9234 (p) REVERT: I 968 MET cc_start: 0.8176 (tpp) cc_final: 0.7869 (tpt) REVERT: I 988 LYS cc_start: 0.8641 (mppt) cc_final: 0.8424 (mppt) outliers start: 38 outliers final: 16 residues processed: 139 average time/residue: 1.5680 time to fit residues: 250.3477 Evaluate side-chains 137 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 504 ASP Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 594 SER Chi-restraints excluded: chain I residue 769 SER Chi-restraints excluded: chain I residue 824 THR Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 909 THR Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 0.6980 chunk 271 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 264 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 238 optimal weight: 0.7980 chunk 249 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 586 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 ASN A 767 ASN I 270 ASN I 586 ASN ** I 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 749 ASN I 767 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24188 Z= 0.191 Angle : 0.468 16.950 32810 Z= 0.252 Chirality : 0.042 0.143 3474 Planarity : 0.003 0.030 4272 Dihedral : 5.358 59.641 3714 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.09 % Allowed : 9.74 % Favored : 89.17 % 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: 0.60 (0.15), residues: 2942 helix: 0.50 (0.20), residues: 678 sheet: 1.07 (0.18), residues: 786 loop : 0.09 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 91 HIS 0.002 0.001 HIS J 132 PHE 0.017 0.001 PHE I 758 TYR 0.011 0.001 TYR A 422 ARG 0.003 0.000 ARG J 100 *********************** 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 142 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 2.920 Fit side-chains REVERT: B 7 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7439 (ttm170) REVERT: B 18 GLN cc_start: 0.8734 (mt0) cc_final: 0.8447 (mt0) REVERT: B 203 TYR cc_start: 0.9483 (OUTLIER) cc_final: 0.8884 (t80) REVERT: A 561 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7598 (tmt) REVERT: A 968 MET cc_start: 0.8153 (tpp) cc_final: 0.7846 (tpt) REVERT: A 988 LYS cc_start: 0.8619 (mppt) cc_final: 0.8410 (mppt) REVERT: J 7 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7434 (ttm170) REVERT: J 18 GLN cc_start: 0.8732 (mt0) cc_final: 0.8447 (mt0) REVERT: J 203 TYR cc_start: 0.9484 (OUTLIER) cc_final: 0.8883 (t80) REVERT: I 502 ARG cc_start: 0.7922 (mtp-110) cc_final: 0.7665 (ttm170) REVERT: I 506 MET cc_start: 0.8721 (ttt) cc_final: 0.8471 (ppp) REVERT: I 561 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7634 (tmt) REVERT: I 968 MET cc_start: 0.8171 (tpp) cc_final: 0.7878 (tpt) REVERT: I 988 LYS cc_start: 0.8617 (mppt) cc_final: 0.8409 (mppt) outliers start: 27 outliers final: 14 residues processed: 132 average time/residue: 1.6003 time to fit residues: 241.8701 Evaluate side-chains 135 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 504 ASP Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 594 SER Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 909 THR Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 292 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 233 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 489 ASN A 586 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 ASN I 489 ASN I 586 ASN ** I 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 749 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24188 Z= 0.186 Angle : 0.458 10.483 32810 Z= 0.248 Chirality : 0.042 0.141 3474 Planarity : 0.003 0.031 4272 Dihedral : 5.196 57.190 3714 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.05 % Allowed : 9.90 % Favored : 89.05 % 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: 0.66 (0.15), residues: 2942 helix: 0.59 (0.20), residues: 666 sheet: 1.05 (0.18), residues: 790 loop : 0.14 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 91 HIS 0.003 0.001 HIS A 362 PHE 0.017 0.001 PHE I 758 TYR 0.011 0.001 TYR B 95 ARG 0.003 0.000 ARG B 100 ********************** 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 140 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 2.622 Fit side-chains REVERT: B 7 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7401 (ttm170) REVERT: B 18 GLN cc_start: 0.8734 (mt0) cc_final: 0.8449 (mt0) REVERT: B 203 TYR cc_start: 0.9479 (OUTLIER) cc_final: 0.8853 (t80) REVERT: A 506 MET cc_start: 0.8716 (ttt) cc_final: 0.8476 (ppp) REVERT: A 561 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7601 (tmt) REVERT: A 968 MET cc_start: 0.8160 (tpp) cc_final: 0.7868 (tpt) REVERT: A 988 LYS cc_start: 0.8630 (mppt) cc_final: 0.8426 (mppt) REVERT: J 7 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7424 (ttm170) REVERT: J 18 GLN cc_start: 0.8734 (mt0) cc_final: 0.8447 (mt0) REVERT: J 203 TYR cc_start: 0.9480 (OUTLIER) cc_final: 0.8852 (t80) REVERT: I 502 ARG cc_start: 0.7912 (mtp-110) cc_final: 0.7651 (ttm170) REVERT: I 506 MET cc_start: 0.8700 (ttt) cc_final: 0.8463 (ppp) REVERT: I 561 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7636 (tmt) REVERT: I 968 MET cc_start: 0.8182 (tpp) cc_final: 0.7863 (tpt) REVERT: I 988 LYS cc_start: 0.8629 (mppt) cc_final: 0.8424 (mppt) outliers start: 26 outliers final: 12 residues processed: 131 average time/residue: 1.5593 time to fit residues: 234.4438 Evaluate side-chains 131 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain J residue 7 ARG Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain I residue 346 MET Chi-restraints excluded: chain I residue 561 MET Chi-restraints excluded: chain I residue 594 SER Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 909 THR Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.0010 chunk 248 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 233 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 ASN A 489 ASN A 586 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 ASN I 306 GLN I 489 ASN I 586 ASN ** I 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 749 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.076000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.061283 restraints weight = 40864.535| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 1.90 r_work: 0.2650 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24188 Z= 0.159 Angle : 0.452 14.257 32810 Z= 0.243 Chirality : 0.041 0.140 3474 Planarity : 0.003 0.030 4272 Dihedral : 4.990 58.983 3714 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.01 % Allowed : 9.94 % Favored : 89.05 % 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: 0.67 (0.15), residues: 2942 helix: 0.58 (0.20), residues: 678 sheet: 1.03 (0.18), residues: 804 loop : 0.16 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 91 HIS 0.003 0.001 HIS A 362 PHE 0.016 0.001 PHE I 758 TYR 0.011 0.001 TYR B 95 ARG 0.003 0.000 ARG B 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5910.44 seconds wall clock time: 108 minutes 0.46 seconds (6480.46 seconds total)