Starting phenix.real_space_refine on Mon Feb 19 04:21:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9y_15288/02_2024/8a9y_15288.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9y_15288/02_2024/8a9y_15288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9y_15288/02_2024/8a9y_15288.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9y_15288/02_2024/8a9y_15288.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9y_15288/02_2024/8a9y_15288.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9y_15288/02_2024/8a9y_15288.pdb" } resolution = 3.5 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 2 5.21 5 S 88 5.16 5 C 14988 2.51 5 N 4004 2.21 5 O 4606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 373": "OE1" <-> "OE2" Residue "T PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 373": "OE1" <-> "OE2" Residue "G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23688 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3982 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 18, 'TRANS': 478} Chain: "T" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 730 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "M" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3982 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 18, 'TRANS': 478} Chain: "G" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 730 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "A" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 903, 7131 Classifications: {'peptide': 903} Link IDs: {'PTRANS': 31, 'TRANS': 871} Chain breaks: 1 Chain: "I" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 903, 7131 Classifications: {'peptide': 903} Link IDs: {'PTRANS': 31, 'TRANS': 871} Chain breaks: 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: "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: 12.30, per 1000 atoms: 0.52 Number of scatterers: 23688 At special positions: 0 Unit cell: (205.545, 112.89, 136.32, 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 88 16.00 Mg 2 11.99 O 4606 8.00 N 4004 7.00 C 14988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.56 Conformation dependent library (CDL) restraints added in 4.7 seconds 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5424 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 44 sheets defined 10.3% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'E' and resid 159 through 162 Processing helix chain 'E' and resid 254 through 261 Processing helix chain 'E' and resid 303 through 307 removed outlier: 3.507A pdb=" N ASP E 307 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 347 removed outlier: 4.010A pdb=" N TYR E 347 " --> pdb=" O ILE E 343 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 162 Processing helix chain 'M' and resid 254 through 261 Processing helix chain 'M' and resid 303 through 307 removed outlier: 3.507A pdb=" N ASP M 307 " --> pdb=" O ALA M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 340 through 347 removed outlier: 4.010A pdb=" N TYR M 347 " --> pdb=" O ILE M 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.705A pdb=" N LYS A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.814A pdb=" N GLU A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.293A pdb=" N ALA A 256 " --> pdb=" O ASN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 409 through 418 Processing helix chain 'A' and resid 602 through 608 removed outlier: 5.559A pdb=" N ASN A 605 " --> pdb=" O THR A 602 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE A 606 " --> pdb=" O GLN A 603 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 608 " --> pdb=" O ASN A 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 602 through 608' Processing helix chain 'A' and resid 779 through 786 Processing helix chain 'A' and resid 789 through 793 removed outlier: 4.504A pdb=" N GLY A 792 " --> pdb=" O GLY A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 822 Processing helix chain 'A' and resid 888 through 895 removed outlier: 3.717A pdb=" N LYS A 892 " --> pdb=" O SER A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 913 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 961 through 969 Processing helix chain 'I' and resid 105 through 113 removed outlier: 3.704A pdb=" N LYS I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY I 113 " --> pdb=" O ILE I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 121 Processing helix chain 'I' and resid 167 through 171 removed outlier: 3.814A pdb=" N GLU I 170 " --> pdb=" O GLY I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'I' and resid 233 through 249 Processing helix chain 'I' and resid 251 through 256 removed outlier: 4.291A pdb=" N ALA I 256 " --> pdb=" O ASN I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 300 Processing helix chain 'I' and resid 376 through 384 Processing helix chain 'I' and resid 409 through 418 Processing helix chain 'I' and resid 602 through 608 removed outlier: 5.557A pdb=" N ASN I 605 " --> pdb=" O THR I 602 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE I 606 " --> pdb=" O GLN I 603 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET I 607 " --> pdb=" O GLU I 604 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS I 608 " --> pdb=" O ASN I 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 602 through 608' Processing helix chain 'I' and resid 779 through 786 Processing helix chain 'I' and resid 789 through 793 removed outlier: 4.504A pdb=" N GLY I 792 " --> pdb=" O GLY I 789 " (cutoff:3.500A) Processing helix chain 'I' and resid 815 through 822 Processing helix chain 'I' and resid 888 through 895 removed outlier: 3.716A pdb=" N LYS I 892 " --> pdb=" O SER I 888 " (cutoff:3.500A) Processing helix chain 'I' and resid 908 through 913 Processing helix chain 'I' and resid 939 through 941 No H-bonds generated for 'chain 'I' and resid 939 through 941' Processing helix chain 'I' and resid 961 through 969 Processing sheet with id=AA1, first strand: chain 'E' and resid 39 through 40 removed outlier: 3.691A pdb=" N ASP E 53 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 39 through 40 removed outlier: 7.320A pdb=" N ILE E 73 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU E 89 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLY E 75 " --> pdb=" O LEU E 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 102 through 111 removed outlier: 3.944A pdb=" N THR E 122 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY E 106 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE E 120 " --> pdb=" O GLY E 106 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR E 108 " --> pdb=" O TYR E 118 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR E 118 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR E 110 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU E 116 " --> pdb=" O TYR E 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 102 through 111 removed outlier: 3.944A pdb=" N THR E 122 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY E 106 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE E 120 " --> pdb=" O GLY E 106 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR E 108 " --> pdb=" O TYR E 118 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR E 118 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR E 110 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU E 116 " --> pdb=" O TYR E 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 168 through 175 removed outlier: 7.064A pdb=" N PHE E 168 " --> pdb=" O ARG E 188 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ARG E 188 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP E 170 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA E 186 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY E 193 " --> pdb=" O MET E 213 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N MET E 213 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE E 195 " --> pdb=" O THR E 211 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N THR E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLU E 197 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 221 through 229 removed outlier: 6.573A pdb=" N ILE E 236 " --> pdb=" O PRO E 224 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL E 226 " --> pdb=" O TYR E 234 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR E 234 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS E 228 " --> pdb=" O TRP E 232 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 283 through 289 removed outlier: 5.831A pdb=" N ALA E 284 " --> pdb=" O TRP E 299 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TRP E 299 " --> pdb=" O ALA E 284 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ARG E 294 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 349 through 351 removed outlier: 4.098A pdb=" N VAL E 500 " --> pdb=" O GLN E 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 349 through 351 removed outlier: 4.098A pdb=" N VAL E 500 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL E 498 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER E 389 " --> pdb=" O VAL E 498 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL E 500 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS E 387 " --> pdb=" O VAL E 500 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR E 502 " --> pdb=" O HIS E 385 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS E 385 " --> pdb=" O THR E 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 357 through 358 removed outlier: 3.846A pdb=" N ALA E 357 " --> pdb=" O ILE E 378 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE E 378 " --> pdb=" O ALA E 357 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TRP E 484 " --> pdb=" O PHE E 379 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE E 401 " --> pdb=" O VAL E 419 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA E 426 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP E 440 " --> pdb=" O ALA E 426 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE E 428 " --> pdb=" O LEU E 438 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 25 through 26 removed outlier: 3.646A pdb=" N SER T 19 " --> pdb=" O ASN T 55 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU T 53 " --> pdb=" O ARG T 21 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 28 through 30 removed outlier: 6.047A pdb=" N ILE T 36 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS T 94 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL T 38 " --> pdb=" O LYS T 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 28 through 30 removed outlier: 6.047A pdb=" N ILE T 36 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS T 94 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL T 38 " --> pdb=" O LYS T 94 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A 262 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET A 276 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA A 260 " --> pdb=" O MET A 276 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 39 through 40 removed outlier: 3.691A pdb=" N ASP M 53 " --> pdb=" O ASP M 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 39 through 40 removed outlier: 7.320A pdb=" N ILE M 73 " --> pdb=" O GLU M 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU M 89 " --> pdb=" O ILE M 73 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLY M 75 " --> pdb=" O LEU M 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 102 through 111 removed outlier: 3.943A pdb=" N THR M 122 " --> pdb=" O GLY M 104 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY M 106 " --> pdb=" O PHE M 120 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE M 120 " --> pdb=" O GLY M 106 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR M 108 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR M 118 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR M 110 " --> pdb=" O LEU M 116 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU M 116 " --> pdb=" O TYR M 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 102 through 111 removed outlier: 3.943A pdb=" N THR M 122 " --> pdb=" O GLY M 104 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY M 106 " --> pdb=" O PHE M 120 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE M 120 " --> pdb=" O GLY M 106 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR M 108 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR M 118 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR M 110 " --> pdb=" O LEU M 116 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU M 116 " --> pdb=" O TYR M 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 168 through 175 removed outlier: 7.065A pdb=" N PHE M 168 " --> pdb=" O ARG M 188 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ARG M 188 " --> pdb=" O PHE M 168 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP M 170 " --> pdb=" O ALA M 186 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA M 186 " --> pdb=" O ASP M 170 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY M 193 " --> pdb=" O MET M 213 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N MET M 213 " --> pdb=" O GLY M 193 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE M 195 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N THR M 211 " --> pdb=" O ILE M 195 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLU M 197 " --> pdb=" O ALA M 209 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 221 through 229 removed outlier: 6.572A pdb=" N ILE M 236 " --> pdb=" O PRO M 224 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL M 226 " --> pdb=" O TYR M 234 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR M 234 " --> pdb=" O VAL M 226 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS M 228 " --> pdb=" O TRP M 232 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP M 232 " --> pdb=" O LYS M 228 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 283 through 289 removed outlier: 5.831A pdb=" N ALA M 284 " --> pdb=" O TRP M 299 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TRP M 299 " --> pdb=" O ALA M 284 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG M 294 " --> pdb=" O LEU M 327 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 349 through 351 removed outlier: 4.098A pdb=" N VAL M 500 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 349 through 351 removed outlier: 4.098A pdb=" N VAL M 500 " --> pdb=" O GLN M 351 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL M 498 " --> pdb=" O SER M 389 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER M 389 " --> pdb=" O VAL M 498 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL M 500 " --> pdb=" O LYS M 387 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS M 387 " --> pdb=" O VAL M 500 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR M 502 " --> pdb=" O HIS M 385 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N HIS M 385 " --> pdb=" O THR M 502 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 357 through 358 removed outlier: 3.846A pdb=" N ALA M 357 " --> pdb=" O ILE M 378 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE M 378 " --> pdb=" O ALA M 357 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TRP M 484 " --> pdb=" O PHE M 379 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE M 401 " --> pdb=" O VAL M 419 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA M 426 " --> pdb=" O ASP M 440 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASP M 440 " --> pdb=" O ALA M 426 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE M 428 " --> pdb=" O LEU M 438 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 25 through 26 removed outlier: 3.646A pdb=" N SER G 19 " --> pdb=" O ASN G 55 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU G 53 " --> pdb=" O ARG G 21 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 28 through 30 removed outlier: 6.047A pdb=" N ILE G 36 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS G 94 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL G 38 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 28 through 30 removed outlier: 6.047A pdb=" N ILE G 36 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS G 94 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL G 38 " --> pdb=" O LYS G 94 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN I 262 " --> pdb=" O TYR I 274 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET I 276 " --> pdb=" O ALA I 260 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA I 260 " --> pdb=" O MET I 276 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 101 through 104 removed outlier: 4.097A pdb=" N ILE A 179 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR A 203 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE A 179 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 201 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 181 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 199 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU A 156 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE A 202 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE A 158 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR A 204 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AD2, first strand: chain 'A' and resid 984 through 986 removed outlier: 3.724A pdb=" N VAL A 304 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ARG A 421 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A 457 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET A 487 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N THR A 591 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY A 626 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN A 879 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU A 951 " --> pdb=" O GLN A 879 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL A 881 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU A 949 " --> pdb=" O VAL A 881 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AD4, first strand: chain 'A' and resid 638 through 640 removed outlier: 6.480A pdb=" N ILE A 638 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 719 through 723 Processing sheet with id=AD6, first strand: chain 'A' and resid 804 through 806 removed outlier: 6.788A pdb=" N GLN A 804 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.448A pdb=" N GLY A 811 " --> pdb=" O ARG A 834 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AD9, first strand: chain 'I' and resid 101 through 104 removed outlier: 4.096A pdb=" N ILE I 179 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR I 203 " --> pdb=" O GLU I 177 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE I 179 " --> pdb=" O ILE I 201 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE I 201 " --> pdb=" O ILE I 179 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL I 181 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL I 199 " --> pdb=" O VAL I 181 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU I 156 " --> pdb=" O ILE I 200 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE I 202 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE I 158 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR I 204 " --> pdb=" O ILE I 158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 128 through 131 Processing sheet with id=AE2, first strand: chain 'I' and resid 984 through 986 removed outlier: 3.724A pdb=" N VAL I 304 " --> pdb=" O LEU I 331 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ARG I 421 " --> pdb=" O ARG I 457 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG I 457 " --> pdb=" O ARG I 421 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET I 487 " --> pdb=" O GLY I 448 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N THR I 591 " --> pdb=" O GLY I 626 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY I 626 " --> pdb=" O THR I 591 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN I 879 " --> pdb=" O LEU I 951 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU I 951 " --> pdb=" O GLN I 879 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL I 881 " --> pdb=" O LEU I 949 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU I 949 " --> pdb=" O VAL I 881 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 464 through 465 Processing sheet with id=AE4, first strand: chain 'I' and resid 638 through 640 removed outlier: 6.480A pdb=" N ILE I 638 " --> pdb=" O ASN I 676 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 719 through 723 Processing sheet with id=AE6, first strand: chain 'I' and resid 804 through 806 removed outlier: 6.788A pdb=" N GLN I 804 " --> pdb=" O ILE I 852 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 809 through 812 removed outlier: 4.447A pdb=" N GLY I 811 " --> pdb=" O ARG I 834 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 885 through 887 1084 hydrogen bonds defined for protein. 2922 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: 10.25 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: 1.22 - 1.34: 7765 1.34 - 1.46: 5876 1.46 - 1.58: 10457 1.58 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 24260 Sorted by residual: bond pdb=" C ALA I 757 " pdb=" N PHE I 758 " ideal model delta sigma weight residual 1.334 1.365 -0.032 1.24e-02 6.50e+03 6.52e+00 bond pdb=" C ALA A 757 " pdb=" N PHE A 758 " ideal model delta sigma weight residual 1.334 1.365 -0.032 1.24e-02 6.50e+03 6.51e+00 bond pdb=" C ALA A 757 " pdb=" O ALA A 757 " ideal model delta sigma weight residual 1.237 1.264 -0.027 1.17e-02 7.31e+03 5.49e+00 bond pdb=" C ALA I 757 " pdb=" O ALA I 757 " ideal model delta sigma weight residual 1.237 1.264 -0.027 1.17e-02 7.31e+03 5.41e+00 bond pdb=" CA ILE M 268 " pdb=" CB ILE M 268 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.15e+00 ... (remaining 24255 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.80: 355 104.80 - 112.11: 11474 112.11 - 119.42: 7926 119.42 - 126.72: 12758 126.72 - 134.03: 377 Bond angle restraints: 32890 Sorted by residual: angle pdb=" N VAL A 86 " pdb=" CA VAL A 86 " pdb=" C VAL A 86 " ideal model delta sigma weight residual 111.77 106.89 4.88 1.04e+00 9.25e-01 2.20e+01 angle pdb=" N VAL I 86 " pdb=" CA VAL I 86 " pdb=" C VAL I 86 " ideal model delta sigma weight residual 111.77 106.93 4.84 1.04e+00 9.25e-01 2.17e+01 angle pdb=" CA MET A 968 " pdb=" CB MET A 968 " pdb=" CG MET A 968 " ideal model delta sigma weight residual 114.10 123.22 -9.12 2.00e+00 2.50e-01 2.08e+01 angle pdb=" CA MET I 968 " pdb=" CB MET I 968 " pdb=" CG MET I 968 " ideal model delta sigma weight residual 114.10 123.20 -9.10 2.00e+00 2.50e-01 2.07e+01 angle pdb=" CA LEU I 121 " pdb=" CB LEU I 121 " pdb=" CG LEU I 121 " ideal model delta sigma weight residual 116.30 130.71 -14.41 3.50e+00 8.16e-02 1.70e+01 ... (remaining 32885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 13293 15.06 - 30.13: 683 30.13 - 45.19: 170 45.19 - 60.26: 22 60.26 - 75.32: 6 Dihedral angle restraints: 14174 sinusoidal: 5590 harmonic: 8584 Sorted by residual: dihedral pdb=" CA MET M 215 " pdb=" C MET M 215 " pdb=" N MET M 216 " pdb=" CA MET M 216 " ideal model delta harmonic sigma weight residual 180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA MET E 215 " pdb=" C MET E 215 " pdb=" N MET E 216 " pdb=" CA MET E 216 " ideal model delta harmonic sigma weight residual 180.00 -162.27 -17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASP A 96 " pdb=" CB ASP A 96 " pdb=" CG ASP A 96 " pdb=" OD1 ASP A 96 " ideal model delta sinusoidal sigma weight residual -30.00 -89.17 59.17 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 14171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2233 0.033 - 0.065: 822 0.065 - 0.098: 203 0.098 - 0.130: 179 0.130 - 0.163: 11 Chirality restraints: 3448 Sorted by residual: chirality pdb=" CA ASP A 717 " pdb=" N ASP A 717 " pdb=" C ASP A 717 " pdb=" CB ASP A 717 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA ASP I 717 " pdb=" N ASP I 717 " pdb=" C ASP I 717 " pdb=" CB ASP I 717 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE E 195 " pdb=" N ILE E 195 " pdb=" C ILE E 195 " pdb=" CB ILE E 195 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 3445 not shown) Planarity restraints: 4300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET I 968 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C MET I 968 " 0.024 2.00e-02 2.50e+03 pdb=" O MET I 968 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG I 969 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 968 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.89e+00 pdb=" C MET A 968 " -0.024 2.00e-02 2.50e+03 pdb=" O MET A 968 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG A 969 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE I 592 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO I 593 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO I 593 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 593 " -0.018 5.00e-02 4.00e+02 ... (remaining 4297 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 412 2.66 - 3.22: 21431 3.22 - 3.78: 36801 3.78 - 4.34: 51772 4.34 - 4.90: 86982 Nonbonded interactions: 197398 Sorted by model distance: nonbonded pdb=" OD2 ASP A 848 " pdb="MG MG A1101 " model vdw 2.100 2.170 nonbonded pdb=" OD2 ASP I 848 " pdb="MG MG I1101 " model vdw 2.100 2.170 nonbonded pdb=" OD1 ASN I 841 " pdb="MG MG I1101 " model vdw 2.103 2.170 nonbonded pdb=" OD1 ASN A 841 " pdb="MG MG A1101 " model vdw 2.103 2.170 nonbonded pdb=" OD1 ASP A 837 " pdb="MG MG A1101 " model vdw 2.115 2.170 ... (remaining 197393 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 'E' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 7.100 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 64.250 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.002 0.032 24260 Z= 0.138 Angle : 0.479 14.411 32890 Z= 0.257 Chirality : 0.043 0.163 3448 Planarity : 0.003 0.032 4300 Dihedral : 9.988 75.322 8750 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.21 % Favored : 95.73 % Rotamer: Outliers : 0.04 % Allowed : 4.96 % Favored : 95.00 % 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: 0.29 (0.16), residues: 2972 helix: 1.57 (0.37), residues: 218 sheet: 0.96 (0.15), residues: 1168 loop : -0.59 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 878 HIS 0.004 0.001 HIS E 71 PHE 0.010 0.001 PHE I 558 TYR 0.010 0.001 TYR I 422 ARG 0.001 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 2.811 Fit side-chains REVERT: M 356 MET cc_start: 0.8538 (mmm) cc_final: 0.8085 (mmp) REVERT: A 241 MET cc_start: 0.8922 (ttt) cc_final: 0.8721 (ttt) REVERT: I 241 MET cc_start: 0.9017 (ttt) cc_final: 0.8697 (ttt) REVERT: I 561 MET cc_start: 0.8232 (tmm) cc_final: 0.7967 (tmm) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.3329 time to fit residues: 49.6383 Evaluate side-chains 77 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 151 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 268 optimal weight: 9.9990 overall best weight: 7.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 ASN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 427 ASN ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN A 197 ASN A 309 ASN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN I 197 ASN ** I 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 627 ASN I 754 ASN ** I 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 24260 Z= 0.439 Angle : 0.601 9.922 32890 Z= 0.321 Chirality : 0.045 0.177 3448 Planarity : 0.004 0.033 4300 Dihedral : 4.427 19.828 3290 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.85 % Rotamer: Outliers : 0.67 % Allowed : 7.62 % Favored : 91.71 % 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: -0.04 (0.15), residues: 2972 helix: 0.52 (0.35), residues: 232 sheet: 0.77 (0.15), residues: 1224 loop : -0.77 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 318 HIS 0.005 0.001 HIS I 482 PHE 0.019 0.002 PHE T 72 TYR 0.021 0.002 TYR A 422 ARG 0.004 0.001 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 2.821 Fit side-chains REVERT: E 215 MET cc_start: 0.7107 (mmm) cc_final: 0.6815 (mmm) REVERT: E 216 MET cc_start: 0.7852 (mmm) cc_final: 0.7436 (tpp) REVERT: M 215 MET cc_start: 0.7004 (mmm) cc_final: 0.6781 (mmm) REVERT: G 14 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7989 (t0) REVERT: A 241 MET cc_start: 0.9121 (ttt) cc_final: 0.8832 (ttt) REVERT: A 534 MET cc_start: 0.9230 (mtp) cc_final: 0.8885 (mtt) REVERT: A 561 MET cc_start: 0.8128 (tmm) cc_final: 0.7760 (tmm) REVERT: A 968 MET cc_start: 0.7827 (tpp) cc_final: 0.7492 (tpp) REVERT: I 241 MET cc_start: 0.9150 (ttt) cc_final: 0.8843 (ttt) REVERT: I 561 MET cc_start: 0.8178 (tmm) cc_final: 0.7889 (tmm) REVERT: I 968 MET cc_start: 0.7839 (tpp) cc_final: 0.7341 (tpp) outliers start: 17 outliers final: 8 residues processed: 86 average time/residue: 0.3152 time to fit residues: 47.9331 Evaluate side-chains 86 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain I residue 427 MET Chi-restraints excluded: chain I residue 487 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 290 optimal weight: 9.9990 chunk 239 optimal weight: 0.9980 chunk 267 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN I 361 GLN ** I 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24260 Z= 0.216 Angle : 0.471 7.200 32890 Z= 0.255 Chirality : 0.043 0.154 3448 Planarity : 0.003 0.033 4300 Dihedral : 4.040 18.964 3290 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.27 % Favored : 95.66 % Rotamer: Outliers : 1.11 % Allowed : 8.13 % Favored : 90.75 % 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: 0.07 (0.15), residues: 2972 helix: 0.95 (0.36), residues: 220 sheet: 0.85 (0.15), residues: 1190 loop : -0.73 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 878 HIS 0.003 0.001 HIS E 71 PHE 0.014 0.001 PHE A 758 TYR 0.015 0.001 TYR I 422 ARG 0.002 0.000 ARG I 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 78 time to evaluate : 2.657 Fit side-chains REVERT: E 215 MET cc_start: 0.6961 (mmm) cc_final: 0.6612 (mmm) REVERT: E 216 MET cc_start: 0.7851 (mmm) cc_final: 0.7484 (tpp) REVERT: M 356 MET cc_start: 0.8894 (mmm) cc_final: 0.8525 (mmm) REVERT: A 241 MET cc_start: 0.9011 (ttt) cc_final: 0.8729 (ttt) REVERT: A 561 MET cc_start: 0.8101 (tmm) cc_final: 0.7700 (tmm) REVERT: A 968 MET cc_start: 0.7799 (tpp) cc_final: 0.7517 (tpp) REVERT: A 970 MET cc_start: 0.8295 (ptp) cc_final: 0.7948 (ptp) REVERT: I 241 MET cc_start: 0.9060 (ttt) cc_final: 0.8758 (ttt) REVERT: I 561 MET cc_start: 0.8132 (tmm) cc_final: 0.7801 (tmm) REVERT: I 968 MET cc_start: 0.7812 (tpp) cc_final: 0.7353 (tpt) outliers start: 28 outliers final: 14 residues processed: 96 average time/residue: 0.3152 time to fit residues: 53.3657 Evaluate side-chains 90 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 270 optimal weight: 9.9990 chunk 286 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 256 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 GLN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 GLN ** I 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 24260 Z= 0.429 Angle : 0.560 10.882 32890 Z= 0.300 Chirality : 0.044 0.161 3448 Planarity : 0.003 0.032 4300 Dihedral : 4.442 20.703 3290 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.35 % Favored : 94.55 % Rotamer: Outliers : 1.71 % Allowed : 8.65 % Favored : 89.64 % 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: -0.14 (0.15), residues: 2972 helix: 0.64 (0.36), residues: 218 sheet: 0.61 (0.15), residues: 1230 loop : -0.78 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 318 HIS 0.004 0.001 HIS I 482 PHE 0.018 0.001 PHE A 758 TYR 0.019 0.002 TYR I 422 ARG 0.003 0.000 ARG A 836 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 76 time to evaluate : 3.005 Fit side-chains REVERT: E 229 MET cc_start: 0.9231 (mmm) cc_final: 0.8787 (ttm) REVERT: E 307 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8084 (p0) REVERT: M 307 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8053 (p0) REVERT: A 241 MET cc_start: 0.9063 (ttt) cc_final: 0.8819 (ttt) REVERT: A 534 MET cc_start: 0.9255 (mtp) cc_final: 0.9004 (mtt) REVERT: A 561 MET cc_start: 0.8152 (tmm) cc_final: 0.7783 (tmm) REVERT: A 968 MET cc_start: 0.7970 (tpp) cc_final: 0.7534 (tpp) REVERT: I 241 MET cc_start: 0.9080 (ttt) cc_final: 0.8832 (ttt) REVERT: I 534 MET cc_start: 0.9297 (mtp) cc_final: 0.9018 (mtt) REVERT: I 561 MET cc_start: 0.8161 (tmm) cc_final: 0.7818 (tmm) REVERT: I 968 MET cc_start: 0.8029 (tpp) cc_final: 0.7376 (tpp) outliers start: 43 outliers final: 25 residues processed: 109 average time/residue: 0.3112 time to fit residues: 60.3624 Evaluate side-chains 102 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 75 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 264 ASN Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 361 GLN Chi-restraints excluded: chain I residue 364 THR Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 796 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 0.9990 chunk 162 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 256 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 444 ASN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 ASN M 444 ASN ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24260 Z= 0.181 Angle : 0.468 8.589 32890 Z= 0.253 Chirality : 0.043 0.141 3448 Planarity : 0.003 0.032 4300 Dihedral : 4.135 20.809 3290 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 1.47 % Allowed : 9.37 % 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: -0.05 (0.15), residues: 2972 helix: 0.76 (0.36), residues: 220 sheet: 0.70 (0.15), residues: 1208 loop : -0.73 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 878 HIS 0.004 0.001 HIS E 71 PHE 0.015 0.001 PHE A 758 TYR 0.013 0.001 TYR I 424 ARG 0.002 0.000 ARG M 475 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 77 time to evaluate : 2.623 Fit side-chains REVERT: E 229 MET cc_start: 0.9215 (mmm) cc_final: 0.8808 (ttm) REVERT: A 241 MET cc_start: 0.8988 (ttt) cc_final: 0.8753 (ttt) REVERT: A 561 MET cc_start: 0.8125 (tmm) cc_final: 0.7733 (tmm) REVERT: A 968 MET cc_start: 0.7972 (tpp) cc_final: 0.7564 (tpt) REVERT: I 241 MET cc_start: 0.8989 (ttt) cc_final: 0.8747 (ttt) REVERT: I 534 MET cc_start: 0.9227 (mtp) cc_final: 0.8983 (mtt) REVERT: I 561 MET cc_start: 0.8129 (tmm) cc_final: 0.7721 (tmm) REVERT: I 968 MET cc_start: 0.7950 (tpp) cc_final: 0.7396 (tpt) outliers start: 37 outliers final: 17 residues processed: 105 average time/residue: 0.2980 time to fit residues: 55.8204 Evaluate side-chains 93 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 574 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 20.0000 chunk 257 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 286 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 94 optimal weight: 30.0000 chunk 150 optimal weight: 4.9990 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 ASN ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 24260 Z= 0.368 Angle : 0.540 10.625 32890 Z= 0.289 Chirality : 0.044 0.150 3448 Planarity : 0.003 0.032 4300 Dihedral : 4.366 20.565 3290 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.68 % Rotamer: Outliers : 1.75 % Allowed : 9.84 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 2972 helix: 0.65 (0.36), residues: 218 sheet: 0.54 (0.15), residues: 1230 loop : -0.78 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 685 HIS 0.003 0.001 HIS A 482 PHE 0.015 0.001 PHE A 758 TYR 0.016 0.001 TYR I 422 ARG 0.002 0.000 ARG M 475 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 77 time to evaluate : 2.882 Fit side-chains REVERT: E 229 MET cc_start: 0.9210 (mmm) cc_final: 0.8636 (ttm) REVERT: A 561 MET cc_start: 0.8123 (tmm) cc_final: 0.7746 (tmm) REVERT: A 968 MET cc_start: 0.7822 (tpp) cc_final: 0.7480 (tpt) REVERT: I 241 MET cc_start: 0.9053 (ttt) cc_final: 0.8826 (ttt) REVERT: I 561 MET cc_start: 0.8122 (tmm) cc_final: 0.7716 (tmm) REVERT: I 968 MET cc_start: 0.7941 (tpp) cc_final: 0.7311 (tpp) outliers start: 44 outliers final: 31 residues processed: 111 average time/residue: 0.3127 time to fit residues: 61.1731 Evaluate side-chains 108 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 77 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 264 ASN Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 770 THR Chi-restraints excluded: chain I residue 796 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 241 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 chunk 285 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 248 GLN E 351 GLN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 351 GLN ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN ** I 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 24260 Z= 0.370 Angle : 0.545 10.880 32890 Z= 0.292 Chirality : 0.044 0.164 3448 Planarity : 0.003 0.031 4300 Dihedral : 4.464 22.289 3290 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.89 % Rotamer: Outliers : 1.83 % Allowed : 10.00 % Favored : 88.17 % 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: -0.30 (0.15), residues: 2972 helix: 0.56 (0.36), residues: 218 sheet: 0.44 (0.15), residues: 1218 loop : -0.82 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 685 HIS 0.003 0.001 HIS A 482 PHE 0.015 0.001 PHE A 758 TYR 0.015 0.001 TYR A 422 ARG 0.003 0.000 ARG I 345 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 77 time to evaluate : 2.676 Fit side-chains REVERT: E 229 MET cc_start: 0.9220 (mmm) cc_final: 0.8658 (ttm) REVERT: M 216 MET cc_start: 0.8434 (mmm) cc_final: 0.8009 (tpp) REVERT: M 229 MET cc_start: 0.9231 (mmm) cc_final: 0.8648 (ttm) REVERT: M 356 MET cc_start: 0.8858 (mmm) cc_final: 0.8418 (mmm) REVERT: G 42 TYR cc_start: 0.5475 (OUTLIER) cc_final: 0.3904 (p90) REVERT: A 561 MET cc_start: 0.8117 (tmm) cc_final: 0.7697 (tmm) REVERT: A 968 MET cc_start: 0.7933 (tpp) cc_final: 0.7580 (tpt) REVERT: I 241 MET cc_start: 0.9064 (ttt) cc_final: 0.8845 (ttt) REVERT: I 561 MET cc_start: 0.8126 (tmm) cc_final: 0.7717 (tmm) REVERT: I 968 MET cc_start: 0.7933 (tpp) cc_final: 0.7341 (tpp) outliers start: 46 outliers final: 34 residues processed: 113 average time/residue: 0.2962 time to fit residues: 58.9825 Evaluate side-chains 112 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 77 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain G residue 42 TYR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 364 THR Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 770 THR Chi-restraints excluded: chain I residue 796 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 224 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 124 ASN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24260 Z= 0.235 Angle : 0.495 9.751 32890 Z= 0.265 Chirality : 0.043 0.142 3448 Planarity : 0.003 0.032 4300 Dihedral : 4.256 21.346 3290 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.68 % Favored : 95.15 % Rotamer: Outliers : 1.43 % Allowed : 10.60 % Favored : 87.98 % 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: -0.23 (0.15), residues: 2972 helix: 0.70 (0.37), residues: 218 sheet: 0.51 (0.15), residues: 1214 loop : -0.80 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 878 HIS 0.003 0.001 HIS M 71 PHE 0.015 0.001 PHE A 758 TYR 0.013 0.001 TYR I 422 ARG 0.002 0.000 ARG I 345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 77 time to evaluate : 2.949 Fit side-chains REVERT: E 216 MET cc_start: 0.8437 (mmm) cc_final: 0.7939 (tpp) REVERT: E 229 MET cc_start: 0.9195 (mmm) cc_final: 0.8666 (ttm) REVERT: T 22 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8407 (mt) REVERT: M 216 MET cc_start: 0.8443 (mmm) cc_final: 0.8083 (tpp) REVERT: M 229 MET cc_start: 0.9205 (mmm) cc_final: 0.8645 (ttm) REVERT: M 356 MET cc_start: 0.8861 (mmm) cc_final: 0.8105 (mpp) REVERT: G 42 TYR cc_start: 0.5400 (OUTLIER) cc_final: 0.3846 (p90) REVERT: A 561 MET cc_start: 0.8094 (tmm) cc_final: 0.7668 (tmm) REVERT: A 968 MET cc_start: 0.7939 (tpp) cc_final: 0.7574 (tpt) REVERT: I 241 MET cc_start: 0.9021 (ttt) cc_final: 0.8820 (ttt) REVERT: I 561 MET cc_start: 0.8108 (tmm) cc_final: 0.7681 (tmm) REVERT: I 968 MET cc_start: 0.7849 (tpp) cc_final: 0.7384 (tpp) outliers start: 36 outliers final: 25 residues processed: 102 average time/residue: 0.3136 time to fit residues: 55.9885 Evaluate side-chains 104 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain G residue 42 TYR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 364 THR Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 796 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 6.9990 chunk 273 optimal weight: 10.0000 chunk 249 optimal weight: 5.9990 chunk 265 optimal weight: 8.9990 chunk 160 optimal weight: 0.0570 chunk 115 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 240 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 264 optimal weight: 6.9990 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 24260 Z= 0.307 Angle : 0.516 10.314 32890 Z= 0.277 Chirality : 0.043 0.142 3448 Planarity : 0.003 0.032 4300 Dihedral : 4.328 21.508 3290 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.98 % Favored : 94.92 % Rotamer: Outliers : 1.59 % Allowed : 10.44 % Favored : 87.98 % 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: -0.27 (0.15), residues: 2972 helix: 0.65 (0.37), residues: 218 sheet: 0.48 (0.15), residues: 1214 loop : -0.82 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 685 HIS 0.003 0.001 HIS A 482 PHE 0.015 0.001 PHE A 758 TYR 0.014 0.001 TYR A 422 ARG 0.002 0.000 ARG M 475 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 77 time to evaluate : 3.019 Fit side-chains REVERT: E 215 MET cc_start: 0.7072 (mmm) cc_final: 0.6844 (mmm) REVERT: E 216 MET cc_start: 0.8409 (mmm) cc_final: 0.7941 (tpp) REVERT: E 229 MET cc_start: 0.9215 (mmm) cc_final: 0.8689 (ttm) REVERT: T 22 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8530 (mt) REVERT: M 215 MET cc_start: 0.7358 (mmm) cc_final: 0.7155 (mmm) REVERT: M 216 MET cc_start: 0.8519 (mmm) cc_final: 0.8198 (tpp) REVERT: M 229 MET cc_start: 0.9211 (mmm) cc_final: 0.8644 (ttm) REVERT: M 356 MET cc_start: 0.8860 (mmm) cc_final: 0.8114 (mpp) REVERT: G 42 TYR cc_start: 0.5380 (OUTLIER) cc_final: 0.3798 (p90) REVERT: A 561 MET cc_start: 0.8103 (tmm) cc_final: 0.7674 (tmm) REVERT: A 968 MET cc_start: 0.7967 (tpp) cc_final: 0.7588 (tpt) REVERT: I 561 MET cc_start: 0.8096 (tmm) cc_final: 0.7671 (tmm) REVERT: I 968 MET cc_start: 0.7865 (tpp) cc_final: 0.7396 (tpp) outliers start: 40 outliers final: 34 residues processed: 109 average time/residue: 0.3074 time to fit residues: 59.5556 Evaluate side-chains 113 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 77 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain G residue 42 TYR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 364 THR Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 770 THR Chi-restraints excluded: chain I residue 796 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 6.9990 chunk 281 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 271 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 181 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 692 ASN ** I 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 24260 Z= 0.360 Angle : 0.543 10.431 32890 Z= 0.290 Chirality : 0.044 0.146 3448 Planarity : 0.003 0.031 4300 Dihedral : 4.471 22.059 3290 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.18 % Favored : 94.65 % Rotamer: Outliers : 1.67 % Allowed : 10.40 % Favored : 87.94 % 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: -0.34 (0.15), residues: 2972 helix: 0.57 (0.36), residues: 218 sheet: 0.40 (0.15), residues: 1236 loop : -0.84 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 685 HIS 0.003 0.001 HIS I 482 PHE 0.015 0.001 PHE A 758 TYR 0.015 0.001 TYR A 422 ARG 0.003 0.000 ARG A 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 77 time to evaluate : 3.040 Fit side-chains REVERT: E 229 MET cc_start: 0.9222 (mmm) cc_final: 0.8690 (ttm) REVERT: E 356 MET cc_start: 0.8265 (mmm) cc_final: 0.7817 (mpp) REVERT: T 22 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8553 (mt) REVERT: T 42 TYR cc_start: 0.5474 (OUTLIER) cc_final: 0.4141 (p90) REVERT: M 229 MET cc_start: 0.9220 (mmm) cc_final: 0.8721 (ttm) REVERT: M 356 MET cc_start: 0.8841 (mmm) cc_final: 0.8097 (mpp) REVERT: G 42 TYR cc_start: 0.5507 (OUTLIER) cc_final: 0.3921 (p90) REVERT: A 427 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7456 (mtt) REVERT: A 561 MET cc_start: 0.8107 (tmm) cc_final: 0.7685 (tmm) REVERT: A 968 MET cc_start: 0.8015 (tpp) cc_final: 0.7684 (tpt) REVERT: I 561 MET cc_start: 0.8117 (tmm) cc_final: 0.7690 (tmm) REVERT: I 968 MET cc_start: 0.7936 (tpp) cc_final: 0.7465 (tpp) outliers start: 42 outliers final: 34 residues processed: 111 average time/residue: 0.3123 time to fit residues: 60.8137 Evaluate side-chains 115 residues out of total 2520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 77 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 42 TYR Chi-restraints excluded: chain T residue 56 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain M residue 272 ASN Chi-restraints excluded: chain G residue 42 TYR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 356 ILE Chi-restraints excluded: chain I residue 364 THR Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 469 THR Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 509 MET Chi-restraints excluded: chain I residue 574 THR Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 770 THR Chi-restraints excluded: chain I residue 796 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 6.9990 chunk 250 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 34 optimal weight: 0.0470 chunk 65 optimal weight: 8.9990 chunk 235 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 overall best weight: 4.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 997 ASN ** 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 = 0.3215 r_free = 0.3215 target = 0.040572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.032893 restraints weight = 149736.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.033634 restraints weight = 64582.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.034061 restraints weight = 36962.802| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24260 Z= 0.271 Angle : 0.519 10.395 32890 Z= 0.278 Chirality : 0.043 0.140 3448 Planarity : 0.003 0.031 4300 Dihedral : 4.416 22.142 3290 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.88 % Favored : 94.92 % Rotamer: Outliers : 1.59 % Allowed : 10.40 % Favored : 88.02 % 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: -0.31 (0.15), residues: 2972 helix: 0.60 (0.37), residues: 218 sheet: 0.42 (0.15), residues: 1236 loop : -0.83 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 685 HIS 0.004 0.001 HIS A 362 PHE 0.015 0.001 PHE A 758 TYR 0.014 0.001 TYR A 422 ARG 0.002 0.000 ARG M 475 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3183.12 seconds wall clock time: 60 minutes 52.53 seconds (3652.53 seconds total)