Starting phenix.real_space_refine on Mon Aug 5 11:38:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k87_36946/08_2024/8k87_36946.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k87_36946/08_2024/8k87_36946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k87_36946/08_2024/8k87_36946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k87_36946/08_2024/8k87_36946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k87_36946/08_2024/8k87_36946.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k87_36946/08_2024/8k87_36946.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 88 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 8248 2.51 5 N 2300 2.21 5 O 2690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 27": "OD1" <-> "OD2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 460": "OD1" <-> "OD2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 496": "OE1" <-> "OE2" Residue "B ASP 515": "OD1" <-> "OD2" Residue "B GLU 518": "OE1" <-> "OE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B ASP 564": "OD1" <-> "OD2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F ASP 65": "OD1" <-> "OD2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 91": "OE1" <-> "OE2" Residue "F GLU 112": "OE1" <-> "OE2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 249": "OD1" <-> "OD2" Residue "F GLU 256": "OE1" <-> "OE2" Residue "F ASP 268": "OD1" <-> "OD2" Residue "F TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 314": "OD1" <-> "OD2" Residue "F GLU 315": "OE1" <-> "OE2" Residue "F PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "F TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 371": "OE1" <-> "OE2" Residue "F TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 358": "OE1" <-> "OE2" Residue "G GLU 361": "OE1" <-> "OE2" Residue "G GLU 376": "OE1" <-> "OE2" Residue "G PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 384": "OE1" <-> "OE2" Residue "G TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 423": "OE1" <-> "OE2" Residue "G GLU 432": "OE1" <-> "OE2" Residue "G GLU 519": "OE1" <-> "OE2" Residue "G PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 564": "OD1" <-> "OD2" Residue "G GLU 570": "OE1" <-> "OE2" Residue "G GLU 572": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13372 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 444 Classifications: {'DNA': 1, 'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 16} Chain: "A" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 439} Chain: "B" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2053 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 247} Chain: "H" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "I" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 444 Classifications: {'DNA': 1, 'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 16} Chain: "F" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 439} Chain: "G" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2053 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 247} 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: "F" 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: 7.94, per 1000 atoms: 0.59 Number of scatterers: 13372 At special positions: 0 Unit cell: (92.828, 107.963, 165.476, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 88 15.00 Mg 2 11.99 O 2690 8.00 N 2300 7.00 C 8248 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: 7.59 Conformation dependent library (CDL) restraints added in 2.4 seconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 20 sheets defined 38.2% alpha, 25.1% beta 33 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 60 through 73 removed outlier: 3.825A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.879A pdb=" N GLY A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 134 through 137 Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 151 through 158 removed outlier: 5.004A pdb=" N LYS A 156 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.859A pdb=" N LEU A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 208 removed outlier: 3.748A pdb=" N VAL A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 295 Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.785A pdb=" N PHE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 428 removed outlier: 4.337A pdb=" N THR A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 Processing helix chain 'A' and resid 460 through 463 removed outlier: 4.071A pdb=" N VAL A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'B' and resid 355 through 367 Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.930A pdb=" N ILE B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 414 Processing helix chain 'B' and resid 414 through 430 Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 458 through 465 Processing helix chain 'B' and resid 513 through 519 removed outlier: 4.829A pdb=" N GLU B 518 " --> pdb=" O ASP B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 528 Processing helix chain 'B' and resid 532 through 549 Processing helix chain 'F' and resid 29 through 37 Processing helix chain 'F' and resid 39 through 43 removed outlier: 3.898A pdb=" N CYS F 43 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 73 removed outlier: 3.792A pdb=" N LEU F 64 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 95 Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 111 through 120 removed outlier: 3.816A pdb=" N GLY F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 133 Processing helix chain 'F' and resid 133 through 140 removed outlier: 3.761A pdb=" N PHE F 137 " --> pdb=" O MET F 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 143 No H-bonds generated for 'chain 'F' and resid 141 through 143' Processing helix chain 'F' and resid 151 through 158 removed outlier: 5.017A pdb=" N LYS F 156 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 174 Processing helix chain 'F' and resid 184 through 189 removed outlier: 3.806A pdb=" N LEU F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 208 removed outlier: 3.905A pdb=" N VAL F 196 " --> pdb=" O CYS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 294 Processing helix chain 'F' and resid 312 through 323 removed outlier: 4.094A pdb=" N PHE F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing helix chain 'F' and resid 417 through 428 removed outlier: 4.641A pdb=" N THR F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 459 Processing helix chain 'F' and resid 460 through 463 removed outlier: 4.215A pdb=" N VAL F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 460 through 463' Processing helix chain 'F' and resid 470 through 472 No H-bonds generated for 'chain 'F' and resid 470 through 472' Processing helix chain 'G' and resid 355 through 367 Processing helix chain 'G' and resid 383 through 391 removed outlier: 3.533A pdb=" N ILE G 387 " --> pdb=" O GLY G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 414 Processing helix chain 'G' and resid 414 through 430 Processing helix chain 'G' and resid 455 through 457 No H-bonds generated for 'chain 'G' and resid 455 through 457' Processing helix chain 'G' and resid 458 through 466 Processing helix chain 'G' and resid 513 through 519 removed outlier: 4.938A pdb=" N GLU G 518 " --> pdb=" O ASP G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 520 through 529 Processing helix chain 'G' and resid 532 through 549 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.535A pdb=" N SER A 12 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 331 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 303 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL A 332 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A 305 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE A 334 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS A 307 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA A 223 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N HIS A 306 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 225 " --> pdb=" O HIS A 306 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 232 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 248 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU A 256 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.688A pdb=" N VAL A 50 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N CYS A 107 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR A 54 " --> pdb=" O CYS A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.688A pdb=" N VAL A 50 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG A 51 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU A 147 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA A 53 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N TYR A 149 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU A 55 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 146 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE A 183 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 148 " --> pdb=" O ILE A 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 356 Processing sheet with id=AA6, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA7, first strand: chain 'B' and resid 335 through 338 removed outlier: 4.816A pdb=" N LEU B 501 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N HIS B 444 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 338 removed outlier: 4.816A pdb=" N LEU B 501 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 371 through 374 removed outlier: 3.584A pdb=" N LEU B 371 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 378 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 346 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 556 through 561 removed outlier: 3.607A pdb=" N ALA B 569 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 12 through 13 removed outlier: 6.626A pdb=" N LEU F 331 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA F 223 " --> pdb=" O PHE F 304 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N HIS F 306 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE F 225 " --> pdb=" O HIS F 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 25 through 27 removed outlier: 3.581A pdb=" N LYS F 214 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 98 through 99 removed outlier: 7.073A pdb=" N VAL F 50 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N CYS F 107 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TYR F 54 " --> pdb=" O CYS F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 98 through 99 removed outlier: 7.073A pdb=" N VAL F 50 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ARG F 51 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU F 147 " --> pdb=" O ARG F 51 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA F 53 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR F 149 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 55 " --> pdb=" O TYR F 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 355 through 356 removed outlier: 3.562A pdb=" N ALA F 355 " --> pdb=" O ASP F 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 381 through 382 removed outlier: 3.523A pdb=" N VAL F 394 " --> pdb=" O VAL F 382 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 335 through 337 removed outlier: 3.979A pdb=" N HIS G 444 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 335 through 337 Processing sheet with id=AC1, first strand: chain 'G' and resid 371 through 374 removed outlier: 3.569A pdb=" N VAL G 378 " --> pdb=" O VAL G 348 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER G 398 " --> pdb=" O THR G 349 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 556 through 561 removed outlier: 3.694A pdb=" N ALA G 569 " --> pdb=" O CYS G 561 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 5.56 Time building geometry restraints manager: 8.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3304 1.33 - 1.45: 3132 1.45 - 1.57: 7192 1.57 - 1.69: 176 1.69 - 1.81: 64 Bond restraints: 13868 Sorted by residual: bond pdb=" CB PRO B 353 " pdb=" CG PRO B 353 " ideal model delta sigma weight residual 1.492 1.635 -0.143 5.00e-02 4.00e+02 8.14e+00 bond pdb=" N3 U I 10 " pdb=" C4 U I 10 " ideal model delta sigma weight residual 1.380 1.331 0.049 2.00e-02 2.50e+03 6.02e+00 bond pdb=" CB PRO F 17 " pdb=" CG PRO F 17 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.94e+00 bond pdb=" CB PRO A 179 " pdb=" CG PRO A 179 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.87e+00 bond pdb=" CB GLU G 432 " pdb=" CG GLU G 432 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.75e+00 ... (remaining 13863 not shown) Histogram of bond angle deviations from ideal: 97.19 - 104.55: 561 104.55 - 111.92: 6727 111.92 - 119.28: 4665 119.28 - 126.65: 6790 126.65 - 134.01: 445 Bond angle restraints: 19188 Sorted by residual: angle pdb=" CA PRO B 353 " pdb=" N PRO B 353 " pdb=" CD PRO B 353 " ideal model delta sigma weight residual 112.00 97.45 14.55 1.40e+00 5.10e-01 1.08e+02 angle pdb=" CA PRO F 17 " pdb=" N PRO F 17 " pdb=" CD PRO F 17 " ideal model delta sigma weight residual 112.00 104.72 7.28 1.40e+00 5.10e-01 2.70e+01 angle pdb=" CA PRO A 179 " pdb=" N PRO A 179 " pdb=" CD PRO A 179 " ideal model delta sigma weight residual 112.00 104.75 7.25 1.40e+00 5.10e-01 2.68e+01 angle pdb=" CA GLU G 432 " pdb=" CB GLU G 432 " pdb=" CG GLU G 432 " ideal model delta sigma weight residual 114.10 122.99 -8.89 2.00e+00 2.50e-01 1.98e+01 angle pdb=" CB MET A 383 " pdb=" CG MET A 383 " pdb=" SD MET A 383 " ideal model delta sigma weight residual 112.70 125.17 -12.47 3.00e+00 1.11e-01 1.73e+01 ... (remaining 19183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 7710 35.24 - 70.48: 492 70.48 - 105.72: 25 105.72 - 140.96: 2 140.96 - 176.20: 5 Dihedral angle restraints: 8234 sinusoidal: 4014 harmonic: 4220 Sorted by residual: dihedral pdb=" O4' U I 10 " pdb=" C1' U I 10 " pdb=" N1 U I 10 " pdb=" C2 U I 10 " ideal model delta sinusoidal sigma weight residual 200.00 23.80 176.20 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U I 8 " pdb=" C1' U I 8 " pdb=" N1 U I 8 " pdb=" C2 U I 8 " ideal model delta sinusoidal sigma weight residual 200.00 30.20 169.80 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U I 2 " pdb=" C1' U I 2 " pdb=" N1 U I 2 " pdb=" C2 U I 2 " ideal model delta sinusoidal sigma weight residual -160.00 -1.21 -158.79 1 1.50e+01 4.44e-03 8.24e+01 ... (remaining 8231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1815 0.057 - 0.113: 291 0.113 - 0.170: 35 0.170 - 0.226: 5 0.226 - 0.283: 2 Chirality restraints: 2148 Sorted by residual: chirality pdb=" C1' G D 7 " pdb=" O4' G D 7 " pdb=" C2' G D 7 " pdb=" N9 G D 7 " both_signs ideal model delta sigma weight residual False 2.46 2.17 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA PRO B 353 " pdb=" N PRO B 353 " pdb=" C PRO B 353 " pdb=" CB PRO B 353 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CG LEU A 46 " pdb=" CB LEU A 46 " pdb=" CD1 LEU A 46 " pdb=" CD2 LEU A 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2145 not shown) Planarity restraints: 2152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 352 " 0.094 5.00e-02 4.00e+02 1.30e-01 2.71e+01 pdb=" N PRO B 353 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO B 353 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO B 353 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 178 " -0.085 5.00e-02 4.00e+02 1.25e-01 2.50e+01 pdb=" N PRO A 179 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 367 " -0.070 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO B 368 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO B 368 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 368 " -0.056 5.00e-02 4.00e+02 ... (remaining 2149 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 125 2.52 - 3.12: 9715 3.12 - 3.71: 21751 3.71 - 4.31: 29834 4.31 - 4.90: 48733 Nonbonded interactions: 110158 Sorted by model distance: nonbonded pdb=" OP2 A D 1 " pdb="MG MG A 501 " model vdw 1.929 2.170 nonbonded pdb=" OXT MET A 473 " pdb="MG MG A 501 " model vdw 1.969 2.170 nonbonded pdb=" ND2 ASN A 434 " pdb="MG MG A 501 " model vdw 2.001 2.250 nonbonded pdb=" OG1 THR F 312 " pdb=" OD1 ASP F 314 " model vdw 2.122 3.040 nonbonded pdb=" O LEU A 426 " pdb=" OG1 THR A 429 " model vdw 2.133 3.040 ... (remaining 110153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 45.620 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.004 0.143 13868 Z= 0.245 Angle : 0.766 14.548 19188 Z= 0.418 Chirality : 0.043 0.283 2148 Planarity : 0.007 0.130 2152 Dihedral : 20.688 176.198 5522 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.09 % Allowed : 36.90 % Favored : 61.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 0.41 (0.22), residues: 1444 helix: 1.50 (0.25), residues: 430 sheet: 0.98 (0.30), residues: 314 loop : -0.86 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 218 HIS 0.008 0.001 HIS A 114 PHE 0.027 0.002 PHE A 143 TYR 0.046 0.002 TYR F 84 ARG 0.014 0.001 ARG G 527 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 250 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8858 (mm) cc_final: 0.8585 (mt) REVERT: A 70 GLU cc_start: 0.8822 (tt0) cc_final: 0.8214 (tt0) REVERT: A 133 MET cc_start: 0.8162 (ptt) cc_final: 0.7912 (ptp) REVERT: A 197 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6245 (mpp) REVERT: A 439 TYR cc_start: 0.7710 (p90) cc_final: 0.7326 (p90) REVERT: B 360 LYS cc_start: 0.8839 (mtpm) cc_final: 0.8469 (pptt) REVERT: B 561 CYS cc_start: 0.7575 (t) cc_final: 0.6489 (p) REVERT: F 214 LYS cc_start: 0.8627 (ptmm) cc_final: 0.8393 (ptpp) REVERT: F 220 LYS cc_start: 0.8374 (ptpt) cc_final: 0.7950 (ptmt) REVERT: F 264 GLU cc_start: 0.8204 (tt0) cc_final: 0.7962 (tp30) REVERT: F 299 MET cc_start: 0.8531 (ptp) cc_final: 0.7886 (ppp) REVERT: F 428 LEU cc_start: 0.8768 (mm) cc_final: 0.8416 (tp) REVERT: F 467 TYR cc_start: 0.7944 (m-80) cc_final: 0.7692 (m-80) REVERT: G 506 LYS cc_start: 0.8825 (mttp) cc_final: 0.8558 (tptp) outliers start: 26 outliers final: 22 residues processed: 270 average time/residue: 0.9474 time to fit residues: 285.9732 Evaluate side-chains 251 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 228 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 478 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 117 optimal weight: 0.0370 chunk 45 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 392 GLN F 184 ASN F 310 HIS G 441 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13868 Z= 0.194 Angle : 0.629 7.953 19188 Z= 0.332 Chirality : 0.042 0.166 2148 Planarity : 0.006 0.069 2152 Dihedral : 19.573 163.539 2777 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.10 % Allowed : 28.54 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 0.51 (0.22), residues: 1444 helix: 1.34 (0.24), residues: 456 sheet: 0.82 (0.28), residues: 352 loop : -0.65 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 510 HIS 0.023 0.001 HIS G 441 PHE 0.027 0.002 PHE A 143 TYR 0.024 0.002 TYR F 84 ARG 0.008 0.001 ARG G 527 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 258 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8788 (tt0) cc_final: 0.8405 (tt0) REVERT: A 221 ASP cc_start: 0.8155 (m-30) cc_final: 0.7886 (m-30) REVERT: A 385 VAL cc_start: 0.8733 (m) cc_final: 0.8467 (t) REVERT: A 392 GLN cc_start: 0.8483 (tt0) cc_final: 0.8253 (tt0) REVERT: B 360 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8435 (pptt) REVERT: B 369 LYS cc_start: 0.8546 (mmpt) cc_final: 0.8240 (mmpt) REVERT: B 384 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: B 401 GLN cc_start: 0.8534 (pm20) cc_final: 0.8095 (pp30) REVERT: B 561 CYS cc_start: 0.7571 (t) cc_final: 0.6692 (p) REVERT: F 61 MET cc_start: 0.8717 (mmt) cc_final: 0.8302 (mmt) REVERT: F 107 CYS cc_start: 0.8014 (t) cc_final: 0.7590 (p) REVERT: F 220 LYS cc_start: 0.8510 (ptpt) cc_final: 0.8203 (ptpt) REVERT: F 299 MET cc_start: 0.8488 (ptp) cc_final: 0.7862 (ppp) REVERT: F 370 THR cc_start: 0.8726 (t) cc_final: 0.8499 (p) REVERT: F 428 LEU cc_start: 0.8541 (mm) cc_final: 0.8248 (tp) REVERT: G 477 ASN cc_start: 0.8669 (m-40) cc_final: 0.8426 (t0) outliers start: 51 outliers final: 24 residues processed: 284 average time/residue: 0.9231 time to fit residues: 294.7674 Evaluate side-chains 262 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 236 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 509 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 147 optimal weight: 0.0670 chunk 121 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN F 195 ASN ** G 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13868 Z= 0.258 Angle : 0.626 8.483 19188 Z= 0.328 Chirality : 0.042 0.166 2148 Planarity : 0.005 0.058 2152 Dihedral : 19.443 170.210 2759 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.78 % Allowed : 30.14 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 0.46 (0.22), residues: 1444 helix: 1.41 (0.24), residues: 442 sheet: 0.69 (0.28), residues: 354 loop : -0.67 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 340 HIS 0.006 0.001 HIS A 114 PHE 0.012 0.002 PHE F 44 TYR 0.028 0.002 TYR F 84 ARG 0.006 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 253 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8455 (t0) cc_final: 0.8233 (t0) REVERT: A 220 LYS cc_start: 0.8103 (mttm) cc_final: 0.7829 (mttt) REVERT: A 392 GLN cc_start: 0.8533 (tt0) cc_final: 0.8248 (tt0) REVERT: B 360 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8409 (pptt) REVERT: B 384 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8344 (mp0) REVERT: B 401 GLN cc_start: 0.8604 (pm20) cc_final: 0.8180 (pp30) REVERT: B 519 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: B 561 CYS cc_start: 0.7528 (t) cc_final: 0.6614 (p) REVERT: F 55 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7742 (tp) REVERT: F 61 MET cc_start: 0.8799 (mmt) cc_final: 0.8397 (mmt) REVERT: F 83 TYR cc_start: 0.8294 (t80) cc_final: 0.8009 (t80) REVERT: F 220 LYS cc_start: 0.8574 (ptpt) cc_final: 0.8262 (ptpt) REVERT: F 232 LYS cc_start: 0.8988 (ttpp) cc_final: 0.8660 (tttm) REVERT: F 370 THR cc_start: 0.8794 (t) cc_final: 0.8580 (p) REVERT: G 377 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8095 (mptt) REVERT: G 401 GLN cc_start: 0.7780 (pp30) cc_final: 0.7576 (pp30) outliers start: 47 outliers final: 29 residues processed: 281 average time/residue: 0.8723 time to fit residues: 275.9127 Evaluate side-chains 272 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 238 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 0.0870 chunk 91 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN B 334 ASN F 195 ASN G 437 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13868 Z= 0.198 Angle : 0.605 9.124 19188 Z= 0.316 Chirality : 0.041 0.189 2148 Planarity : 0.005 0.053 2152 Dihedral : 19.272 168.577 2755 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.18 % Allowed : 29.58 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 0.64 (0.22), residues: 1444 helix: 1.66 (0.25), residues: 430 sheet: 0.67 (0.28), residues: 354 loop : -0.51 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 340 HIS 0.006 0.001 HIS A 114 PHE 0.028 0.002 PHE A 143 TYR 0.027 0.002 TYR A 439 ARG 0.009 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 256 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8677 (tt0) cc_final: 0.8453 (tt0) REVERT: A 121 ASN cc_start: 0.8433 (t0) cc_final: 0.8179 (t0) REVERT: A 220 LYS cc_start: 0.7985 (mttm) cc_final: 0.7717 (mttt) REVERT: A 221 ASP cc_start: 0.7973 (m-30) cc_final: 0.7515 (p0) REVERT: A 222 GLU cc_start: 0.6443 (mm-30) cc_final: 0.5953 (mm-30) REVERT: A 375 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8537 (mp) REVERT: A 392 GLN cc_start: 0.8489 (tt0) cc_final: 0.8235 (tt0) REVERT: B 360 LYS cc_start: 0.8835 (mtpm) cc_final: 0.8387 (pptt) REVERT: B 384 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8318 (mp0) REVERT: B 401 GLN cc_start: 0.8652 (pm20) cc_final: 0.8227 (pp30) REVERT: B 561 CYS cc_start: 0.7467 (t) cc_final: 0.6580 (p) REVERT: F 61 MET cc_start: 0.8787 (mmt) cc_final: 0.8397 (mmt) REVERT: F 107 CYS cc_start: 0.8080 (t) cc_final: 0.7603 (p) REVERT: F 214 LYS cc_start: 0.9037 (ptmm) cc_final: 0.8540 (ptmm) REVERT: F 220 LYS cc_start: 0.8567 (ptpt) cc_final: 0.8128 (ptmt) REVERT: F 370 THR cc_start: 0.8769 (t) cc_final: 0.8547 (p) REVERT: G 377 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8056 (mptt) REVERT: G 401 GLN cc_start: 0.7827 (pp30) cc_final: 0.7581 (pp30) REVERT: G 477 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8367 (t0) REVERT: G 512 LYS cc_start: 0.8741 (tttt) cc_final: 0.8528 (tttp) outliers start: 52 outliers final: 33 residues processed: 287 average time/residue: 0.9055 time to fit residues: 291.8200 Evaluate side-chains 277 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 240 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 396 ILE Chi-restraints excluded: chain G residue 477 ASN Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN B 534 GLN ** F 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13868 Z= 0.336 Angle : 0.657 9.178 19188 Z= 0.345 Chirality : 0.044 0.200 2148 Planarity : 0.005 0.055 2152 Dihedral : 19.174 175.037 2755 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.98 % Allowed : 29.58 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 0.32 (0.22), residues: 1444 helix: 1.39 (0.25), residues: 442 sheet: 0.62 (0.29), residues: 342 loop : -0.81 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 340 HIS 0.005 0.001 HIS A 114 PHE 0.023 0.002 PHE A 143 TYR 0.024 0.002 TYR F 84 ARG 0.010 0.001 ARG F 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 253 time to evaluate : 1.333 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8612 (tp) REVERT: A 70 GLU cc_start: 0.8726 (tt0) cc_final: 0.8173 (tt0) REVERT: A 121 ASN cc_start: 0.8552 (t0) cc_final: 0.8263 (t0) REVERT: A 197 MET cc_start: 0.7915 (tpp) cc_final: 0.7462 (mpp) REVERT: A 248 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.7287 (p90) REVERT: A 285 SER cc_start: 0.8507 (m) cc_final: 0.8104 (p) REVERT: A 392 GLN cc_start: 0.8538 (tt0) cc_final: 0.8290 (tt0) REVERT: B 384 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: B 401 GLN cc_start: 0.8681 (pm20) cc_final: 0.8078 (pp30) REVERT: B 442 ARG cc_start: 0.8728 (ttm110) cc_final: 0.8340 (mtp-110) REVERT: B 561 CYS cc_start: 0.7596 (t) cc_final: 0.6742 (p) REVERT: F 55 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7821 (tp) REVERT: F 61 MET cc_start: 0.8818 (mmt) cc_final: 0.8453 (mmt) REVERT: F 214 LYS cc_start: 0.9055 (ptmm) cc_final: 0.8562 (ptmm) REVERT: F 220 LYS cc_start: 0.8643 (ptpt) cc_final: 0.8305 (ptpt) REVERT: F 233 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8330 (tppt) REVERT: F 370 THR cc_start: 0.8837 (t) cc_final: 0.8611 (p) REVERT: G 342 SER cc_start: 0.8473 (p) cc_final: 0.8179 (m) REVERT: G 357 SER cc_start: 0.9348 (OUTLIER) cc_final: 0.9085 (p) REVERT: G 377 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8077 (mptt) REVERT: G 401 GLN cc_start: 0.7959 (pp30) cc_final: 0.7753 (pp30) REVERT: G 441 HIS cc_start: 0.7846 (t-90) cc_final: 0.7587 (t70) REVERT: G 477 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8409 (t0) outliers start: 62 outliers final: 38 residues processed: 290 average time/residue: 0.8376 time to fit residues: 275.6694 Evaluate side-chains 296 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 251 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 477 ASN Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN F 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13868 Z= 0.284 Angle : 0.655 9.493 19188 Z= 0.344 Chirality : 0.043 0.212 2148 Planarity : 0.005 0.054 2152 Dihedral : 19.140 172.361 2754 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.74 % Allowed : 30.71 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 0.28 (0.22), residues: 1444 helix: 1.38 (0.25), residues: 444 sheet: 0.52 (0.29), residues: 342 loop : -0.82 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 340 HIS 0.005 0.001 HIS A 114 PHE 0.026 0.002 PHE F 265 TYR 0.046 0.002 TYR F 84 ARG 0.012 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 261 time to evaluate : 1.431 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8748 (tt0) cc_final: 0.8222 (tt0) REVERT: A 121 ASN cc_start: 0.8572 (t0) cc_final: 0.8242 (t0) REVERT: A 197 MET cc_start: 0.7912 (tpp) cc_final: 0.7463 (mpp) REVERT: A 285 SER cc_start: 0.8467 (m) cc_final: 0.8076 (p) REVERT: A 392 GLN cc_start: 0.8488 (tt0) cc_final: 0.8254 (tt0) REVERT: B 371 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8572 (pp) REVERT: B 384 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8357 (mp0) REVERT: B 401 GLN cc_start: 0.8652 (pm20) cc_final: 0.8434 (pm20) REVERT: B 442 ARG cc_start: 0.8730 (ttm110) cc_final: 0.8306 (mtp-110) REVERT: B 561 CYS cc_start: 0.7585 (t) cc_final: 0.6784 (p) REVERT: F 55 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7826 (tp) REVERT: F 61 MET cc_start: 0.8776 (mmt) cc_final: 0.8455 (mmt) REVERT: F 214 LYS cc_start: 0.9064 (ptmm) cc_final: 0.8560 (ptmm) REVERT: F 370 THR cc_start: 0.8824 (t) cc_final: 0.8587 (p) REVERT: G 342 SER cc_start: 0.8453 (p) cc_final: 0.8175 (m) REVERT: G 357 SER cc_start: 0.9339 (OUTLIER) cc_final: 0.9083 (p) REVERT: G 377 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8063 (mptt) REVERT: G 401 GLN cc_start: 0.8002 (pp30) cc_final: 0.7679 (pp30) REVERT: G 441 HIS cc_start: 0.7838 (t-90) cc_final: 0.7600 (t70) REVERT: G 477 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8398 (t0) REVERT: G 504 MET cc_start: 0.9172 (mmm) cc_final: 0.8668 (mmp) outliers start: 59 outliers final: 37 residues processed: 293 average time/residue: 0.8834 time to fit residues: 292.1254 Evaluate side-chains 293 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 250 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 355 THR Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 477 ASN Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.3980 chunk 82 optimal weight: 0.1980 chunk 105 optimal weight: 0.1980 chunk 122 optimal weight: 0.0970 chunk 81 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 0.0270 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.1836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13868 Z= 0.179 Angle : 0.639 10.398 19188 Z= 0.334 Chirality : 0.042 0.199 2148 Planarity : 0.004 0.048 2152 Dihedral : 19.098 167.574 2752 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.46 % Allowed : 32.56 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 0.61 (0.22), residues: 1444 helix: 1.79 (0.25), residues: 432 sheet: 0.55 (0.29), residues: 342 loop : -0.56 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 543 HIS 0.004 0.001 HIS A 114 PHE 0.028 0.001 PHE A 143 TYR 0.025 0.002 TYR F 240 ARG 0.008 0.000 ARG F 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 269 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8685 (tt0) cc_final: 0.8279 (tt0) REVERT: A 121 ASN cc_start: 0.8482 (t0) cc_final: 0.8190 (t0) REVERT: A 197 MET cc_start: 0.7805 (tpp) cc_final: 0.7377 (mpp) REVERT: A 285 SER cc_start: 0.8560 (m) cc_final: 0.8165 (p) REVERT: A 385 VAL cc_start: 0.8741 (m) cc_final: 0.8489 (t) REVERT: B 371 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8561 (pp) REVERT: B 384 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: B 401 GLN cc_start: 0.8626 (pm20) cc_final: 0.8012 (pp30) REVERT: B 442 ARG cc_start: 0.8678 (ttm110) cc_final: 0.8255 (mtp-110) REVERT: B 561 CYS cc_start: 0.7513 (t) cc_final: 0.6702 (p) REVERT: F 46 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8380 (pp) REVERT: F 61 MET cc_start: 0.8760 (mmt) cc_final: 0.8390 (mmt) REVERT: F 69 ARG cc_start: 0.8294 (mtp-110) cc_final: 0.8059 (ptm-80) REVERT: F 107 CYS cc_start: 0.8024 (t) cc_final: 0.7682 (p) REVERT: F 214 LYS cc_start: 0.9016 (ptmm) cc_final: 0.8467 (ptmm) REVERT: F 220 LYS cc_start: 0.8600 (ptpt) cc_final: 0.8299 (ptpt) REVERT: F 328 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: F 370 THR cc_start: 0.8760 (t) cc_final: 0.8532 (p) REVERT: G 342 SER cc_start: 0.8379 (p) cc_final: 0.8094 (m) REVERT: G 377 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8249 (mptt) REVERT: G 401 GLN cc_start: 0.7999 (pp30) cc_final: 0.7593 (pp30) REVERT: G 441 HIS cc_start: 0.7714 (t-90) cc_final: 0.7464 (t70) REVERT: G 477 ASN cc_start: 0.8509 (m-40) cc_final: 0.8303 (t0) outliers start: 43 outliers final: 26 residues processed: 294 average time/residue: 0.9052 time to fit residues: 299.8494 Evaluate side-chains 285 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 254 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 355 THR Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 478 VAL Chi-restraints excluded: chain G residue 485 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 113 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN G 437 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13868 Z= 0.238 Angle : 0.670 11.629 19188 Z= 0.349 Chirality : 0.042 0.182 2148 Planarity : 0.005 0.056 2152 Dihedral : 18.993 171.497 2750 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.30 % Allowed : 32.96 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 0.47 (0.22), residues: 1444 helix: 1.62 (0.25), residues: 444 sheet: 0.54 (0.29), residues: 342 loop : -0.70 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 340 HIS 0.005 0.001 HIS A 114 PHE 0.025 0.002 PHE F 323 TYR 0.022 0.002 TYR F 240 ARG 0.014 0.001 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 256 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8692 (tt0) cc_final: 0.8160 (tt0) REVERT: A 121 ASN cc_start: 0.8528 (t0) cc_final: 0.8261 (t0) REVERT: A 197 MET cc_start: 0.7856 (tpp) cc_final: 0.7422 (mpp) REVERT: A 285 SER cc_start: 0.8606 (m) cc_final: 0.8197 (p) REVERT: A 376 LEU cc_start: 0.8814 (tm) cc_final: 0.8577 (tt) REVERT: B 371 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8475 (pp) REVERT: B 384 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: B 401 GLN cc_start: 0.8648 (pm20) cc_final: 0.8069 (pp30) REVERT: B 442 ARG cc_start: 0.8704 (ttm110) cc_final: 0.8276 (mtp-110) REVERT: B 561 CYS cc_start: 0.7557 (t) cc_final: 0.6720 (p) REVERT: F 46 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8379 (pp) REVERT: F 61 MET cc_start: 0.8794 (mmt) cc_final: 0.8486 (mmt) REVERT: F 69 ARG cc_start: 0.8319 (mtp-110) cc_final: 0.8099 (ptm-80) REVERT: F 107 CYS cc_start: 0.8061 (t) cc_final: 0.7738 (p) REVERT: F 133 MET cc_start: 0.8549 (ptp) cc_final: 0.8325 (ttp) REVERT: F 214 LYS cc_start: 0.9032 (ptmm) cc_final: 0.8499 (ptmm) REVERT: F 220 LYS cc_start: 0.8696 (ptpt) cc_final: 0.8376 (ptpt) REVERT: F 328 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7849 (mm-30) REVERT: F 370 THR cc_start: 0.8787 (t) cc_final: 0.8565 (p) REVERT: G 342 SER cc_start: 0.8431 (p) cc_final: 0.8176 (m) REVERT: G 357 SER cc_start: 0.9340 (OUTLIER) cc_final: 0.9086 (p) REVERT: G 377 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8074 (mptt) REVERT: G 401 GLN cc_start: 0.8046 (pp30) cc_final: 0.7631 (pp30) REVERT: G 441 HIS cc_start: 0.7804 (t-90) cc_final: 0.7546 (t70) REVERT: G 477 ASN cc_start: 0.8554 (m-40) cc_final: 0.8343 (t0) outliers start: 41 outliers final: 26 residues processed: 278 average time/residue: 0.8606 time to fit residues: 270.5527 Evaluate side-chains 278 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 246 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 355 THR Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 0.0170 chunk 41 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13868 Z= 0.204 Angle : 0.669 12.402 19188 Z= 0.350 Chirality : 0.042 0.211 2148 Planarity : 0.005 0.060 2152 Dihedral : 18.983 169.573 2750 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.22 % Allowed : 33.12 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 0.52 (0.22), residues: 1444 helix: 1.70 (0.25), residues: 440 sheet: 0.54 (0.29), residues: 342 loop : -0.67 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 340 HIS 0.004 0.001 HIS A 114 PHE 0.030 0.001 PHE F 323 TYR 0.033 0.002 TYR F 240 ARG 0.014 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 265 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8697 (tt0) cc_final: 0.8129 (tt0) REVERT: A 121 ASN cc_start: 0.8512 (t0) cc_final: 0.8235 (t0) REVERT: A 197 MET cc_start: 0.7847 (tpp) cc_final: 0.7368 (mpp) REVERT: A 220 LYS cc_start: 0.7820 (tppt) cc_final: 0.7557 (tppt) REVERT: A 285 SER cc_start: 0.8664 (m) cc_final: 0.8287 (p) REVERT: A 376 LEU cc_start: 0.8800 (tm) cc_final: 0.8566 (tt) REVERT: B 371 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8486 (pp) REVERT: B 384 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8335 (mp0) REVERT: B 401 GLN cc_start: 0.8646 (pm20) cc_final: 0.8077 (pp30) REVERT: B 442 ARG cc_start: 0.8665 (ttm110) cc_final: 0.8224 (mtp-110) REVERT: B 480 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8131 (t0) REVERT: B 561 CYS cc_start: 0.7556 (t) cc_final: 0.6709 (p) REVERT: F 46 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8475 (pp) REVERT: F 61 MET cc_start: 0.8781 (mmt) cc_final: 0.8488 (mmt) REVERT: F 133 MET cc_start: 0.8482 (ptp) cc_final: 0.8281 (ttp) REVERT: F 214 LYS cc_start: 0.9035 (ptmm) cc_final: 0.8496 (ptmm) REVERT: F 220 LYS cc_start: 0.8710 (ptpt) cc_final: 0.8385 (ptpt) REVERT: F 328 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7871 (mm-30) REVERT: F 370 THR cc_start: 0.8776 (t) cc_final: 0.8551 (p) REVERT: G 342 SER cc_start: 0.8372 (p) cc_final: 0.8098 (m) REVERT: G 377 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8070 (mptt) REVERT: G 401 GLN cc_start: 0.8024 (pp30) cc_final: 0.7568 (pp30) REVERT: G 441 HIS cc_start: 0.7768 (t-90) cc_final: 0.7500 (t70) REVERT: G 477 ASN cc_start: 0.8520 (m-40) cc_final: 0.8316 (t0) outliers start: 40 outliers final: 31 residues processed: 286 average time/residue: 0.9028 time to fit residues: 291.2094 Evaluate side-chains 292 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 255 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 355 THR Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13868 Z= 0.230 Angle : 0.690 12.851 19188 Z= 0.360 Chirality : 0.043 0.232 2148 Planarity : 0.005 0.059 2152 Dihedral : 18.957 171.203 2750 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.22 % Allowed : 33.76 % Favored : 63.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 0.55 (0.22), residues: 1444 helix: 1.82 (0.25), residues: 416 sheet: 0.48 (0.29), residues: 342 loop : -0.58 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 340 HIS 0.004 0.001 HIS A 114 PHE 0.025 0.002 PHE A 143 TYR 0.030 0.002 TYR F 240 ARG 0.017 0.001 ARG A 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 256 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8801 (mm) cc_final: 0.8523 (mt) REVERT: A 70 GLU cc_start: 0.8676 (tt0) cc_final: 0.8132 (tt0) REVERT: A 121 ASN cc_start: 0.8511 (t0) cc_final: 0.8227 (t0) REVERT: A 197 MET cc_start: 0.7849 (tpp) cc_final: 0.7366 (mpp) REVERT: A 285 SER cc_start: 0.8732 (m) cc_final: 0.8311 (p) REVERT: A 302 LYS cc_start: 0.8211 (tttt) cc_final: 0.7970 (tttm) REVERT: A 376 LEU cc_start: 0.8786 (tm) cc_final: 0.8543 (tt) REVERT: B 371 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8474 (pp) REVERT: B 384 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: B 401 GLN cc_start: 0.8637 (pm20) cc_final: 0.8095 (pp30) REVERT: B 403 TYR cc_start: 0.8118 (m-10) cc_final: 0.7860 (m-10) REVERT: B 442 ARG cc_start: 0.8681 (ttm110) cc_final: 0.8241 (mtp-110) REVERT: B 480 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8164 (t0) REVERT: B 561 CYS cc_start: 0.7575 (t) cc_final: 0.6707 (p) REVERT: F 46 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8439 (pp) REVERT: F 61 MET cc_start: 0.8788 (mmt) cc_final: 0.8440 (mmt) REVERT: F 70 GLU cc_start: 0.8882 (pt0) cc_final: 0.8598 (pp20) REVERT: F 133 MET cc_start: 0.8498 (ptp) cc_final: 0.8274 (ttp) REVERT: F 214 LYS cc_start: 0.9039 (ptmm) cc_final: 0.8491 (ptmm) REVERT: F 220 LYS cc_start: 0.8735 (ptpt) cc_final: 0.8400 (ptpt) REVERT: F 328 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7870 (mm-30) REVERT: F 370 THR cc_start: 0.8787 (t) cc_final: 0.8564 (p) REVERT: G 342 SER cc_start: 0.8371 (p) cc_final: 0.8086 (m) REVERT: G 377 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8037 (mptt) REVERT: G 401 GLN cc_start: 0.8038 (pp30) cc_final: 0.7578 (pp30) REVERT: G 441 HIS cc_start: 0.7810 (t-90) cc_final: 0.7547 (t70) REVERT: G 477 ASN cc_start: 0.8537 (m-40) cc_final: 0.8330 (t0) outliers start: 40 outliers final: 31 residues processed: 274 average time/residue: 0.8721 time to fit residues: 269.4232 Evaluate side-chains 292 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 255 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 401 THR Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 347 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 355 THR Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 119 ASN F 73 ASN F 131 GLN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.101458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.087162 restraints weight = 26640.421| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.04 r_work: 0.3387 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13868 Z= 0.206 Angle : 0.677 12.623 19188 Z= 0.353 Chirality : 0.042 0.219 2148 Planarity : 0.005 0.050 2152 Dihedral : 18.941 169.383 2750 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.97 % Allowed : 34.16 % Favored : 62.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 0.61 (0.22), residues: 1444 helix: 1.87 (0.25), residues: 416 sheet: 0.49 (0.29), residues: 342 loop : -0.54 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 543 HIS 0.004 0.001 HIS A 114 PHE 0.025 0.001 PHE A 143 TYR 0.025 0.002 TYR F 240 ARG 0.009 0.001 ARG A 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4927.89 seconds wall clock time: 87 minutes 7.06 seconds (5227.06 seconds total)