Starting phenix.real_space_refine on Fri Mar 15 09:54:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/03_2024/6zn2_11309_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/03_2024/6zn2_11309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/03_2024/6zn2_11309.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/03_2024/6zn2_11309.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/03_2024/6zn2_11309_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/03_2024/6zn2_11309_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 36 5.16 5 C 7192 2.51 5 N 1932 2.21 5 O 2156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11320 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "B" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 130 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "C" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "D" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 130 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "E" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "F" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 130 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "G" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "H" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 130 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.47, per 1000 atoms: 0.57 Number of scatterers: 11320 At special positions: 0 Unit cell: (106.05, 87.15, 121.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 36 16.00 O 2156 8.00 N 1932 7.00 C 7192 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: 4.91 Conformation dependent library (CDL) restraints added in 2.3 seconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 16 sheets defined 51.6% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.531A pdb=" N ASP A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 226 through 243 removed outlier: 3.707A pdb=" N GLY A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 261 removed outlier: 3.840A pdb=" N GLU A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 282 removed outlier: 3.585A pdb=" N LYS A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 437 through 450 removed outlier: 3.852A pdb=" N LEU A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 495 removed outlier: 3.581A pdb=" N ARG A 477 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLY A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 485 " --> pdb=" O GLY A 481 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 486 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS A 491 " --> pdb=" O ASP A 487 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 492 " --> pdb=" O THR A 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'C' and resid 170 through 179 removed outlier: 3.531A pdb=" N ASP C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 226 through 243 removed outlier: 3.706A pdb=" N GLY C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 242 " --> pdb=" O THR C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 261 removed outlier: 3.840A pdb=" N GLU C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 282 removed outlier: 3.586A pdb=" N LYS C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 305 Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 360 through 373 Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 414 through 418 Processing helix chain 'C' and resid 437 through 450 removed outlier: 3.852A pdb=" N LEU C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 495 removed outlier: 3.581A pdb=" N ARG C 477 " --> pdb=" O GLN C 473 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU C 480 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLY C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU C 485 " --> pdb=" O GLY C 481 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU C 486 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS C 491 " --> pdb=" O ASP C 487 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 492 " --> pdb=" O THR C 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'E' and resid 170 through 179 removed outlier: 3.531A pdb=" N ASP E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 226 through 243 removed outlier: 3.706A pdb=" N GLY E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 242 " --> pdb=" O THR E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 261 removed outlier: 3.840A pdb=" N GLU E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA E 254 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 282 removed outlier: 3.585A pdb=" N LYS E 280 " --> pdb=" O SER E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 305 Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 360 through 373 Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 414 through 418 Processing helix chain 'E' and resid 437 through 450 removed outlier: 3.852A pdb=" N LEU E 444 " --> pdb=" O ALA E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 495 removed outlier: 3.582A pdb=" N ARG E 477 " --> pdb=" O GLN E 473 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER E 478 " --> pdb=" O ALA E 474 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLY E 481 " --> pdb=" O ARG E 477 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU E 485 " --> pdb=" O GLY E 481 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU E 486 " --> pdb=" O VAL E 482 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA E 490 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS E 491 " --> pdb=" O ASP E 487 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA E 492 " --> pdb=" O THR E 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 48 through 56 Processing helix chain 'G' and resid 170 through 179 removed outlier: 3.530A pdb=" N ASP G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS G 176 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 211 Processing helix chain 'G' and resid 226 through 243 removed outlier: 3.706A pdb=" N GLY G 241 " --> pdb=" O THR G 237 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G 242 " --> pdb=" O THR G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 261 removed outlier: 3.840A pdb=" N GLU G 253 " --> pdb=" O GLY G 249 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA G 254 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 282 removed outlier: 3.585A pdb=" N LYS G 280 " --> pdb=" O SER G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 305 Processing helix chain 'G' and resid 317 through 319 No H-bonds generated for 'chain 'G' and resid 317 through 319' Processing helix chain 'G' and resid 328 through 334 Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 360 through 373 Processing helix chain 'G' and resid 392 through 394 No H-bonds generated for 'chain 'G' and resid 392 through 394' Processing helix chain 'G' and resid 396 through 402 Processing helix chain 'G' and resid 414 through 418 Processing helix chain 'G' and resid 437 through 450 removed outlier: 3.852A pdb=" N LEU G 444 " --> pdb=" O ALA G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 495 removed outlier: 3.581A pdb=" N ARG G 477 " --> pdb=" O GLN G 473 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER G 478 " --> pdb=" O ALA G 474 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLY G 481 " --> pdb=" O ARG G 477 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU G 485 " --> pdb=" O GLY G 481 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU G 486 " --> pdb=" O VAL G 482 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA G 490 " --> pdb=" O LEU G 486 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS G 491 " --> pdb=" O ASP G 487 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA G 492 " --> pdb=" O THR G 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 46 Processing helix chain 'H' and resid 48 through 56 Processing sheet with id= A, first strand: chain 'A' and resid 286 through 289 Processing sheet with id= B, first strand: chain 'A' and resid 378 through 380 Processing sheet with id= C, first strand: chain 'A' and resid 408 through 411 Processing sheet with id= D, first strand: chain 'A' and resid 456 through 460 removed outlier: 3.511A pdb=" N LYS A 458 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 286 through 289 Processing sheet with id= F, first strand: chain 'C' and resid 378 through 380 Processing sheet with id= G, first strand: chain 'C' and resid 408 through 411 Processing sheet with id= H, first strand: chain 'C' and resid 456 through 460 removed outlier: 3.511A pdb=" N LYS C 458 " --> pdb=" O ASP C 467 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 286 through 289 Processing sheet with id= J, first strand: chain 'E' and resid 378 through 380 Processing sheet with id= K, first strand: chain 'E' and resid 408 through 411 Processing sheet with id= L, first strand: chain 'E' and resid 456 through 460 removed outlier: 3.511A pdb=" N LYS E 458 " --> pdb=" O ASP E 467 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 286 through 289 Processing sheet with id= N, first strand: chain 'G' and resid 378 through 380 Processing sheet with id= O, first strand: chain 'G' and resid 408 through 411 Processing sheet with id= P, first strand: chain 'G' and resid 456 through 460 removed outlier: 3.511A pdb=" N LYS G 458 " --> pdb=" O ASP G 467 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 5.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3772 1.34 - 1.46: 2157 1.46 - 1.58: 5615 1.58 - 1.69: 4 1.69 - 1.81: 44 Bond restraints: 11592 Sorted by residual: bond pdb=" CB ASN A 268 " pdb=" CG ASN A 268 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.46e+00 bond pdb=" C3 LDP G 501 " pdb=" O1 LDP G 501 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" CB ASN C 268 " pdb=" CG ASN C 268 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.42e+00 bond pdb=" CB ASN G 268 " pdb=" CG ASN G 268 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.39e+00 bond pdb=" CB ASN E 268 " pdb=" CG ASN E 268 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.38e+00 ... (remaining 11587 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.98: 356 106.98 - 113.74: 6117 113.74 - 120.49: 4712 120.49 - 127.24: 4392 127.24 - 134.00: 135 Bond angle restraints: 15712 Sorted by residual: angle pdb=" CA GLU C 227 " pdb=" CB GLU C 227 " pdb=" CG GLU C 227 " ideal model delta sigma weight residual 114.10 126.90 -12.80 2.00e+00 2.50e-01 4.10e+01 angle pdb=" CA GLU A 227 " pdb=" CB GLU A 227 " pdb=" CG GLU A 227 " ideal model delta sigma weight residual 114.10 126.87 -12.77 2.00e+00 2.50e-01 4.08e+01 angle pdb=" CA GLU G 227 " pdb=" CB GLU G 227 " pdb=" CG GLU G 227 " ideal model delta sigma weight residual 114.10 126.86 -12.76 2.00e+00 2.50e-01 4.07e+01 angle pdb=" CA GLU E 227 " pdb=" CB GLU E 227 " pdb=" CG GLU E 227 " ideal model delta sigma weight residual 114.10 126.85 -12.75 2.00e+00 2.50e-01 4.06e+01 angle pdb=" CA GLU C 480 " pdb=" CB GLU C 480 " pdb=" CG GLU C 480 " ideal model delta sigma weight residual 114.10 125.06 -10.96 2.00e+00 2.50e-01 3.01e+01 ... (remaining 15707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.66: 5973 14.66 - 29.33: 650 29.33 - 43.99: 229 43.99 - 58.65: 80 58.65 - 73.31: 8 Dihedral angle restraints: 6940 sinusoidal: 2788 harmonic: 4152 Sorted by residual: dihedral pdb=" CA GLU D 48 " pdb=" C GLU D 48 " pdb=" N ARG D 49 " pdb=" CA ARG D 49 " ideal model delta harmonic sigma weight residual -180.00 -150.76 -29.24 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA GLU F 48 " pdb=" C GLU F 48 " pdb=" N ARG F 49 " pdb=" CA ARG F 49 " ideal model delta harmonic sigma weight residual -180.00 -150.77 -29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA GLU B 48 " pdb=" C GLU B 48 " pdb=" N ARG B 49 " pdb=" CA ARG B 49 " ideal model delta harmonic sigma weight residual -180.00 -150.82 -29.18 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 6937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1113 0.038 - 0.076: 426 0.076 - 0.114: 119 0.114 - 0.152: 22 0.152 - 0.190: 4 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CB VAL C 275 " pdb=" CA VAL C 275 " pdb=" CG1 VAL C 275 " pdb=" CG2 VAL C 275 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.98e-01 chirality pdb=" CB VAL A 275 " pdb=" CA VAL A 275 " pdb=" CG1 VAL A 275 " pdb=" CG2 VAL A 275 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.93e-01 chirality pdb=" CB VAL E 275 " pdb=" CA VAL E 275 " pdb=" CG1 VAL E 275 " pdb=" CG2 VAL E 275 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 1681 not shown) Planarity restraints: 2068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 477 " 0.166 9.50e-02 1.11e+02 7.48e-02 3.71e+00 pdb=" NE ARG A 477 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 477 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 477 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 477 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 477 " -0.165 9.50e-02 1.11e+02 7.44e-02 3.69e+00 pdb=" NE ARG G 477 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG G 477 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 477 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 477 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 477 " 0.166 9.50e-02 1.11e+02 7.47e-02 3.69e+00 pdb=" NE ARG E 477 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG E 477 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 477 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 477 " 0.009 2.00e-02 2.50e+03 ... (remaining 2065 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 319 2.58 - 3.16: 10449 3.16 - 3.74: 19852 3.74 - 4.32: 26286 4.32 - 4.90: 39967 Nonbonded interactions: 96873 Sorted by model distance: nonbonded pdb=" N GLU E 480 " pdb=" OE1 GLU E 480 " model vdw 2.001 2.520 nonbonded pdb=" N GLU C 480 " pdb=" OE1 GLU C 480 " model vdw 2.001 2.520 nonbonded pdb=" N GLU A 480 " pdb=" OE1 GLU A 480 " model vdw 2.001 2.520 nonbonded pdb=" N GLU G 480 " pdb=" OE1 GLU G 480 " model vdw 2.002 2.520 nonbonded pdb=" N GLU A 227 " pdb=" OE1 GLU A 227 " model vdw 2.025 2.520 ... (remaining 96868 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 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: 1.820 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 34.820 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 0.067 11592 Z= 0.264 Angle : 0.929 14.360 15712 Z= 0.492 Chirality : 0.043 0.190 1684 Planarity : 0.005 0.075 2068 Dihedral : 15.059 73.314 4252 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.35 % Allowed : 3.01 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1396 helix: -0.86 (0.20), residues: 632 sheet: -1.08 (0.43), residues: 160 loop : -0.78 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 371 HIS 0.006 0.001 HIS E 491 PHE 0.024 0.001 PHE C 344 TYR 0.009 0.001 TYR C 243 ARG 0.010 0.001 ARG G 477 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 569 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LYS cc_start: 0.8656 (mppt) cc_final: 0.8178 (mtpt) REVERT: A 172 GLU cc_start: 0.9163 (pm20) cc_final: 0.8688 (pm20) REVERT: A 186 ASP cc_start: 0.7957 (t0) cc_final: 0.7629 (t0) REVERT: A 208 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9058 (mm-30) REVERT: A 212 GLN cc_start: 0.9353 (pt0) cc_final: 0.9133 (tp40) REVERT: A 242 LEU cc_start: 0.9414 (tp) cc_final: 0.9120 (pp) REVERT: A 341 ASP cc_start: 0.8499 (t0) cc_final: 0.7841 (p0) REVERT: A 379 CYS cc_start: 0.9387 (p) cc_final: 0.9084 (p) REVERT: A 393 LEU cc_start: 0.9209 (mp) cc_final: 0.8580 (mp) REVERT: A 413 ASP cc_start: 0.9513 (t0) cc_final: 0.9236 (t0) REVERT: C 182 LYS cc_start: 0.8687 (pttm) cc_final: 0.8467 (ptpp) REVERT: C 186 ASP cc_start: 0.7997 (t0) cc_final: 0.7650 (t0) REVERT: C 212 GLN cc_start: 0.9385 (pt0) cc_final: 0.9178 (tp40) REVERT: C 242 LEU cc_start: 0.9357 (tp) cc_final: 0.9100 (pp) REVERT: C 243 TYR cc_start: 0.9285 (m-10) cc_final: 0.9077 (m-10) REVERT: C 269 ILE cc_start: 0.8196 (tt) cc_final: 0.7979 (tt) REVERT: C 338 MET cc_start: 0.9048 (mmp) cc_final: 0.8792 (mmp) REVERT: C 341 ASP cc_start: 0.8435 (t0) cc_final: 0.7990 (p0) REVERT: C 393 LEU cc_start: 0.9148 (mp) cc_final: 0.8546 (mp) REVERT: C 463 THR cc_start: 0.8345 (t) cc_final: 0.8060 (t) REVERT: E 182 LYS cc_start: 0.8540 (pttm) cc_final: 0.8299 (ptpp) REVERT: E 186 ASP cc_start: 0.7914 (t0) cc_final: 0.7574 (t0) REVERT: E 212 GLN cc_start: 0.9379 (pt0) cc_final: 0.9173 (tp40) REVERT: E 242 LEU cc_start: 0.9378 (tp) cc_final: 0.9091 (pp) REVERT: E 338 MET cc_start: 0.8688 (mmp) cc_final: 0.8296 (mmp) REVERT: E 341 ASP cc_start: 0.8472 (t0) cc_final: 0.7992 (p0) REVERT: E 349 GLN cc_start: 0.9236 (tt0) cc_final: 0.8929 (tt0) REVERT: E 393 LEU cc_start: 0.9132 (mp) cc_final: 0.8610 (mp) REVERT: E 463 THR cc_start: 0.8166 (t) cc_final: 0.7911 (t) REVERT: G 186 ASP cc_start: 0.7918 (t0) cc_final: 0.7616 (t0) REVERT: G 212 GLN cc_start: 0.9366 (pt0) cc_final: 0.9154 (tp40) REVERT: G 242 LEU cc_start: 0.9361 (tp) cc_final: 0.9111 (pp) REVERT: G 341 ASP cc_start: 0.8458 (t0) cc_final: 0.8061 (p0) REVERT: G 393 LEU cc_start: 0.9184 (mp) cc_final: 0.8563 (mp) outliers start: 76 outliers final: 33 residues processed: 609 average time/residue: 0.2799 time to fit residues: 225.8596 Evaluate side-chains 458 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 425 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 0.0980 chunk 69 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11592 Z= 0.240 Angle : 0.731 8.715 15712 Z= 0.368 Chirality : 0.044 0.138 1684 Planarity : 0.005 0.070 2068 Dihedral : 5.020 21.974 1568 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.59 % Allowed : 3.85 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.22), residues: 1396 helix: -1.01 (0.18), residues: 776 sheet: -0.43 (0.62), residues: 88 loop : -0.84 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 371 HIS 0.010 0.002 HIS E 251 PHE 0.020 0.002 PHE A 278 TYR 0.016 0.002 TYR C 264 ARG 0.011 0.001 ARG H 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 499 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ASP cc_start: 0.7829 (t0) cc_final: 0.7531 (t0) REVERT: A 212 GLN cc_start: 0.9363 (pt0) cc_final: 0.9142 (tp40) REVERT: A 213 TYR cc_start: 0.9028 (t80) cc_final: 0.8681 (t80) REVERT: A 236 TYR cc_start: 0.8818 (t80) cc_final: 0.8355 (t80) REVERT: A 242 LEU cc_start: 0.9387 (tp) cc_final: 0.9148 (pp) REVERT: A 251 HIS cc_start: 0.8704 (m170) cc_final: 0.8475 (m90) REVERT: A 308 PHE cc_start: 0.8613 (t80) cc_final: 0.8379 (t80) REVERT: A 338 MET cc_start: 0.9239 (mmp) cc_final: 0.8915 (mmp) REVERT: A 341 ASP cc_start: 0.8401 (t0) cc_final: 0.7730 (p0) REVERT: A 369 LEU cc_start: 0.8972 (mm) cc_final: 0.8738 (mm) REVERT: A 393 LEU cc_start: 0.9037 (mp) cc_final: 0.8735 (mp) REVERT: A 460 ASP cc_start: 0.9157 (t0) cc_final: 0.8955 (t0) REVERT: C 175 LYS cc_start: 0.8221 (pptt) cc_final: 0.7957 (tptt) REVERT: C 186 ASP cc_start: 0.7925 (t0) cc_final: 0.7698 (t0) REVERT: C 212 GLN cc_start: 0.9387 (pt0) cc_final: 0.9165 (tp40) REVERT: C 213 TYR cc_start: 0.9070 (t80) cc_final: 0.8842 (t80) REVERT: C 236 TYR cc_start: 0.8745 (t80) cc_final: 0.8430 (t80) REVERT: C 242 LEU cc_start: 0.9312 (tp) cc_final: 0.9106 (pp) REVERT: C 338 MET cc_start: 0.9166 (mmp) cc_final: 0.8923 (mmp) REVERT: C 341 ASP cc_start: 0.8562 (t0) cc_final: 0.7819 (p0) REVERT: C 369 LEU cc_start: 0.8661 (mm) cc_final: 0.8427 (mm) REVERT: C 393 LEU cc_start: 0.8994 (mp) cc_final: 0.8628 (mp) REVERT: C 463 THR cc_start: 0.8498 (t) cc_final: 0.8166 (t) REVERT: E 186 ASP cc_start: 0.7910 (t0) cc_final: 0.7680 (t0) REVERT: E 212 GLN cc_start: 0.9397 (pt0) cc_final: 0.9182 (tp40) REVERT: E 213 TYR cc_start: 0.9069 (t80) cc_final: 0.8733 (t80) REVERT: E 242 LEU cc_start: 0.9334 (tp) cc_final: 0.9132 (pp) REVERT: E 308 PHE cc_start: 0.8664 (t80) cc_final: 0.8432 (t80) REVERT: E 341 ASP cc_start: 0.8565 (t0) cc_final: 0.7853 (p0) REVERT: E 349 GLN cc_start: 0.9286 (tt0) cc_final: 0.8785 (tt0) REVERT: E 369 LEU cc_start: 0.8904 (mm) cc_final: 0.8646 (mm) REVERT: E 393 LEU cc_start: 0.9055 (mp) cc_final: 0.8709 (mp) REVERT: E 455 PHE cc_start: 0.8783 (p90) cc_final: 0.8262 (p90) REVERT: E 460 ASP cc_start: 0.9045 (t0) cc_final: 0.8831 (t0) REVERT: G 186 ASP cc_start: 0.7904 (t0) cc_final: 0.7648 (t0) REVERT: G 212 GLN cc_start: 0.9359 (pt0) cc_final: 0.9132 (tp40) REVERT: G 213 TYR cc_start: 0.9038 (t80) cc_final: 0.8707 (t80) REVERT: G 308 PHE cc_start: 0.8704 (t80) cc_final: 0.8494 (t80) REVERT: G 341 ASP cc_start: 0.8593 (t0) cc_final: 0.7983 (p0) REVERT: G 369 LEU cc_start: 0.8913 (mm) cc_final: 0.8702 (mm) REVERT: G 393 LEU cc_start: 0.9081 (mp) cc_final: 0.8739 (mp) outliers start: 7 outliers final: 4 residues processed: 499 average time/residue: 0.2618 time to fit residues: 176.4176 Evaluate side-chains 414 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 410 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 ASN ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 ASN E 491 HIS ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 382 ASN G 491 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 11592 Z= 0.273 Angle : 0.672 6.359 15712 Z= 0.350 Chirality : 0.043 0.139 1684 Planarity : 0.005 0.038 2068 Dihedral : 4.979 20.545 1568 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 23.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.59 % Allowed : 5.85 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.22), residues: 1396 helix: -0.92 (0.18), residues: 776 sheet: -0.46 (0.57), residues: 96 loop : -0.82 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP G 371 HIS 0.011 0.002 HIS E 251 PHE 0.023 0.002 PHE A 372 TYR 0.025 0.002 TYR A 462 ARG 0.006 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 462 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.9199 (pm20) cc_final: 0.8774 (pm20) REVERT: A 186 ASP cc_start: 0.7882 (t0) cc_final: 0.7586 (t0) REVERT: A 212 GLN cc_start: 0.9362 (pt0) cc_final: 0.9131 (tp40) REVERT: A 213 TYR cc_start: 0.8971 (t80) cc_final: 0.8645 (t80) REVERT: A 242 LEU cc_start: 0.9450 (tp) cc_final: 0.9203 (pp) REVERT: A 308 PHE cc_start: 0.8650 (t80) cc_final: 0.8418 (t80) REVERT: A 338 MET cc_start: 0.9266 (mmp) cc_final: 0.9022 (mmp) REVERT: A 341 ASP cc_start: 0.8386 (t0) cc_final: 0.7699 (p0) REVERT: A 392 LEU cc_start: 0.9531 (mt) cc_final: 0.9078 (mt) REVERT: A 393 LEU cc_start: 0.8990 (mp) cc_final: 0.8436 (mp) REVERT: C 175 LYS cc_start: 0.8240 (pptt) cc_final: 0.8006 (mttm) REVERT: C 186 ASP cc_start: 0.7983 (t0) cc_final: 0.7757 (t0) REVERT: C 212 GLN cc_start: 0.9345 (pt0) cc_final: 0.9122 (tp40) REVERT: C 213 TYR cc_start: 0.9008 (t80) cc_final: 0.8708 (t80) REVERT: C 242 LEU cc_start: 0.9373 (tp) cc_final: 0.9141 (pp) REVERT: C 341 ASP cc_start: 0.8714 (t0) cc_final: 0.8013 (p0) REVERT: C 369 LEU cc_start: 0.9058 (mm) cc_final: 0.8821 (mm) REVERT: C 393 LEU cc_start: 0.9007 (mp) cc_final: 0.8711 (mp) REVERT: C 455 PHE cc_start: 0.8864 (p90) cc_final: 0.8349 (p90) REVERT: C 456 SER cc_start: 0.8400 (t) cc_final: 0.8024 (t) REVERT: C 462 TYR cc_start: 0.8638 (m-10) cc_final: 0.8217 (m-10) REVERT: E 175 LYS cc_start: 0.8222 (pptt) cc_final: 0.7992 (tptt) REVERT: E 213 TYR cc_start: 0.9013 (t80) cc_final: 0.8713 (t80) REVERT: E 251 HIS cc_start: 0.8707 (m-70) cc_final: 0.8465 (m-70) REVERT: E 274 ASP cc_start: 0.8913 (p0) cc_final: 0.8627 (t70) REVERT: E 338 MET cc_start: 0.9046 (mmp) cc_final: 0.8611 (mmt) REVERT: E 341 ASP cc_start: 0.8727 (t0) cc_final: 0.7916 (p0) REVERT: E 349 GLN cc_start: 0.9272 (tt0) cc_final: 0.8680 (tp40) REVERT: E 369 LEU cc_start: 0.9133 (mm) cc_final: 0.8875 (mm) REVERT: E 393 LEU cc_start: 0.8994 (mp) cc_final: 0.8708 (mp) REVERT: E 450 ARG cc_start: 0.9072 (mtt90) cc_final: 0.8802 (ttm110) REVERT: E 455 PHE cc_start: 0.8867 (p90) cc_final: 0.8359 (p90) REVERT: G 172 GLU cc_start: 0.9202 (pm20) cc_final: 0.8643 (pm20) REVERT: G 212 GLN cc_start: 0.9297 (pt0) cc_final: 0.9084 (tp40) REVERT: G 213 TYR cc_start: 0.9011 (t80) cc_final: 0.8683 (t80) REVERT: G 251 HIS cc_start: 0.8667 (m-70) cc_final: 0.8407 (m-70) REVERT: G 267 ASP cc_start: 0.9455 (OUTLIER) cc_final: 0.9142 (p0) REVERT: G 331 GLU cc_start: 0.9441 (pt0) cc_final: 0.9114 (mp0) REVERT: G 338 MET cc_start: 0.9005 (mmp) cc_final: 0.8567 (mmp) REVERT: G 341 ASP cc_start: 0.8742 (t0) cc_final: 0.7990 (p0) REVERT: G 369 LEU cc_start: 0.9060 (mm) cc_final: 0.8847 (mm) REVERT: G 393 LEU cc_start: 0.8983 (mp) cc_final: 0.8727 (mp) REVERT: G 450 ARG cc_start: 0.9138 (mtt90) cc_final: 0.8882 (ttm110) REVERT: G 455 PHE cc_start: 0.8777 (p90) cc_final: 0.8350 (p90) REVERT: G 460 ASP cc_start: 0.9193 (t0) cc_final: 0.8992 (t0) outliers start: 7 outliers final: 0 residues processed: 462 average time/residue: 0.2521 time to fit residues: 159.5480 Evaluate side-chains 402 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 401 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.0970 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 11592 Z= 0.214 Angle : 0.651 7.241 15712 Z= 0.329 Chirality : 0.043 0.228 1684 Planarity : 0.004 0.055 2068 Dihedral : 4.859 17.856 1568 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.42 % Allowed : 5.27 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.22), residues: 1396 helix: -0.81 (0.18), residues: 780 sheet: -0.46 (0.50), residues: 128 loop : -0.71 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP G 371 HIS 0.008 0.001 HIS C 251 PHE 0.019 0.001 PHE A 372 TYR 0.017 0.002 TYR A 462 ARG 0.005 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 467 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.9180 (pm20) cc_final: 0.8794 (pm20) REVERT: A 186 ASP cc_start: 0.7891 (t0) cc_final: 0.7615 (t0) REVERT: A 212 GLN cc_start: 0.9319 (pt0) cc_final: 0.9093 (tp40) REVERT: A 213 TYR cc_start: 0.9032 (t80) cc_final: 0.8669 (t80) REVERT: A 242 LEU cc_start: 0.9453 (tp) cc_final: 0.9230 (pp) REVERT: A 251 HIS cc_start: 0.8439 (m90) cc_final: 0.8122 (m-70) REVERT: A 273 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8323 (tp30) REVERT: A 305 PHE cc_start: 0.8892 (m-80) cc_final: 0.8657 (m-80) REVERT: A 331 GLU cc_start: 0.9370 (pt0) cc_final: 0.8953 (mp0) REVERT: A 338 MET cc_start: 0.9263 (mmp) cc_final: 0.8763 (mmt) REVERT: A 341 ASP cc_start: 0.8448 (t0) cc_final: 0.7602 (p0) REVERT: A 369 LEU cc_start: 0.9072 (mm) cc_final: 0.8861 (mm) REVERT: A 393 LEU cc_start: 0.8952 (mp) cc_final: 0.8706 (mp) REVERT: A 460 ASP cc_start: 0.9117 (t0) cc_final: 0.8752 (t0) REVERT: C 212 GLN cc_start: 0.9290 (pt0) cc_final: 0.9070 (tp40) REVERT: C 242 LEU cc_start: 0.9395 (tp) cc_final: 0.9193 (pp) REVERT: C 338 MET cc_start: 0.9203 (mmp) cc_final: 0.8827 (mmp) REVERT: C 341 ASP cc_start: 0.8715 (t0) cc_final: 0.7865 (p0) REVERT: C 369 LEU cc_start: 0.8986 (mm) cc_final: 0.8777 (mm) REVERT: C 393 LEU cc_start: 0.8788 (mp) cc_final: 0.8541 (mp) REVERT: C 450 ARG cc_start: 0.9034 (mtt90) cc_final: 0.8790 (ttm110) REVERT: C 455 PHE cc_start: 0.8797 (p90) cc_final: 0.8342 (p90) REVERT: C 456 SER cc_start: 0.8442 (t) cc_final: 0.8142 (t) REVERT: E 166 PHE cc_start: 0.9351 (p90) cc_final: 0.9138 (p90) REVERT: E 186 ASP cc_start: 0.7384 (t0) cc_final: 0.7178 (t0) REVERT: E 274 ASP cc_start: 0.8913 (p0) cc_final: 0.8577 (t0) REVERT: E 308 PHE cc_start: 0.8590 (t80) cc_final: 0.8373 (t80) REVERT: E 341 ASP cc_start: 0.8670 (t0) cc_final: 0.7844 (p0) REVERT: E 349 GLN cc_start: 0.9274 (tt0) cc_final: 0.8867 (tp40) REVERT: E 369 LEU cc_start: 0.9095 (mm) cc_final: 0.8851 (mm) REVERT: E 393 LEU cc_start: 0.8940 (mp) cc_final: 0.8725 (mp) REVERT: E 450 ARG cc_start: 0.9074 (mtt90) cc_final: 0.8821 (ttm110) REVERT: E 455 PHE cc_start: 0.8841 (p90) cc_final: 0.8331 (p90) REVERT: E 456 SER cc_start: 0.8406 (t) cc_final: 0.8004 (t) REVERT: G 172 GLU cc_start: 0.9170 (pm20) cc_final: 0.8734 (pm20) REVERT: G 212 GLN cc_start: 0.9263 (pt0) cc_final: 0.9062 (tp40) REVERT: G 213 TYR cc_start: 0.9131 (t80) cc_final: 0.8818 (t80) REVERT: G 331 GLU cc_start: 0.9406 (pt0) cc_final: 0.9139 (mp0) REVERT: G 338 MET cc_start: 0.9132 (mmp) cc_final: 0.8787 (mmp) REVERT: G 341 ASP cc_start: 0.8698 (t0) cc_final: 0.7859 (p0) REVERT: G 361 GLU cc_start: 0.9665 (tp30) cc_final: 0.9428 (tm-30) REVERT: G 450 ARG cc_start: 0.9123 (mtt90) cc_final: 0.8888 (ttm110) REVERT: G 455 PHE cc_start: 0.8743 (p90) cc_final: 0.8371 (p90) REVERT: G 456 SER cc_start: 0.8394 (t) cc_final: 0.8153 (t) REVERT: G 460 ASP cc_start: 0.9294 (t0) cc_final: 0.9091 (t0) outliers start: 5 outliers final: 5 residues processed: 467 average time/residue: 0.2494 time to fit residues: 159.0484 Evaluate side-chains 400 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 395 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11592 Z= 0.298 Angle : 0.702 6.415 15712 Z= 0.373 Chirality : 0.045 0.217 1684 Planarity : 0.005 0.035 2068 Dihedral : 5.065 18.902 1568 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.22), residues: 1396 helix: -1.01 (0.17), residues: 764 sheet: -0.95 (0.79), residues: 56 loop : -0.54 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP E 371 HIS 0.015 0.002 HIS E 401 PHE 0.023 0.002 PHE C 376 TYR 0.020 0.002 TYR A 462 ARG 0.006 0.001 ARG G 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLN cc_start: 0.9283 (pt0) cc_final: 0.9033 (tp40) REVERT: A 242 LEU cc_start: 0.9490 (tp) cc_final: 0.9281 (pp) REVERT: A 243 TYR cc_start: 0.9237 (m-10) cc_final: 0.9034 (m-10) REVERT: A 308 PHE cc_start: 0.8623 (t80) cc_final: 0.8397 (t80) REVERT: A 349 GLN cc_start: 0.9262 (tt0) cc_final: 0.8967 (tt0) REVERT: A 369 LEU cc_start: 0.9154 (mm) cc_final: 0.8930 (mm) REVERT: A 462 TYR cc_start: 0.8728 (m-10) cc_final: 0.8201 (m-10) REVERT: C 166 PHE cc_start: 0.9462 (p90) cc_final: 0.9243 (p90) REVERT: C 212 GLN cc_start: 0.9283 (pt0) cc_final: 0.9078 (tp40) REVERT: C 341 ASP cc_start: 0.8730 (t0) cc_final: 0.8522 (t0) REVERT: C 369 LEU cc_start: 0.9119 (mm) cc_final: 0.8899 (mm) REVERT: C 393 LEU cc_start: 0.8811 (mp) cc_final: 0.8595 (mp) REVERT: C 450 ARG cc_start: 0.9126 (mtt90) cc_final: 0.8881 (ttm110) REVERT: C 455 PHE cc_start: 0.8902 (p90) cc_final: 0.8432 (p90) REVERT: C 460 ASP cc_start: 0.9364 (t0) cc_final: 0.8907 (t0) REVERT: E 240 LYS cc_start: 0.8838 (mttt) cc_final: 0.8517 (mmmm) REVERT: E 308 PHE cc_start: 0.8651 (t80) cc_final: 0.8437 (t80) REVERT: E 341 ASP cc_start: 0.8699 (t0) cc_final: 0.8496 (t0) REVERT: E 349 GLN cc_start: 0.9382 (tt0) cc_final: 0.9090 (tt0) REVERT: E 369 LEU cc_start: 0.9202 (mm) cc_final: 0.8972 (mm) REVERT: E 450 ARG cc_start: 0.9054 (mtt90) cc_final: 0.8808 (ttm110) REVERT: E 460 ASP cc_start: 0.9228 (t0) cc_final: 0.8746 (t0) REVERT: G 240 LYS cc_start: 0.9186 (tttp) cc_final: 0.8903 (mmmm) REVERT: G 308 PHE cc_start: 0.8685 (t80) cc_final: 0.8431 (t80) REVERT: G 450 ARG cc_start: 0.9068 (mtt90) cc_final: 0.8839 (ttm110) REVERT: G 455 PHE cc_start: 0.8846 (p90) cc_final: 0.8465 (p90) REVERT: G 460 ASP cc_start: 0.9379 (t0) cc_final: 0.8981 (t0) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.2508 time to fit residues: 150.9873 Evaluate side-chains 371 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.0970 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 0.0970 chunk 10 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11592 Z= 0.203 Angle : 0.671 10.092 15712 Z= 0.338 Chirality : 0.044 0.260 1684 Planarity : 0.005 0.066 2068 Dihedral : 4.945 19.269 1568 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.22), residues: 1396 helix: -0.75 (0.18), residues: 760 sheet: -0.26 (0.86), residues: 48 loop : -0.65 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP E 371 HIS 0.010 0.001 HIS A 251 PHE 0.016 0.002 PHE A 305 TYR 0.017 0.002 TYR E 236 ARG 0.007 0.001 ARG G 477 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLN cc_start: 0.9193 (pt0) cc_final: 0.8972 (tp40) REVERT: A 213 TYR cc_start: 0.9091 (t80) cc_final: 0.8619 (t80) REVERT: A 240 LYS cc_start: 0.9131 (tptm) cc_final: 0.8880 (mmmm) REVERT: A 242 LEU cc_start: 0.9481 (tp) cc_final: 0.9271 (pp) REVERT: A 308 PHE cc_start: 0.8594 (t80) cc_final: 0.8389 (t80) REVERT: A 349 GLN cc_start: 0.8966 (tt0) cc_final: 0.8673 (tt0) REVERT: A 369 LEU cc_start: 0.9073 (mm) cc_final: 0.8827 (mm) REVERT: A 460 ASP cc_start: 0.9191 (t0) cc_final: 0.8882 (t0) REVERT: A 462 TYR cc_start: 0.8667 (m-10) cc_final: 0.8138 (m-10) REVERT: C 213 TYR cc_start: 0.9108 (t80) cc_final: 0.8687 (t80) REVERT: C 338 MET cc_start: 0.9246 (mmp) cc_final: 0.8999 (mmp) REVERT: C 369 LEU cc_start: 0.9068 (mm) cc_final: 0.8826 (mm) REVERT: C 450 ARG cc_start: 0.8982 (mtt90) cc_final: 0.8755 (ttm110) REVERT: C 455 PHE cc_start: 0.8798 (p90) cc_final: 0.8371 (p90) REVERT: C 466 ILE cc_start: 0.8859 (mm) cc_final: 0.8639 (mm) REVERT: E 186 ASP cc_start: 0.7344 (t0) cc_final: 0.7118 (t0) REVERT: E 213 TYR cc_start: 0.9064 (t80) cc_final: 0.8804 (t80) REVERT: E 240 LYS cc_start: 0.8819 (mttt) cc_final: 0.8505 (mmmm) REVERT: E 276 SER cc_start: 0.8811 (m) cc_final: 0.8555 (p) REVERT: E 308 PHE cc_start: 0.8637 (t80) cc_final: 0.8429 (t80) REVERT: E 341 ASP cc_start: 0.8670 (t0) cc_final: 0.8455 (t0) REVERT: E 369 LEU cc_start: 0.9157 (mm) cc_final: 0.8901 (mm) REVERT: E 455 PHE cc_start: 0.8762 (p90) cc_final: 0.8322 (p90) REVERT: E 460 ASP cc_start: 0.9171 (t0) cc_final: 0.8814 (t0) REVERT: G 166 PHE cc_start: 0.9458 (p90) cc_final: 0.9192 (p90) REVERT: G 213 TYR cc_start: 0.9158 (t80) cc_final: 0.8886 (t80) REVERT: G 240 LYS cc_start: 0.9111 (tttp) cc_final: 0.8836 (mmmm) REVERT: G 308 PHE cc_start: 0.8671 (t80) cc_final: 0.8428 (t80) REVERT: G 338 MET cc_start: 0.9019 (mmp) cc_final: 0.8457 (mmp) REVERT: G 341 ASP cc_start: 0.8752 (t0) cc_final: 0.7961 (p0) REVERT: G 450 ARG cc_start: 0.9166 (mtt90) cc_final: 0.8930 (ttm110) REVERT: G 455 PHE cc_start: 0.8767 (p90) cc_final: 0.8414 (p90) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.2526 time to fit residues: 156.6326 Evaluate side-chains 385 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 73 optimal weight: 0.1980 chunk 131 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11592 Z= 0.194 Angle : 0.687 10.316 15712 Z= 0.341 Chirality : 0.044 0.233 1684 Planarity : 0.004 0.039 2068 Dihedral : 4.873 20.285 1568 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.22), residues: 1396 helix: -0.65 (0.18), residues: 756 sheet: -0.44 (0.84), residues: 48 loop : -0.65 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.005 TRP E 371 HIS 0.016 0.002 HIS C 401 PHE 0.017 0.002 PHE C 305 TYR 0.021 0.002 TYR G 388 ARG 0.007 0.001 ARG E 297 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 PHE cc_start: 0.8599 (t80) cc_final: 0.8397 (t80) REVERT: A 369 LEU cc_start: 0.9057 (mm) cc_final: 0.8808 (mm) REVERT: A 462 TYR cc_start: 0.8755 (m-10) cc_final: 0.8068 (m-10) REVERT: C 213 TYR cc_start: 0.9071 (t80) cc_final: 0.8820 (t80) REVERT: C 346 GLN cc_start: 0.9018 (tp40) cc_final: 0.8729 (tp-100) REVERT: C 349 GLN cc_start: 0.9322 (tt0) cc_final: 0.8925 (tp40) REVERT: C 450 ARG cc_start: 0.9009 (mtt90) cc_final: 0.8727 (ttm110) REVERT: C 455 PHE cc_start: 0.8748 (p90) cc_final: 0.8362 (p90) REVERT: C 460 ASP cc_start: 0.9374 (t0) cc_final: 0.9038 (t0) REVERT: E 213 TYR cc_start: 0.9070 (t80) cc_final: 0.8832 (t80) REVERT: E 338 MET cc_start: 0.8956 (mmp) cc_final: 0.8525 (mmp) REVERT: E 369 LEU cc_start: 0.9055 (mm) cc_final: 0.8819 (mm) REVERT: E 455 PHE cc_start: 0.8718 (p90) cc_final: 0.8298 (p90) REVERT: E 460 ASP cc_start: 0.9221 (t0) cc_final: 0.8874 (t0) REVERT: G 213 TYR cc_start: 0.9151 (t80) cc_final: 0.8818 (t80) REVERT: G 240 LYS cc_start: 0.9084 (tttp) cc_final: 0.8778 (mmmm) REVERT: G 331 GLU cc_start: 0.9357 (pt0) cc_final: 0.9045 (mp0) REVERT: G 338 MET cc_start: 0.9047 (mmp) cc_final: 0.8374 (mmp) REVERT: G 341 ASP cc_start: 0.8632 (t0) cc_final: 0.7967 (p0) REVERT: G 346 GLN cc_start: 0.8917 (tp-100) cc_final: 0.8683 (tp40) REVERT: G 349 GLN cc_start: 0.9240 (tt0) cc_final: 0.8812 (tp40) REVERT: G 450 ARG cc_start: 0.9143 (mtt90) cc_final: 0.8883 (ttm110) REVERT: G 455 PHE cc_start: 0.8734 (p90) cc_final: 0.8438 (p90) REVERT: G 460 ASP cc_start: 0.9288 (t0) cc_final: 0.8891 (t0) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.2539 time to fit residues: 149.6930 Evaluate side-chains 375 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11592 Z= 0.210 Angle : 0.687 10.715 15712 Z= 0.349 Chirality : 0.044 0.210 1684 Planarity : 0.004 0.035 2068 Dihedral : 4.853 20.920 1568 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1396 helix: -0.65 (0.18), residues: 784 sheet: -0.63 (0.82), residues: 48 loop : -0.69 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP C 371 HIS 0.016 0.002 HIS G 401 PHE 0.025 0.002 PHE C 255 TYR 0.029 0.002 TYR A 213 ARG 0.008 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ARG cc_start: 0.8706 (mmt90) cc_final: 0.8476 (mmm-85) REVERT: A 331 GLU cc_start: 0.9323 (pt0) cc_final: 0.9023 (mp0) REVERT: A 338 MET cc_start: 0.9200 (mmp) cc_final: 0.8545 (mmp) REVERT: A 369 LEU cc_start: 0.9058 (mm) cc_final: 0.8812 (mm) REVERT: A 462 TYR cc_start: 0.8725 (m-10) cc_final: 0.8125 (m-10) REVERT: C 275 VAL cc_start: 0.8937 (p) cc_final: 0.8733 (m) REVERT: C 349 GLN cc_start: 0.9318 (tt0) cc_final: 0.8919 (tp40) REVERT: C 369 LEU cc_start: 0.8995 (mm) cc_final: 0.8768 (mm) REVERT: C 455 PHE cc_start: 0.8780 (p90) cc_final: 0.8397 (p90) REVERT: C 460 ASP cc_start: 0.9375 (t0) cc_final: 0.9164 (t0) REVERT: E 186 ASP cc_start: 0.7361 (t0) cc_final: 0.7155 (t0) REVERT: E 369 LEU cc_start: 0.9058 (mm) cc_final: 0.8828 (mm) REVERT: E 455 PHE cc_start: 0.8741 (p90) cc_final: 0.8329 (p90) REVERT: E 460 ASP cc_start: 0.9222 (t0) cc_final: 0.8881 (t0) REVERT: G 166 PHE cc_start: 0.9443 (p90) cc_final: 0.9232 (p90) REVERT: G 240 LYS cc_start: 0.9115 (tttp) cc_final: 0.8804 (mmmm) REVERT: G 297 ARG cc_start: 0.8930 (tpp80) cc_final: 0.8687 (mmt90) REVERT: G 331 GLU cc_start: 0.9349 (pt0) cc_final: 0.9026 (mp0) REVERT: G 341 ASP cc_start: 0.8613 (t0) cc_final: 0.8380 (t0) REVERT: G 455 PHE cc_start: 0.8723 (p90) cc_final: 0.8411 (p90) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.2539 time to fit residues: 149.2976 Evaluate side-chains 386 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11592 Z= 0.263 Angle : 0.722 9.962 15712 Z= 0.375 Chirality : 0.046 0.202 1684 Planarity : 0.005 0.057 2068 Dihedral : 5.073 23.365 1568 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.22), residues: 1396 helix: -0.69 (0.18), residues: 768 sheet: -0.47 (0.57), residues: 92 loop : -1.02 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.006 TRP E 371 HIS 0.016 0.002 HIS C 401 PHE 0.024 0.002 PHE C 412 TYR 0.026 0.002 TYR G 213 ARG 0.016 0.001 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ASP cc_start: 0.7173 (t0) cc_final: 0.6962 (t0) REVERT: A 213 TYR cc_start: 0.9034 (t80) cc_final: 0.8613 (t80) REVERT: A 308 PHE cc_start: 0.8603 (t80) cc_final: 0.8352 (t80) REVERT: A 338 MET cc_start: 0.9156 (mmp) cc_final: 0.8568 (mmp) REVERT: A 341 ASP cc_start: 0.8543 (t0) cc_final: 0.8291 (t0) REVERT: A 369 LEU cc_start: 0.9105 (mm) cc_final: 0.8870 (mm) REVERT: A 462 TYR cc_start: 0.8859 (m-10) cc_final: 0.8233 (m-10) REVERT: C 275 VAL cc_start: 0.9120 (p) cc_final: 0.8590 (m) REVERT: C 369 LEU cc_start: 0.9123 (mm) cc_final: 0.8918 (mm) REVERT: C 455 PHE cc_start: 0.8839 (p90) cc_final: 0.8427 (p90) REVERT: C 460 ASP cc_start: 0.9346 (t0) cc_final: 0.8943 (t0) REVERT: E 213 TYR cc_start: 0.9050 (t80) cc_final: 0.8708 (t80) REVERT: E 369 LEU cc_start: 0.9152 (mm) cc_final: 0.8925 (mm) REVERT: G 166 PHE cc_start: 0.9510 (p90) cc_final: 0.9277 (p90) REVERT: G 186 ASP cc_start: 0.7225 (t0) cc_final: 0.7015 (t0) REVERT: G 240 LYS cc_start: 0.9134 (tttp) cc_final: 0.8854 (mmmm) REVERT: G 297 ARG cc_start: 0.9031 (tpp80) cc_final: 0.8813 (mmt90) REVERT: G 308 PHE cc_start: 0.8702 (t80) cc_final: 0.8440 (t80) REVERT: G 341 ASP cc_start: 0.8611 (t0) cc_final: 0.8405 (t0) REVERT: G 455 PHE cc_start: 0.8814 (p90) cc_final: 0.8467 (p90) REVERT: G 460 ASP cc_start: 0.9284 (t0) cc_final: 0.8908 (t0) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.2364 time to fit residues: 139.1847 Evaluate side-chains 365 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 85 optimal weight: 0.1980 chunk 114 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11592 Z= 0.247 Angle : 0.740 11.550 15712 Z= 0.376 Chirality : 0.046 0.238 1684 Planarity : 0.006 0.161 2068 Dihedral : 5.086 23.244 1568 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 24.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.22), residues: 1396 helix: -0.68 (0.18), residues: 764 sheet: -0.09 (0.46), residues: 132 loop : -1.16 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.005 TRP A 371 HIS 0.018 0.002 HIS E 401 PHE 0.023 0.002 PHE E 255 TYR 0.028 0.002 TYR A 213 ARG 0.007 0.001 ARG A 297 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.9529 (tp30) cc_final: 0.9322 (tp30) REVERT: A 308 PHE cc_start: 0.8572 (t80) cc_final: 0.8351 (t80) REVERT: A 338 MET cc_start: 0.9196 (mmp) cc_final: 0.8649 (mmp) REVERT: A 369 LEU cc_start: 0.9062 (mm) cc_final: 0.8818 (mm) REVERT: A 462 TYR cc_start: 0.8858 (m-10) cc_final: 0.8256 (m-10) REVERT: C 338 MET cc_start: 0.9279 (mmp) cc_final: 0.8967 (mmp) REVERT: C 349 GLN cc_start: 0.9292 (tt0) cc_final: 0.8930 (tp40) REVERT: C 369 LEU cc_start: 0.9141 (mm) cc_final: 0.8931 (mm) REVERT: C 455 PHE cc_start: 0.8832 (p90) cc_final: 0.8418 (p90) REVERT: E 213 TYR cc_start: 0.9086 (t80) cc_final: 0.8808 (t80) REVERT: E 275 VAL cc_start: 0.9142 (p) cc_final: 0.8616 (m) REVERT: E 338 MET cc_start: 0.8924 (mmp) cc_final: 0.8526 (mmp) REVERT: E 369 LEU cc_start: 0.9130 (mm) cc_final: 0.8901 (mm) REVERT: E 455 PHE cc_start: 0.8837 (p90) cc_final: 0.8413 (p90) REVERT: E 460 ASP cc_start: 0.9277 (t0) cc_final: 0.8888 (t0) REVERT: G 166 PHE cc_start: 0.9513 (p90) cc_final: 0.9280 (p90) REVERT: G 213 TYR cc_start: 0.9103 (t80) cc_final: 0.8698 (t80) REVERT: G 297 ARG cc_start: 0.9008 (tpp80) cc_final: 0.8790 (mmt90) REVERT: G 308 PHE cc_start: 0.8696 (t80) cc_final: 0.8435 (t80) REVERT: G 427 TYR cc_start: 0.8485 (m-80) cc_final: 0.7933 (m-80) REVERT: G 455 PHE cc_start: 0.8797 (p90) cc_final: 0.8451 (p90) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.2474 time to fit residues: 139.3061 Evaluate side-chains 365 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 110 optimal weight: 0.0070 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN C 178 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 HIS ** E 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.124170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.095418 restraints weight = 25656.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.099302 restraints weight = 17001.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.102247 restraints weight = 12315.206| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11592 Z= 0.195 Angle : 0.743 12.743 15712 Z= 0.367 Chirality : 0.045 0.197 1684 Planarity : 0.005 0.096 2068 Dihedral : 4.931 22.146 1568 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1396 helix: -0.43 (0.19), residues: 732 sheet: 0.15 (0.47), residues: 132 loop : -1.33 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.005 TRP G 371 HIS 0.019 0.002 HIS E 401 PHE 0.026 0.002 PHE E 255 TYR 0.030 0.002 TYR G 213 ARG 0.007 0.001 ARG G 445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3184.78 seconds wall clock time: 57 minutes 49.49 seconds (3469.49 seconds total)