Starting phenix.real_space_refine on Wed Nov 15 09:27:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/11_2023/6zn2_11309_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/11_2023/6zn2_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_11309/11_2023/6zn2_11309.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/11_2023/6zn2_11309.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/11_2023/6zn2_11309_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn2_11309/11_2023/6zn2_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 6.71, per 1000 atoms: 0.59 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: 4.93 Conformation dependent library (CDL) restraints added in 2.5 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: 3.05 Time building geometry restraints manager: 5.25 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.910 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 35.240 Find NCS groups from input model: 0.700 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.280 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.279 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 outliers start: 76 outliers final: 33 residues processed: 609 average time/residue: 0.2828 time to fit residues: 227.6434 Evaluate side-chains 440 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 407 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1418 time to fit residues: 9.5395 ------------------------------------------------------------------------------- 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: 9.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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** A 491 HIS ** 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** ** E 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 11592 Z= 0.399 Angle : 0.834 9.673 15712 Z= 0.441 Chirality : 0.047 0.168 1684 Planarity : 0.006 0.057 2068 Dihedral : 5.460 22.983 1568 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 26.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.59 % Allowed : 6.10 % Favored : 93.31 % 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: -1.98 (0.22), residues: 1396 helix: -1.47 (0.17), residues: 776 sheet: -0.86 (0.51), residues: 128 loop : -0.80 (0.30), residues: 492 *********************** 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 482 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 475 time to evaluate : 1.317 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 outliers start: 7 outliers final: 0 residues processed: 478 average time/residue: 0.2694 time to fit residues: 175.4138 Evaluate side-chains 368 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8955 ------------------------------------------------------------------------------- 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: 0.1980 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 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 246 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 420 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** E 382 ASN ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11592 Z= 0.230 Angle : 0.673 6.448 15712 Z= 0.344 Chirality : 0.043 0.186 1684 Planarity : 0.004 0.035 2068 Dihedral : 5.180 20.905 1568 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.33 % Allowed : 4.85 % Favored : 94.82 % 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: -1.49 (0.22), residues: 1396 helix: -1.06 (0.18), residues: 760 sheet: -0.66 (0.50), residues: 128 loop : -0.62 (0.29), residues: 508 *********************** 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 473 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 469 time to evaluate : 1.287 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 outliers start: 4 outliers final: 3 residues processed: 469 average time/residue: 0.2473 time to fit residues: 160.2225 Evaluate side-chains 392 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 389 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1403 time to fit residues: 2.4486 ------------------------------------------------------------------------------- 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: 1.9990 chunk 93 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 131 optimal weight: 0.4980 chunk 117 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 GLN ** E 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 HIS ** G 246 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: 0.7889 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 11592 Z= 0.199 Angle : 0.670 8.025 15712 Z= 0.334 Chirality : 0.043 0.235 1684 Planarity : 0.004 0.042 2068 Dihedral : 4.987 17.908 1568 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.42 % Allowed : 4.77 % Favored : 94.82 % 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: -1.28 (0.22), residues: 1396 helix: -0.78 (0.18), residues: 768 sheet: -0.17 (0.48), residues: 120 loop : -0.85 (0.29), residues: 508 *********************** 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 : 1.297 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 outliers start: 5 outliers final: 4 residues processed: 467 average time/residue: 0.2482 time to fit residues: 161.4992 Evaluate side-chains 405 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 401 time to evaluate : 1.319 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1403 time to fit residues: 2.7028 ------------------------------------------------------------------------------- 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: 0.9980 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 117 optimal weight: 0.0370 chunk 33 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.7662 ------------------------------------------------------------------------------- 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 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 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 246 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: 0.7926 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11592 Z= 0.227 Angle : 0.669 8.115 15712 Z= 0.341 Chirality : 0.044 0.214 1684 Planarity : 0.005 0.044 2068 Dihedral : 4.922 18.474 1568 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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: -0.79 (0.18), residues: 768 sheet: -0.09 (0.57), residues: 88 loop : -0.89 (0.27), residues: 540 *********************** 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 442 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 1.297 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 outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.2530 time to fit residues: 155.1280 Evaluate side-chains 380 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9117 ------------------------------------------------------------------------------- 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: 1.9990 chunk 25 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 10 optimal weight: 0.0010 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 overall best weight: 1.9192 ------------------------------------------------------------------------------- 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** ** C 246 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 246 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: 0.7933 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11592 Z= 0.228 Angle : 0.678 8.760 15712 Z= 0.344 Chirality : 0.044 0.216 1684 Planarity : 0.004 0.039 2068 Dihedral : 4.971 17.272 1568 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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: -1.35 (0.22), residues: 1396 helix: -0.87 (0.18), residues: 780 sheet: -0.08 (0.56), residues: 88 loop : -0.81 (0.28), residues: 528 *********************** 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 447 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 447 time to evaluate : 1.314 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 outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.2383 time to fit residues: 149.4525 Evaluate side-chains 380 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6187 ------------------------------------------------------------------------------- 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: 0.9980 chunk 74 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 81 optimal weight: 0.0970 chunk 52 optimal weight: 4.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 ASN ** C 401 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5664 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= 0.185 Angle : 0.674 10.496 15712 Z= 0.333 Chirality : 0.044 0.232 1684 Planarity : 0.004 0.037 2068 Dihedral : 4.813 16.646 1568 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -1.23 (0.22), residues: 1396 helix: -0.68 (0.18), residues: 768 sheet: -0.76 (0.45), residues: 136 loop : -0.74 (0.29), residues: 492 *********************** 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 463 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 1.280 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 outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.2505 time to fit residues: 160.4866 Evaluate side-chains 402 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7936 ------------------------------------------------------------------------------- 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: 1.9990 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 chunk 83 optimal weight: 8.9990 chunk 89 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 125 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** E 251 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.5873 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= 0.196 Angle : 0.707 11.309 15712 Z= 0.351 Chirality : 0.044 0.219 1684 Planarity : 0.004 0.044 2068 Dihedral : 4.732 16.266 1568 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.08 % Allowed : 1.92 % Favored : 97.99 % 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: -1.23 (0.22), residues: 1396 helix: -0.67 (0.18), residues: 772 sheet: -0.70 (0.46), residues: 136 loop : -0.78 (0.29), residues: 488 *********************** 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 443 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 442 time to evaluate : 1.172 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 outliers start: 1 outliers final: 0 residues processed: 443 average time/residue: 0.2426 time to fit residues: 149.6126 Evaluate side-chains 387 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 1.375 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8311 ------------------------------------------------------------------------------- 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: 0.9990 chunk 125 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** C 178 HIS ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 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: 0.7930 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11592 Z= 0.248 Angle : 0.730 10.440 15712 Z= 0.375 Chirality : 0.045 0.202 1684 Planarity : 0.005 0.048 2068 Dihedral : 4.897 20.823 1568 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -1.25 (0.22), residues: 1396 helix: -0.71 (0.18), residues: 756 sheet: -0.26 (0.53), residues: 96 loop : -0.89 (0.28), residues: 544 *********************** 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 433 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 1.352 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 outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.2678 time to fit residues: 162.2231 Evaluate side-chains 371 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7324 ------------------------------------------------------------------------------- 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: 4.9990 chunk 61 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 85 optimal weight: 0.0770 chunk 114 optimal weight: 7.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- 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** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 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: 0.7918 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11592 Z= 0.222 Angle : 0.748 12.248 15712 Z= 0.377 Chirality : 0.045 0.195 1684 Planarity : 0.005 0.145 2068 Dihedral : 4.909 20.509 1568 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 22.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1396 helix: -0.78 (0.18), residues: 780 sheet: -0.23 (0.44), residues: 140 loop : -1.37 (0.29), residues: 476 ********************** 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 433 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 1.201 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 outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.2372 time to fit residues: 142.4279 Evaluate side-chains 380 residues out of total 1196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6355 ------------------------------------------------------------------------------- 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: 7.9990 chunk 99 optimal weight: 0.0970 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.9982 ------------------------------------------------------------------------------- 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** ** C 251 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** ** G 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.121629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.093231 restraints weight = 25996.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.096944 restraints weight = 17295.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.099731 restraints weight = 12553.399| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11592 Z= 0.241 Angle : 0.760 11.473 15712 Z= 0.385 Chirality : 0.046 0.196 1684 Planarity : 0.005 0.100 2068 Dihedral : 4.977 18.398 1568 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -1.46 (0.22), residues: 1396 helix: -0.74 (0.18), residues: 760 sheet: -0.35 (0.44), residues: 140 loop : -1.27 (0.28), residues: 496 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3205.90 seconds wall clock time: 58 minutes 39.36 seconds (3519.36 seconds total)