Starting phenix.real_space_refine on Sat Feb 17 15:40:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ec6_28013/02_2024/8ec6_28013.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ec6_28013/02_2024/8ec6_28013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ec6_28013/02_2024/8ec6_28013.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ec6_28013/02_2024/8ec6_28013.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ec6_28013/02_2024/8ec6_28013.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ec6_28013/02_2024/8ec6_28013.pdb" } resolution = 3.1 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= 0.157 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 P 8 5.49 5 S 184 5.16 5 C 12207 2.51 5 N 3159 2.21 5 O 3575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B ASP 511": "OD1" <-> "OD2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 274": "OD1" <-> "OD2" Residue "C GLU 408": "OE1" <-> "OE2" Residue "E ASP 228": "OD1" <-> "OD2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 388": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19133 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2388 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "B" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2388 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "C" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2388 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "D" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2388 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "E" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2377 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 15, 'TRANS': 293} Chain: "F" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2388 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "G" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2388 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "H" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2388 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 15, 'TRANS': 294} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.22, per 1000 atoms: 0.53 Number of scatterers: 19133 At special positions: 0 Unit cell: (97.9, 124.3, 159.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 8 15.00 O 3575 8.00 N 3159 7.00 C 12207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.86 Conformation dependent library (CDL) restraints added in 3.9 seconds 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4510 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 16 sheets defined 52.6% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.889A pdb=" N LYS A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 339 through 350 removed outlier: 3.626A pdb=" N ILE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 371 Processing helix chain 'A' and resid 379 through 388 removed outlier: 3.506A pdb=" N GLU A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.684A pdb=" N PHE A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 424 Processing helix chain 'A' and resid 428 through 442 Processing helix chain 'A' and resid 454 through 469 Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 516 through 530 Processing helix chain 'B' and resid 230 through 245 removed outlier: 3.862A pdb=" N LYS B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 292 through 306 removed outlier: 4.523A pdb=" N LEU B 296 " --> pdb=" O CYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 355 through 371 Processing helix chain 'B' and resid 379 through 388 Processing helix chain 'B' and resid 390 through 403 Processing helix chain 'B' and resid 411 through 424 Processing helix chain 'B' and resid 428 through 442 Processing helix chain 'B' and resid 454 through 469 Processing helix chain 'B' and resid 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'B' and resid 473 through 481 Processing helix chain 'B' and resid 516 through 530 Processing helix chain 'C' and resid 232 through 244 Processing helix chain 'C' and resid 293 through 305 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 355 through 371 Processing helix chain 'C' and resid 379 through 388 removed outlier: 3.539A pdb=" N GLU C 388 " --> pdb=" O GLN C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 403 removed outlier: 3.712A pdb=" N PHE C 394 " --> pdb=" O GLY C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 424 Processing helix chain 'C' and resid 428 through 442 Processing helix chain 'C' and resid 454 through 469 Processing helix chain 'C' and resid 470 through 472 No H-bonds generated for 'chain 'C' and resid 470 through 472' Processing helix chain 'C' and resid 473 through 481 Processing helix chain 'C' and resid 516 through 530 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 306 through 312 Processing helix chain 'D' and resid 339 through 349 Processing helix chain 'D' and resid 355 through 371 Processing helix chain 'D' and resid 379 through 388 removed outlier: 3.768A pdb=" N GLU D 388 " --> pdb=" O GLN D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 403 Processing helix chain 'D' and resid 411 through 424 Processing helix chain 'D' and resid 428 through 442 Processing helix chain 'D' and resid 454 through 469 Processing helix chain 'D' and resid 470 through 472 No H-bonds generated for 'chain 'D' and resid 470 through 472' Processing helix chain 'D' and resid 473 through 481 Processing helix chain 'D' and resid 516 through 530 Processing helix chain 'E' and resid 230 through 245 removed outlier: 3.702A pdb=" N GLU E 241 " --> pdb=" O ASP E 237 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 305 Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 339 through 349 Processing helix chain 'E' and resid 355 through 371 Processing helix chain 'E' and resid 379 through 388 Processing helix chain 'E' and resid 390 through 403 Processing helix chain 'E' and resid 411 through 424 Processing helix chain 'E' and resid 428 through 442 Processing helix chain 'E' and resid 454 through 469 Processing helix chain 'E' and resid 470 through 472 No H-bonds generated for 'chain 'E' and resid 470 through 472' Processing helix chain 'E' and resid 473 through 481 Processing helix chain 'E' and resid 516 through 530 Processing helix chain 'F' and resid 230 through 245 removed outlier: 3.890A pdb=" N LYS F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 260 Processing helix chain 'F' and resid 293 through 306 Processing helix chain 'F' and resid 306 through 311 Processing helix chain 'F' and resid 339 through 350 removed outlier: 3.588A pdb=" N ILE F 350 " --> pdb=" O VAL F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 371 Processing helix chain 'F' and resid 379 through 390 Processing helix chain 'F' and resid 390 through 404 removed outlier: 3.733A pdb=" N PHE F 394 " --> pdb=" O GLY F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 424 Processing helix chain 'F' and resid 428 through 442 removed outlier: 3.560A pdb=" N LEU F 439 " --> pdb=" O MET F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 469 Processing helix chain 'F' and resid 470 through 472 No H-bonds generated for 'chain 'F' and resid 470 through 472' Processing helix chain 'F' and resid 473 through 481 Processing helix chain 'F' and resid 516 through 530 Processing helix chain 'G' and resid 230 through 245 removed outlier: 3.843A pdb=" N LYS G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 260 Processing helix chain 'G' and resid 293 through 306 Processing helix chain 'G' and resid 306 through 311 Processing helix chain 'G' and resid 339 through 349 Processing helix chain 'G' and resid 355 through 371 Processing helix chain 'G' and resid 379 through 388 removed outlier: 3.558A pdb=" N GLU G 388 " --> pdb=" O GLN G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 403 Processing helix chain 'G' and resid 411 through 424 Processing helix chain 'G' and resid 428 through 442 Processing helix chain 'G' and resid 454 through 469 Processing helix chain 'G' and resid 470 through 472 No H-bonds generated for 'chain 'G' and resid 470 through 472' Processing helix chain 'G' and resid 473 through 481 Processing helix chain 'G' and resid 516 through 530 Processing helix chain 'H' and resid 230 through 245 removed outlier: 3.872A pdb=" N LYS H 245 " --> pdb=" O GLU H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 305 Processing helix chain 'H' and resid 306 through 311 Processing helix chain 'H' and resid 339 through 350 removed outlier: 3.587A pdb=" N ILE H 350 " --> pdb=" O VAL H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 371 Processing helix chain 'H' and resid 379 through 388 removed outlier: 3.603A pdb=" N GLU H 388 " --> pdb=" O GLN H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 403 removed outlier: 3.683A pdb=" N PHE H 394 " --> pdb=" O GLY H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 424 Processing helix chain 'H' and resid 428 through 442 removed outlier: 3.527A pdb=" N LEU H 439 " --> pdb=" O MET H 435 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 469 Processing helix chain 'H' and resid 470 through 472 No H-bonds generated for 'chain 'H' and resid 470 through 472' Processing helix chain 'H' and resid 473 through 481 Processing helix chain 'H' and resid 516 through 530 Processing sheet with id=AA1, first strand: chain 'A' and resid 277 through 281 Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AA3, first strand: chain 'B' and resid 277 through 281 removed outlier: 3.956A pdb=" N GLY B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 287 through 288 Processing sheet with id=AA5, first strand: chain 'C' and resid 277 through 281 Processing sheet with id=AA6, first strand: chain 'C' and resid 287 through 288 Processing sheet with id=AA7, first strand: chain 'D' and resid 277 through 281 Processing sheet with id=AA8, first strand: chain 'D' and resid 287 through 288 Processing sheet with id=AA9, first strand: chain 'E' and resid 277 through 281 removed outlier: 3.876A pdb=" N GLY E 492 " --> pdb=" O GLY E 488 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 287 through 288 Processing sheet with id=AB2, first strand: chain 'F' and resid 277 through 281 Processing sheet with id=AB3, first strand: chain 'F' and resid 287 through 288 Processing sheet with id=AB4, first strand: chain 'G' and resid 277 through 281 removed outlier: 3.862A pdb=" N GLY G 492 " --> pdb=" O GLY G 488 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 287 through 288 Processing sheet with id=AB6, first strand: chain 'H' and resid 277 through 280 removed outlier: 3.784A pdb=" N GLY H 492 " --> pdb=" O GLY H 488 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 287 through 288 1038 hydrogen bonds defined for protein. 3042 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: 5.87 Time building geometry restraints manager: 8.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5878 1.34 - 1.46: 3031 1.46 - 1.57: 10407 1.57 - 1.69: 0 1.69 - 1.81: 280 Bond restraints: 19596 Sorted by residual: bond pdb=" O3 PO4 F 701 " pdb=" P PO4 F 701 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.07e+00 bond pdb=" O3 PO4 B 701 " pdb=" P PO4 B 701 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.95e+00 bond pdb=" O3 PO4 C 701 " pdb=" P PO4 C 701 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.88e+00 bond pdb=" O3 PO4 H 701 " pdb=" P PO4 H 701 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" O3 PO4 D 701 " pdb=" P PO4 D 701 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.84e+00 ... (remaining 19591 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.41: 476 105.41 - 112.59: 9826 112.59 - 119.77: 6450 119.77 - 126.95: 9539 126.95 - 134.13: 213 Bond angle restraints: 26504 Sorted by residual: angle pdb=" N MET F 501 " pdb=" CA MET F 501 " pdb=" C MET F 501 " ideal model delta sigma weight residual 107.88 114.40 -6.52 1.41e+00 5.03e-01 2.14e+01 angle pdb=" N MET C 501 " pdb=" CA MET C 501 " pdb=" C MET C 501 " ideal model delta sigma weight residual 107.88 114.05 -6.17 1.41e+00 5.03e-01 1.91e+01 angle pdb=" CA PRO E 509 " pdb=" N PRO E 509 " pdb=" CD PRO E 509 " ideal model delta sigma weight residual 112.00 105.90 6.10 1.40e+00 5.10e-01 1.90e+01 angle pdb=" C TYR F 471 " pdb=" CA TYR F 471 " pdb=" CB TYR F 471 " ideal model delta sigma weight residual 116.34 111.52 4.82 1.40e+00 5.10e-01 1.18e+01 angle pdb=" CA PRO F 509 " pdb=" N PRO F 509 " pdb=" CD PRO F 509 " ideal model delta sigma weight residual 112.00 107.18 4.82 1.40e+00 5.10e-01 1.18e+01 ... (remaining 26499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 10401 15.76 - 31.52: 872 31.52 - 47.28: 240 47.28 - 63.03: 43 63.03 - 78.79: 7 Dihedral angle restraints: 11563 sinusoidal: 4494 harmonic: 7069 Sorted by residual: dihedral pdb=" CA VAL A 500 " pdb=" C VAL A 500 " pdb=" N MET A 501 " pdb=" CA MET A 501 " ideal model delta harmonic sigma weight residual 180.00 -161.63 -18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA PRO C 227 " pdb=" C PRO C 227 " pdb=" N ASP C 228 " pdb=" CA ASP C 228 " ideal model delta harmonic sigma weight residual 180.00 162.66 17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB MET F 501 " pdb=" CG MET F 501 " pdb=" SD MET F 501 " pdb=" CE MET F 501 " ideal model delta sinusoidal sigma weight residual -180.00 -122.33 -57.67 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 11560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1932 0.035 - 0.071: 672 0.071 - 0.106: 174 0.106 - 0.142: 77 0.142 - 0.177: 8 Chirality restraints: 2863 Sorted by residual: chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA MET E 230 " pdb=" N MET E 230 " pdb=" C MET E 230 " pdb=" CB MET E 230 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA LEU B 510 " pdb=" N LEU B 510 " pdb=" C LEU B 510 " pdb=" CB LEU B 510 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 2860 not shown) Planarity restraints: 3438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 508 " 0.066 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO E 509 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO E 509 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 509 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 508 " -0.058 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO C 509 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 509 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 509 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 262 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO E 263 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 263 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 263 " 0.036 5.00e-02 4.00e+02 ... (remaining 3435 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 135 2.62 - 3.19: 17055 3.19 - 3.76: 29060 3.76 - 4.33: 40890 4.33 - 4.90: 70620 Nonbonded interactions: 157760 Sorted by model distance: nonbonded pdb=" O ASP A 274 " pdb=" OD1 ASP A 274 " model vdw 2.049 3.040 nonbonded pdb=" O VAL A 345 " pdb=" OG SER A 348 " model vdw 2.261 2.440 nonbonded pdb=" O ASP C 228 " pdb=" N MET C 230 " model vdw 2.286 2.520 nonbonded pdb=" OG SER C 262 " pdb=" OD1 ASP C 264 " model vdw 2.300 2.440 nonbonded pdb=" OD1 ASP H 228 " pdb=" N PHE H 229 " model vdw 2.301 2.520 ... (remaining 157755 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' and (resid 225 through 533 or resid 701)) selection = (chain 'B' and (resid 225 through 533 or resid 701)) selection = (chain 'C' and (resid 225 through 533 or resid 701)) selection = (chain 'D' and (resid 225 through 533 or resid 701)) selection = chain 'E' selection = (chain 'F' and (resid 225 through 533 or resid 701)) selection = (chain 'G' and (resid 225 through 533 or resid 701)) selection = (chain 'H' and (resid 225 through 533 or resid 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.430 Check model and map are aligned: 0.290 Set scattering table: 0.160 Process input model: 51.580 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.090 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 0.069 19596 Z= 0.224 Angle : 0.487 7.869 26504 Z= 0.269 Chirality : 0.041 0.177 2863 Planarity : 0.005 0.097 3438 Dihedral : 12.897 78.792 7053 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.72 % Favored : 94.15 % Rotamer: Outliers : 0.05 % Allowed : 12.41 % Favored : 87.54 % 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 (0.18), residues: 2463 helix: 1.91 (0.15), residues: 1271 sheet: 0.69 (0.34), residues: 241 loop : -0.65 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 266 HIS 0.007 0.001 HIS G 235 PHE 0.030 0.001 PHE C 232 TYR 0.011 0.001 TYR H 240 ARG 0.010 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 2.205 Fit side-chains REVERT: F 386 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8109 (mt-10) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.3112 time to fit residues: 111.3106 Evaluate side-chains 229 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 103 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 193 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 0.1980 chunk 144 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN E 365 GLN F 515 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.0483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19596 Z= 0.169 Angle : 0.463 6.814 26504 Z= 0.244 Chirality : 0.041 0.168 2863 Planarity : 0.005 0.069 3438 Dihedral : 3.495 18.511 2615 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 1.71 % Allowed : 11.17 % Favored : 87.11 % 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 (0.18), residues: 2463 helix: 2.19 (0.15), residues: 1275 sheet: 0.63 (0.33), residues: 241 loop : -0.55 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 266 HIS 0.005 0.001 HIS A 521 PHE 0.012 0.001 PHE G 473 TYR 0.011 0.001 TYR H 240 ARG 0.005 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 251 time to evaluate : 2.055 Fit side-chains REVERT: C 232 PHE cc_start: 0.7723 (t80) cc_final: 0.7496 (t80) REVERT: C 512 LYS cc_start: 0.8492 (ptpp) cc_final: 0.8207 (ptmt) REVERT: F 386 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7977 (mt-10) outliers start: 36 outliers final: 18 residues processed: 274 average time/residue: 0.2966 time to fit residues: 125.7976 Evaluate side-chains 252 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 234 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 527 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 0.0970 chunk 69 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 242 optimal weight: 0.5980 chunk 200 optimal weight: 0.6980 chunk 222 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 ASN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN E 365 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19596 Z= 0.177 Angle : 0.462 6.531 26504 Z= 0.243 Chirality : 0.042 0.166 2863 Planarity : 0.004 0.063 3438 Dihedral : 3.511 19.227 2615 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.97 % Favored : 93.95 % Rotamer: Outliers : 2.47 % Allowed : 11.13 % Favored : 86.40 % 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: 1.55 (0.18), residues: 2463 helix: 2.21 (0.15), residues: 1275 sheet: 0.59 (0.33), residues: 241 loop : -0.50 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 266 HIS 0.004 0.001 HIS A 521 PHE 0.028 0.001 PHE D 473 TYR 0.012 0.001 TYR C 240 ARG 0.004 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 246 time to evaluate : 2.324 Fit side-chains REVERT: C 512 LYS cc_start: 0.8465 (ptpp) cc_final: 0.8191 (ptmt) REVERT: D 387 ARG cc_start: 0.8167 (mtm180) cc_final: 0.7929 (mtm110) REVERT: G 503 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7987 (mtm) outliers start: 52 outliers final: 32 residues processed: 282 average time/residue: 0.3006 time to fit residues: 130.2772 Evaluate side-chains 273 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 240 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 527 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 0.0000 chunk 168 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN H 515 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19596 Z= 0.158 Angle : 0.452 6.313 26504 Z= 0.237 Chirality : 0.041 0.163 2863 Planarity : 0.004 0.060 3438 Dihedral : 3.452 18.258 2615 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.60 % Favored : 94.32 % Rotamer: Outliers : 2.52 % Allowed : 11.65 % Favored : 85.83 % 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: 1.62 (0.18), residues: 2463 helix: 2.26 (0.15), residues: 1281 sheet: 0.57 (0.33), residues: 241 loop : -0.47 (0.22), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 266 HIS 0.004 0.000 HIS G 235 PHE 0.018 0.001 PHE D 473 TYR 0.010 0.001 TYR H 240 ARG 0.005 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 250 time to evaluate : 1.948 Fit side-chains REVERT: A 305 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8417 (mp) REVERT: B 495 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8249 (tt) REVERT: C 512 LYS cc_start: 0.8482 (ptpp) cc_final: 0.8176 (ptmt) REVERT: D 387 ARG cc_start: 0.8176 (mtm180) cc_final: 0.7952 (mtm110) REVERT: G 282 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7796 (p0) REVERT: G 503 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7994 (mtm) outliers start: 53 outliers final: 35 residues processed: 285 average time/residue: 0.3007 time to fit residues: 131.3844 Evaluate side-chains 283 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 244 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 165 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 121 optimal weight: 0.0270 chunk 214 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN G 235 HIS H 515 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19596 Z= 0.169 Angle : 0.457 6.241 26504 Z= 0.239 Chirality : 0.041 0.161 2863 Planarity : 0.004 0.050 3438 Dihedral : 3.464 18.532 2615 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.21 % Favored : 93.71 % Rotamer: Outliers : 2.81 % Allowed : 11.65 % Favored : 85.54 % 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: 1.63 (0.18), residues: 2463 helix: 2.33 (0.15), residues: 1274 sheet: 0.32 (0.33), residues: 248 loop : -0.46 (0.22), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 266 HIS 0.005 0.000 HIS G 235 PHE 0.015 0.001 PHE D 473 TYR 0.010 0.001 TYR H 240 ARG 0.006 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 250 time to evaluate : 2.286 Fit side-chains REVERT: A 305 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8432 (mp) REVERT: B 495 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8290 (tt) REVERT: C 305 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8459 (mp) REVERT: C 512 LYS cc_start: 0.8482 (ptpp) cc_final: 0.8153 (ptmt) REVERT: D 279 SER cc_start: 0.9186 (p) cc_final: 0.8716 (m) REVERT: D 387 ARG cc_start: 0.8231 (mtm180) cc_final: 0.7995 (mtm110) REVERT: E 230 MET cc_start: 0.6557 (mmm) cc_final: 0.5868 (mtp) REVERT: G 282 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7798 (p0) REVERT: G 503 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7998 (mtm) REVERT: H 238 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7382 (mp0) outliers start: 59 outliers final: 45 residues processed: 288 average time/residue: 0.3020 time to fit residues: 134.1188 Evaluate side-chains 295 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 244 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 238 GLU Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 489 VAL Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 238 optimal weight: 0.9980 chunk 198 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19596 Z= 0.195 Angle : 0.474 6.212 26504 Z= 0.248 Chirality : 0.042 0.160 2863 Planarity : 0.004 0.048 3438 Dihedral : 3.539 18.697 2615 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.72 % Favored : 94.19 % Rotamer: Outliers : 2.76 % Allowed : 12.22 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.18), residues: 2463 helix: 2.31 (0.15), residues: 1274 sheet: 0.47 (0.33), residues: 241 loop : -0.50 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 266 HIS 0.004 0.001 HIS G 235 PHE 0.014 0.001 PHE D 473 TYR 0.011 0.001 TYR H 240 ARG 0.006 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 252 time to evaluate : 2.172 Fit side-chains REVERT: A 305 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8407 (mp) REVERT: C 305 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8465 (mp) REVERT: C 512 LYS cc_start: 0.8472 (ptpp) cc_final: 0.8097 (mmtm) REVERT: D 279 SER cc_start: 0.9195 (p) cc_final: 0.8745 (m) REVERT: D 387 ARG cc_start: 0.8272 (mtm180) cc_final: 0.8045 (mtm110) REVERT: E 464 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8461 (mm) REVERT: E 495 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8643 (pp) REVERT: F 232 PHE cc_start: 0.7330 (t80) cc_final: 0.7055 (t80) REVERT: F 386 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8135 (mt-10) REVERT: G 282 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7815 (p0) REVERT: G 503 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7974 (mtm) REVERT: H 238 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7406 (mp0) outliers start: 58 outliers final: 48 residues processed: 291 average time/residue: 0.3242 time to fit residues: 146.9879 Evaluate side-chains 304 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 249 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 472 ASP Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 238 GLU Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 489 VAL Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Chi-restraints excluded: chain H residue 529 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 201 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN G 235 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19596 Z= 0.224 Angle : 0.488 6.164 26504 Z= 0.255 Chirality : 0.042 0.158 2863 Planarity : 0.004 0.048 3438 Dihedral : 3.622 18.831 2615 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.25 % Favored : 93.67 % Rotamer: Outliers : 2.90 % Allowed : 12.65 % Favored : 84.45 % 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: 1.55 (0.18), residues: 2463 helix: 2.26 (0.15), residues: 1274 sheet: 0.45 (0.33), residues: 241 loop : -0.53 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 266 HIS 0.006 0.001 HIS G 235 PHE 0.013 0.001 PHE D 473 TYR 0.012 0.001 TYR A 240 ARG 0.007 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 253 time to evaluate : 2.157 Fit side-chains REVERT: A 305 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8404 (mp) REVERT: C 305 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8467 (mp) REVERT: C 512 LYS cc_start: 0.8471 (ptpp) cc_final: 0.8143 (ptmt) REVERT: D 279 SER cc_start: 0.9173 (p) cc_final: 0.8703 (m) REVERT: D 387 ARG cc_start: 0.8285 (mtm180) cc_final: 0.8049 (mtm110) REVERT: E 464 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8468 (mm) REVERT: E 495 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8654 (pp) REVERT: F 232 PHE cc_start: 0.7242 (t80) cc_final: 0.6857 (t80) REVERT: F 274 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7389 (t0) REVERT: F 386 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8099 (mt-10) REVERT: G 282 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7816 (p0) REVERT: H 238 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7361 (mp0) outliers start: 61 outliers final: 49 residues processed: 294 average time/residue: 0.2901 time to fit residues: 130.8948 Evaluate side-chains 296 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 240 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 472 ASP Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 238 GLU Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 489 VAL Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Chi-restraints excluded: chain H residue 529 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 0.0270 chunk 95 optimal weight: 8.9990 chunk 142 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 216 optimal weight: 6.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN F 521 HIS G 235 HIS H 515 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19596 Z= 0.175 Angle : 0.471 6.097 26504 Z= 0.247 Chirality : 0.041 0.153 2863 Planarity : 0.004 0.047 3438 Dihedral : 3.558 18.664 2615 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 2.71 % Allowed : 13.03 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.18), residues: 2463 helix: 2.30 (0.15), residues: 1274 sheet: 0.48 (0.33), residues: 241 loop : -0.52 (0.22), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 266 HIS 0.007 0.000 HIS G 235 PHE 0.021 0.001 PHE D 473 TYR 0.012 0.001 TYR A 240 ARG 0.007 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 250 time to evaluate : 2.329 Fit side-chains REVERT: A 305 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8413 (mp) REVERT: B 495 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8272 (tt) REVERT: C 305 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8463 (mp) REVERT: C 512 LYS cc_start: 0.8468 (ptpp) cc_final: 0.8111 (mmtm) REVERT: D 279 SER cc_start: 0.9192 (p) cc_final: 0.8734 (m) REVERT: D 387 ARG cc_start: 0.8261 (mtm180) cc_final: 0.8020 (mtm110) REVERT: E 464 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8460 (mm) REVERT: F 232 PHE cc_start: 0.7195 (t80) cc_final: 0.6869 (t80) REVERT: F 274 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7373 (t0) REVERT: F 525 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7328 (m-30) REVERT: G 282 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7817 (p0) REVERT: H 238 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7378 (mp0) outliers start: 57 outliers final: 47 residues processed: 286 average time/residue: 0.3099 time to fit residues: 136.6743 Evaluate side-chains 300 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 245 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 525 ASP Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 238 GLU Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 489 VAL Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Chi-restraints excluded: chain H residue 529 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 0.5980 chunk 208 optimal weight: 0.5980 chunk 221 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 200 optimal weight: 0.0970 chunk 209 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 234 optimal weight: 5.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN G 235 HIS H 278 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19596 Z= 0.167 Angle : 0.469 6.127 26504 Z= 0.245 Chirality : 0.041 0.152 2863 Planarity : 0.004 0.047 3438 Dihedral : 3.526 18.599 2615 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 2.85 % Allowed : 12.79 % Favored : 84.36 % 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: 1.62 (0.18), residues: 2463 helix: 2.33 (0.15), residues: 1274 sheet: 0.45 (0.33), residues: 241 loop : -0.52 (0.22), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 266 HIS 0.007 0.000 HIS G 235 PHE 0.019 0.001 PHE D 473 TYR 0.016 0.001 TYR A 240 ARG 0.007 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 250 time to evaluate : 2.217 Fit side-chains REVERT: A 305 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8442 (mp) REVERT: B 388 GLU cc_start: 0.7605 (mp0) cc_final: 0.7307 (mp0) REVERT: B 495 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8302 (tt) REVERT: C 305 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8462 (mp) REVERT: C 512 LYS cc_start: 0.8466 (ptpp) cc_final: 0.8113 (mmtm) REVERT: D 279 SER cc_start: 0.9191 (p) cc_final: 0.8745 (m) REVERT: D 387 ARG cc_start: 0.8249 (mtm180) cc_final: 0.8002 (mtm110) REVERT: E 230 MET cc_start: 0.6686 (mmm) cc_final: 0.6026 (mtp) REVERT: E 245 LYS cc_start: 0.8886 (mtmt) cc_final: 0.8441 (mmtt) REVERT: E 388 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6928 (mm-30) REVERT: E 464 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8451 (mm) REVERT: E 495 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8547 (pp) REVERT: F 274 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7327 (t0) REVERT: F 525 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: G 282 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7807 (p0) REVERT: H 238 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7377 (mp0) outliers start: 60 outliers final: 49 residues processed: 288 average time/residue: 0.3001 time to fit residues: 133.4609 Evaluate side-chains 307 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 249 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 472 ASP Chi-restraints excluded: chain F residue 525 ASP Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 238 GLU Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 489 VAL Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Chi-restraints excluded: chain H residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 0.8980 chunk 111 optimal weight: 0.0570 chunk 163 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 226 optimal weight: 5.9990 chunk 195 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 208 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN G 235 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19596 Z= 0.159 Angle : 0.465 6.125 26504 Z= 0.242 Chirality : 0.041 0.152 2863 Planarity : 0.004 0.046 3438 Dihedral : 3.493 18.520 2615 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.15 % Rotamer: Outliers : 2.66 % Allowed : 12.98 % Favored : 84.36 % 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: 1.65 (0.18), residues: 2463 helix: 2.37 (0.15), residues: 1274 sheet: 0.44 (0.33), residues: 241 loop : -0.50 (0.22), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 266 HIS 0.008 0.000 HIS G 235 PHE 0.019 0.001 PHE D 473 TYR 0.015 0.001 TYR A 240 ARG 0.008 0.000 ARG B 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4926 Ramachandran restraints generated. 2463 Oldfield, 0 Emsley, 2463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 258 time to evaluate : 2.191 Fit side-chains REVERT: A 276 GLN cc_start: 0.8101 (mt0) cc_final: 0.7735 (mt0) REVERT: A 305 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8450 (mp) REVERT: B 495 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8277 (tt) REVERT: C 305 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8456 (mp) REVERT: C 512 LYS cc_start: 0.8461 (ptpp) cc_final: 0.8113 (mmtm) REVERT: D 279 SER cc_start: 0.9165 (p) cc_final: 0.8715 (m) REVERT: D 387 ARG cc_start: 0.8237 (mtm180) cc_final: 0.8001 (mtm110) REVERT: E 230 MET cc_start: 0.6704 (mmm) cc_final: 0.6040 (mtp) REVERT: E 245 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8440 (mmtt) REVERT: E 388 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6955 (mm-30) REVERT: E 495 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8540 (pp) REVERT: F 232 PHE cc_start: 0.7281 (t80) cc_final: 0.6944 (t80) REVERT: F 269 SER cc_start: 0.8544 (m) cc_final: 0.8252 (m) REVERT: F 274 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7319 (t0) REVERT: F 330 GLU cc_start: 0.8014 (mp0) cc_final: 0.7779 (mp0) REVERT: F 503 MET cc_start: 0.8041 (mtm) cc_final: 0.7804 (mtp) REVERT: F 525 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7241 (m-30) REVERT: G 282 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7802 (p0) REVERT: G 503 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8069 (mtm) REVERT: H 238 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7368 (mp0) outliers start: 56 outliers final: 46 residues processed: 292 average time/residue: 0.2931 time to fit residues: 132.1738 Evaluate side-chains 308 residues out of total 2103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 253 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 472 ASP Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 472 ASP Chi-restraints excluded: chain F residue 525 ASP Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 529 LEU Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 450 GLU Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 503 MET Chi-restraints excluded: chain H residue 238 GLU Chi-restraints excluded: chain H residue 274 ASP Chi-restraints excluded: chain H residue 424 SER Chi-restraints excluded: chain H residue 472 ASP Chi-restraints excluded: chain H residue 489 VAL Chi-restraints excluded: chain H residue 495 LEU Chi-restraints excluded: chain H residue 503 MET Chi-restraints excluded: chain H residue 527 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 201 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 11 optimal weight: 0.0670 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN G 235 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.141621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118564 restraints weight = 21861.442| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.33 r_work: 0.3169 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19596 Z= 0.205 Angle : 0.491 6.136 26504 Z= 0.256 Chirality : 0.042 0.154 2863 Planarity : 0.004 0.047 3438 Dihedral : 3.590 19.710 2615 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 2.66 % Allowed : 12.93 % Favored : 84.40 % 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: 1.57 (0.18), residues: 2463 helix: 2.31 (0.15), residues: 1272 sheet: 0.39 (0.33), residues: 241 loop : -0.55 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 266 HIS 0.008 0.001 HIS G 235 PHE 0.019 0.001 PHE D 473 TYR 0.019 0.001 TYR A 240 ARG 0.007 0.000 ARG B 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4040.26 seconds wall clock time: 75 minutes 2.07 seconds (4502.07 seconds total)