Starting phenix.real_space_refine on Sun Apr 7 12:43:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/04_2024/7lh2_23334_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/04_2024/7lh2_23334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/04_2024/7lh2_23334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/04_2024/7lh2_23334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/04_2024/7lh2_23334_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/04_2024/7lh2_23334_updated.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6930 2.51 5 N 1690 2.21 5 O 1860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 31": "NH1" <-> "NH2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 686": "OD1" <-> "OD2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 502": "NH1" <-> "NH2" Residue "B TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 558": "NH1" <-> "NH2" Residue "B TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 686": "OD1" <-> "OD2" Residue "B ARG 689": "NH1" <-> "NH2" Residue "B GLU 694": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10528 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'CLR': 1, 'SAL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'CLR': 1, 'SAL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.87, per 1000 atoms: 0.56 Number of scatterers: 10528 At special positions: 0 Unit cell: (102.16, 120.379, 113.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1860 8.00 N 1690 7.00 C 6930 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: 4.46 Conformation dependent library (CDL) restraints added in 1.8 seconds 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 4 sheets defined 61.9% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.886A pdb=" N ARG A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 50 removed outlier: 4.170A pdb=" N GLN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ALA A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 50' Processing helix chain 'A' and resid 54 through 64 Processing helix chain 'A' and resid 66 through 70 removed outlier: 4.030A pdb=" N TRP A 70 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 105 removed outlier: 5.451A pdb=" N LEU A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 118 through 126 removed outlier: 3.664A pdb=" N PHE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 169 through 195 Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.549A pdb=" N ALA A 202 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 203 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 224 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 242 through 256 removed outlier: 5.029A pdb=" N LYS A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASN A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 281 Processing helix chain 'A' and resid 292 through 307 Processing helix chain 'A' and resid 309 through 312 No H-bonds generated for 'chain 'A' and resid 309 through 312' Processing helix chain 'A' and resid 336 through 365 removed outlier: 6.494A pdb=" N VAL A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 388 Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 412 through 426 Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 449 through 464 removed outlier: 4.380A pdb=" N GLN A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N PHE A 455 " --> pdb=" O MET A 451 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N SER A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEU A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Proline residue: A 459 - end of helix Processing helix chain 'A' and resid 466 through 480 Processing helix chain 'A' and resid 484 through 504 removed outlier: 3.866A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 Processing helix chain 'A' and resid 564 through 578 Processing helix chain 'A' and resid 627 through 632 removed outlier: 4.008A pdb=" N PHE A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 669 Processing helix chain 'A' and resid 681 through 689 Processing helix chain 'A' and resid 696 through 701 removed outlier: 3.928A pdb=" N GLU A 700 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 724 Processing helix chain 'B' and resid 25 through 31 removed outlier: 3.885A pdb=" N ARG B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 50 removed outlier: 4.170A pdb=" N GLN B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ALA B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 50' Processing helix chain 'B' and resid 54 through 64 Processing helix chain 'B' and resid 66 through 70 removed outlier: 4.030A pdb=" N TRP B 70 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 105 removed outlier: 5.451A pdb=" N LEU B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 118 through 126 removed outlier: 3.665A pdb=" N PHE B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'B' and resid 169 through 195 Processing helix chain 'B' and resid 198 through 204 removed outlier: 3.549A pdb=" N ALA B 202 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 203 " --> pdb=" O PHE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 224 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 242 through 256 removed outlier: 5.029A pdb=" N LYS B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASN B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 281 Processing helix chain 'B' and resid 292 through 307 Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 336 through 365 removed outlier: 6.493A pdb=" N VAL B 341 " --> pdb=" O HIS B 337 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASP B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 388 Processing helix chain 'B' and resid 397 through 405 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 449 through 464 removed outlier: 4.379A pdb=" N GLN B 454 " --> pdb=" O GLY B 450 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N PHE B 455 " --> pdb=" O MET B 451 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N SER B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LEU B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Proline residue: B 459 - end of helix Processing helix chain 'B' and resid 466 through 480 Processing helix chain 'B' and resid 484 through 504 removed outlier: 3.866A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 564 through 578 Processing helix chain 'B' and resid 627 through 632 removed outlier: 4.008A pdb=" N PHE B 632 " --> pdb=" O GLU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 669 Processing helix chain 'B' and resid 681 through 689 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.928A pdb=" N GLU B 700 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 724 Processing sheet with id= A, first strand: chain 'A' and resid 511 through 513 Processing sheet with id= B, first strand: chain 'A' and resid 535 through 539 removed outlier: 6.746A pdb=" N THR A 641 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N PHE A 538 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 643 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR A 673 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU A 644 " --> pdb=" O TYR A 673 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR A 675 " --> pdb=" O LEU A 644 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 511 through 513 Processing sheet with id= D, first strand: chain 'B' and resid 535 through 539 removed outlier: 6.746A pdb=" N THR B 641 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N PHE B 538 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE B 643 " --> pdb=" O PHE B 538 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR B 673 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU B 644 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR B 675 " --> pdb=" O LEU B 644 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 542 hydrogen bonds defined for protein. 1578 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: 2.91 Time building geometry restraints manager: 4.84 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: 3242 1.34 - 1.46: 2346 1.46 - 1.58: 5104 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 10770 Sorted by residual: bond pdb=" C1 SAL A 801 " pdb=" C2 SAL A 801 " ideal model delta sigma weight residual 1.409 1.484 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C1 SAL B 801 " pdb=" C2 SAL B 801 " ideal model delta sigma weight residual 1.409 1.484 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" N VAL B 402 " pdb=" CA VAL B 402 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.49e+00 bond pdb=" N SER B 398 " pdb=" CA SER B 398 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.66e+00 bond pdb=" N GLN B 403 " pdb=" CA GLN B 403 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.83e+00 ... (remaining 10765 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.00: 294 106.00 - 113.00: 5913 113.00 - 120.00: 3689 120.00 - 126.99: 4658 126.99 - 133.99: 100 Bond angle restraints: 14654 Sorted by residual: angle pdb=" O VAL B 402 " pdb=" C VAL B 402 " pdb=" N GLN B 403 " ideal model delta sigma weight residual 121.87 124.67 -2.80 9.70e-01 1.06e+00 8.32e+00 angle pdb=" CA LEU A 448 " pdb=" CB LEU A 448 " pdb=" CG LEU A 448 " ideal model delta sigma weight residual 116.30 125.79 -9.49 3.50e+00 8.16e-02 7.36e+00 angle pdb=" CA LEU B 448 " pdb=" CB LEU B 448 " pdb=" CG LEU B 448 " ideal model delta sigma weight residual 116.30 125.74 -9.44 3.50e+00 8.16e-02 7.27e+00 angle pdb=" CA SER B 398 " pdb=" C SER B 398 " pdb=" O SER B 398 " ideal model delta sigma weight residual 120.82 118.04 2.78 1.05e+00 9.07e-01 7.00e+00 angle pdb=" CA ARG B 399 " pdb=" C ARG B 399 " pdb=" O ARG B 399 " ideal model delta sigma weight residual 120.55 117.84 2.71 1.06e+00 8.90e-01 6.52e+00 ... (remaining 14649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 5809 16.06 - 32.13: 527 32.13 - 48.19: 100 48.19 - 64.25: 22 64.25 - 80.32: 12 Dihedral angle restraints: 6470 sinusoidal: 2546 harmonic: 3924 Sorted by residual: dihedral pdb=" CA PHE A 23 " pdb=" C PHE A 23 " pdb=" N SER A 24 " pdb=" CA SER A 24 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PHE B 23 " pdb=" C PHE B 23 " pdb=" N SER B 24 " pdb=" CA SER B 24 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ASP B 686 " pdb=" CB ASP B 686 " pdb=" CG ASP B 686 " pdb=" OD1 ASP B 686 " ideal model delta sinusoidal sigma weight residual -30.00 -87.57 57.57 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 6467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1174 0.039 - 0.077: 427 0.077 - 0.116: 123 0.116 - 0.154: 16 0.154 - 0.193: 4 Chirality restraints: 1744 Sorted by residual: chirality pdb=" CG LEU A 193 " pdb=" CB LEU A 193 " pdb=" CD1 LEU A 193 " pdb=" CD2 LEU A 193 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CG LEU B 193 " pdb=" CB LEU B 193 " pdb=" CD1 LEU B 193 " pdb=" CD2 LEU B 193 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA VAL B 402 " pdb=" N VAL B 402 " pdb=" C VAL B 402 " pdb=" CB VAL B 402 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.28e-01 ... (remaining 1741 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 633 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO B 634 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 634 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 634 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 633 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 634 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 634 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 634 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 198 " 0.015 2.00e-02 2.50e+03 1.47e-02 3.78e+00 pdb=" CG PHE B 198 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 198 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 198 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 198 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 198 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 198 " 0.000 2.00e-02 2.50e+03 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 64 2.60 - 3.18: 9520 3.18 - 3.75: 16221 3.75 - 4.33: 21775 4.33 - 4.90: 36224 Nonbonded interactions: 83804 Sorted by model distance: nonbonded pdb=" OG SER A 398 " pdb=" O2' SAL A 801 " model vdw 2.030 2.440 nonbonded pdb=" OG SER B 86 " pdb=" O GLN B 403 " model vdw 2.164 2.440 nonbonded pdb=" OD2 ASP A 83 " pdb=" OG1 THR A 410 " model vdw 2.223 2.440 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 410 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR B 503 " pdb=" OH TYR B 545 " model vdw 2.226 2.440 ... (remaining 83799 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 'B' } 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: 0.980 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: 4.100 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 30.730 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.003 0.075 10770 Z= 0.202 Angle : 0.558 9.493 14654 Z= 0.304 Chirality : 0.043 0.193 1744 Planarity : 0.004 0.053 1812 Dihedral : 13.017 80.315 3958 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.18 % Allowed : 0.53 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.24), residues: 1352 helix: 1.34 (0.18), residues: 894 sheet: 1.90 (0.69), residues: 52 loop : -1.07 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 472 HIS 0.002 0.001 HIS A 25 PHE 0.034 0.001 PHE B 198 TYR 0.014 0.001 TYR B 237 ARG 0.008 0.001 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 1.039 Fit side-chains REVERT: A 545 TYR cc_start: 0.8268 (p90) cc_final: 0.7954 (p90) outliers start: 2 outliers final: 2 residues processed: 146 average time/residue: 0.1844 time to fit residues: 41.0622 Evaluate side-chains 105 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain B residue 453 MET 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: 8.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 0.0370 chunk 55 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10770 Z= 0.196 Angle : 0.518 11.040 14654 Z= 0.251 Chirality : 0.042 0.147 1744 Planarity : 0.004 0.050 1812 Dihedral : 5.130 47.877 1594 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.76 % Allowed : 7.14 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1352 helix: 1.47 (0.18), residues: 900 sheet: 1.89 (0.68), residues: 52 loop : -1.11 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 472 HIS 0.007 0.001 HIS A 704 PHE 0.025 0.001 PHE A 198 TYR 0.012 0.001 TYR A 237 ARG 0.005 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.148 Fit side-chains REVERT: A 545 TYR cc_start: 0.8413 (p90) cc_final: 0.8051 (p90) REVERT: A 575 MET cc_start: 0.7159 (tmm) cc_final: 0.6908 (tmm) REVERT: B 198 PHE cc_start: 0.7049 (t80) cc_final: 0.6638 (t80) REVERT: B 694 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6485 (mp0) outliers start: 20 outliers final: 18 residues processed: 131 average time/residue: 0.1992 time to fit residues: 39.2645 Evaluate side-chains 123 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 550 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10770 Z= 0.165 Angle : 0.493 9.557 14654 Z= 0.238 Chirality : 0.041 0.126 1744 Planarity : 0.004 0.053 1812 Dihedral : 4.385 40.752 1594 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.20 % Allowed : 8.29 % Favored : 89.51 % 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: 1.31 (0.24), residues: 1352 helix: 1.61 (0.18), residues: 890 sheet: 2.01 (0.69), residues: 52 loop : -0.90 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 472 HIS 0.004 0.001 HIS A 704 PHE 0.011 0.001 PHE B 200 TYR 0.010 0.001 TYR A 545 ARG 0.003 0.000 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.299 Fit side-chains REVERT: A 575 MET cc_start: 0.7215 (tmm) cc_final: 0.6845 (tmm) REVERT: B 198 PHE cc_start: 0.7044 (t80) cc_final: 0.6597 (t80) REVERT: B 694 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6555 (mp0) outliers start: 25 outliers final: 20 residues processed: 134 average time/residue: 0.2005 time to fit residues: 40.9033 Evaluate side-chains 126 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 550 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.5980 chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 124 optimal weight: 40.0000 chunk 131 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 109 optimal weight: 0.3980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10770 Z= 0.253 Angle : 0.528 8.888 14654 Z= 0.258 Chirality : 0.042 0.127 1744 Planarity : 0.004 0.055 1812 Dihedral : 4.159 35.874 1588 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.65 % Allowed : 10.93 % Favored : 86.42 % 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: 1.22 (0.24), residues: 1352 helix: 1.51 (0.18), residues: 900 sheet: 1.89 (0.68), residues: 52 loop : -0.93 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 70 HIS 0.004 0.001 HIS A 704 PHE 0.012 0.001 PHE B 391 TYR 0.014 0.001 TYR A 545 ARG 0.003 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 MET cc_start: 0.7415 (tmm) cc_final: 0.7026 (tmm) REVERT: A 694 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6538 (mp0) REVERT: B 198 PHE cc_start: 0.7096 (t80) cc_final: 0.6632 (t80) REVERT: B 227 LYS cc_start: 0.7824 (ptmt) cc_final: 0.7421 (ptpp) outliers start: 30 outliers final: 27 residues processed: 133 average time/residue: 0.2074 time to fit residues: 42.5499 Evaluate side-chains 129 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 723 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 723 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 90 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10770 Z= 0.250 Angle : 0.528 9.248 14654 Z= 0.259 Chirality : 0.042 0.145 1744 Planarity : 0.004 0.055 1812 Dihedral : 4.054 33.950 1588 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.26 % Allowed : 11.73 % Favored : 85.01 % 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: 1.22 (0.24), residues: 1352 helix: 1.51 (0.18), residues: 900 sheet: 1.83 (0.69), residues: 52 loop : -0.92 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 70 HIS 0.004 0.001 HIS A 704 PHE 0.017 0.001 PHE A 198 TYR 0.014 0.001 TYR A 545 ARG 0.005 0.000 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 1.266 Fit side-chains REVERT: A 227 LYS cc_start: 0.7793 (ptmt) cc_final: 0.7443 (ptpt) REVERT: A 575 MET cc_start: 0.7469 (tmm) cc_final: 0.7060 (tmm) REVERT: B 198 PHE cc_start: 0.7139 (t80) cc_final: 0.6643 (t80) REVERT: B 227 LYS cc_start: 0.7800 (ptmt) cc_final: 0.7467 (ptpt) REVERT: B 694 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6538 (mp0) outliers start: 37 outliers final: 31 residues processed: 137 average time/residue: 0.1888 time to fit residues: 39.3243 Evaluate side-chains 132 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 550 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 69 optimal weight: 0.5980 chunk 126 optimal weight: 40.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10770 Z= 0.225 Angle : 0.530 9.776 14654 Z= 0.255 Chirality : 0.042 0.124 1744 Planarity : 0.004 0.056 1812 Dihedral : 4.101 43.873 1588 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.47 % Allowed : 13.49 % Favored : 84.04 % 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 (0.24), residues: 1352 helix: 1.57 (0.18), residues: 894 sheet: 1.74 (0.69), residues: 52 loop : -0.95 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 70 HIS 0.003 0.001 HIS A 704 PHE 0.021 0.001 PHE A 198 TYR 0.013 0.001 TYR A 545 ARG 0.008 0.000 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 1.118 Fit side-chains REVERT: A 227 LYS cc_start: 0.7776 (ptmt) cc_final: 0.7432 (ptpt) REVERT: A 575 MET cc_start: 0.7539 (tmm) cc_final: 0.7126 (tmm) REVERT: A 694 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6527 (mp0) REVERT: B 198 PHE cc_start: 0.7134 (t80) cc_final: 0.6616 (t80) REVERT: B 227 LYS cc_start: 0.7827 (ptmt) cc_final: 0.7480 (ptpt) outliers start: 28 outliers final: 25 residues processed: 127 average time/residue: 0.1900 time to fit residues: 36.5192 Evaluate side-chains 127 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 550 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10770 Z= 0.301 Angle : 0.566 8.199 14654 Z= 0.278 Chirality : 0.043 0.133 1744 Planarity : 0.004 0.057 1812 Dihedral : 4.310 50.962 1588 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.56 % Allowed : 14.55 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1352 helix: 1.49 (0.18), residues: 894 sheet: 1.99 (0.78), residues: 38 loop : -0.94 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 70 HIS 0.003 0.001 HIS A 704 PHE 0.014 0.002 PHE A 50 TYR 0.016 0.001 TYR B 545 ARG 0.006 0.001 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 1.651 Fit side-chains REVERT: A 227 LYS cc_start: 0.7800 (ptmt) cc_final: 0.7458 (ptpt) REVERT: A 575 MET cc_start: 0.7659 (tmm) cc_final: 0.7292 (tmm) REVERT: B 198 PHE cc_start: 0.7178 (t80) cc_final: 0.6638 (t80) REVERT: B 227 LYS cc_start: 0.7814 (ptmt) cc_final: 0.7476 (ptpt) REVERT: B 694 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6613 (mp0) outliers start: 29 outliers final: 28 residues processed: 132 average time/residue: 0.1967 time to fit residues: 39.0454 Evaluate side-chains 133 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 550 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 125 optimal weight: 0.0370 chunk 114 optimal weight: 8.9990 overall best weight: 1.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10770 Z= 0.155 Angle : 0.516 8.719 14654 Z= 0.247 Chirality : 0.041 0.126 1744 Planarity : 0.004 0.055 1812 Dihedral : 4.196 53.001 1588 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.29 % Allowed : 15.52 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.24), residues: 1352 helix: 1.71 (0.18), residues: 882 sheet: 1.75 (0.71), residues: 52 loop : -0.86 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 472 HIS 0.002 0.001 HIS A 704 PHE 0.011 0.001 PHE A 269 TYR 0.016 0.001 TYR A 578 ARG 0.006 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 1.103 Fit side-chains REVERT: A 227 LYS cc_start: 0.7773 (ptmt) cc_final: 0.7404 (ptpt) REVERT: A 575 MET cc_start: 0.7640 (tmm) cc_final: 0.7204 (tmm) REVERT: A 694 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6523 (mp0) REVERT: B 198 PHE cc_start: 0.7142 (t80) cc_final: 0.6576 (t80) REVERT: B 227 LYS cc_start: 0.7777 (ptmt) cc_final: 0.7412 (ptpt) REVERT: B 441 SER cc_start: 0.7600 (t) cc_final: 0.7068 (p) REVERT: B 694 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6587 (mp0) outliers start: 26 outliers final: 24 residues processed: 131 average time/residue: 0.1874 time to fit residues: 37.3048 Evaluate side-chains 132 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 550 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10770 Z= 0.174 Angle : 0.515 9.692 14654 Z= 0.248 Chirality : 0.041 0.124 1744 Planarity : 0.004 0.055 1812 Dihedral : 4.167 54.428 1588 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.94 % Allowed : 16.05 % Favored : 82.01 % 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 (0.24), residues: 1352 helix: 1.75 (0.18), residues: 882 sheet: 1.73 (0.71), residues: 52 loop : -0.81 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 472 HIS 0.002 0.001 HIS A 704 PHE 0.010 0.001 PHE A 269 TYR 0.014 0.001 TYR A 578 ARG 0.009 0.000 ARG A 576 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.190 Fit side-chains REVERT: A 227 LYS cc_start: 0.7750 (ptmt) cc_final: 0.7391 (ptpt) REVERT: A 575 MET cc_start: 0.7618 (tmm) cc_final: 0.7166 (tmm) REVERT: A 694 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6491 (mp0) REVERT: B 198 PHE cc_start: 0.7171 (t80) cc_final: 0.6582 (t80) REVERT: B 227 LYS cc_start: 0.7785 (ptmt) cc_final: 0.7428 (ptpt) REVERT: B 694 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6581 (mp0) outliers start: 22 outliers final: 22 residues processed: 126 average time/residue: 0.2035 time to fit residues: 39.3018 Evaluate side-chains 129 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 550 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10770 Z= 0.401 Angle : 0.623 8.105 14654 Z= 0.310 Chirality : 0.045 0.145 1744 Planarity : 0.004 0.056 1812 Dihedral : 4.546 57.692 1588 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.20 % Allowed : 15.96 % Favored : 81.83 % 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: 1.01 (0.24), residues: 1352 helix: 1.34 (0.18), residues: 904 sheet: 1.81 (0.80), residues: 38 loop : -0.89 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 70 HIS 0.003 0.001 HIS A 704 PHE 0.016 0.002 PHE B 111 TYR 0.017 0.002 TYR A 545 ARG 0.009 0.001 ARG B 576 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 1.106 Fit side-chains REVERT: A 227 LYS cc_start: 0.7808 (ptmt) cc_final: 0.7461 (ptpt) REVERT: A 575 MET cc_start: 0.7673 (tmm) cc_final: 0.7221 (tmm) REVERT: B 198 PHE cc_start: 0.7243 (t80) cc_final: 0.6634 (t80) REVERT: B 227 LYS cc_start: 0.7813 (ptmt) cc_final: 0.7475 (ptpt) outliers start: 25 outliers final: 24 residues processed: 122 average time/residue: 0.1960 time to fit residues: 36.0623 Evaluate side-chains 121 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 550 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 chunk 6 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 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 = 0.3875 r_free = 0.3875 target = 0.136912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.111260 restraints weight = 16595.058| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.03 r_work: 0.3382 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10770 Z= 0.250 Angle : 0.559 10.609 14654 Z= 0.272 Chirality : 0.042 0.129 1744 Planarity : 0.004 0.055 1812 Dihedral : 4.526 59.880 1588 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.20 % Allowed : 16.40 % Favored : 81.39 % 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: 1.06 (0.24), residues: 1352 helix: 1.40 (0.18), residues: 906 sheet: 1.76 (0.80), residues: 38 loop : -0.92 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 472 HIS 0.002 0.001 HIS A 704 PHE 0.012 0.001 PHE B 391 TYR 0.013 0.001 TYR A 578 ARG 0.010 0.001 ARG A 576 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2254.98 seconds wall clock time: 42 minutes 7.36 seconds (2527.36 seconds total)