Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:49:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/12_2022/7lh2_23334_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/12_2022/7lh2_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_23334/12_2022/7lh2_23334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/12_2022/7lh2_23334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/12_2022/7lh2_23334_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/12_2022/7lh2_23334_updated_updated.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 6.43, per 1000 atoms: 0.61 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: 4.28 Conformation dependent library (CDL) restraints added in 1.5 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: 1.31 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: 3.17 Time building geometry restraints manager: 4.64 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: 5700 16.06 - 32.13: 524 32.13 - 48.19: 100 48.19 - 64.25: 22 64.25 - 80.32: 12 Dihedral angle restraints: 6358 sinusoidal: 2434 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 6355 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 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. 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: 0.730 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: 4.750 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.100 Process input model: 30.370 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 13.177 80.315 3846 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 % 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 *********************** 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 : 1.291 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 146 average time/residue: 0.1872 time to fit residues: 41.6291 Evaluate side-chains 104 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1159 time to fit residues: 2.0702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 9.9990 chunk 103 optimal weight: 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: 4.9990 chunk 123 optimal weight: 6.9990 overall best weight: 3.0064 ------------------------------------------------------------------------------- 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: 0.8298 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 10770 Z= 0.212 Angle : 0.526 10.966 14654 Z= 0.256 Chirality : 0.042 0.133 1744 Planarity : 0.004 0.050 1812 Dihedral : 4.076 52.581 1476 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 1.59 % 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: 1.11 (0.24), residues: 1352 helix: 1.45 (0.18), residues: 900 sheet: 1.86 (0.68), residues: 52 loop : -1.05 (0.32), residues: 400 *********************** 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 131 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.283 Fit side-chains outliers start: 18 outliers final: 16 residues processed: 125 average time/residue: 0.1879 time to fit residues: 35.6899 Evaluate side-chains 117 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 1.271 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0976 time to fit residues: 4.6500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 42 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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: 0.8315 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10770 Z= 0.216 Angle : 0.517 9.519 14654 Z= 0.251 Chirality : 0.042 0.124 1744 Planarity : 0.004 0.054 1812 Dihedral : 3.934 41.900 1476 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.06 % 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: 1.17 (0.24), residues: 1352 helix: 1.47 (0.18), residues: 900 sheet: 1.94 (0.69), residues: 52 loop : -0.95 (0.32), residues: 400 *********************** 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 127 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.349 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 126 average time/residue: 0.1892 time to fit residues: 36.3750 Evaluate side-chains 111 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0927 time to fit residues: 2.7053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.0040 chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 124 optimal weight: 40.0000 chunk 131 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 overall best weight: 3.3398 ------------------------------------------------------------------------------- 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: 0.8329 moved from start: 0.1355 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= 0.227 Angle : 0.513 8.762 14654 Z= 0.252 Chirality : 0.042 0.124 1744 Planarity : 0.004 0.055 1812 Dihedral : 3.928 44.765 1476 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 1.50 % 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: 1.51 (0.18), residues: 896 sheet: 1.89 (0.69), residues: 52 loop : -0.84 (0.32), residues: 404 *********************** 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 128 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 124 average time/residue: 0.1959 time to fit residues: 36.8280 Evaluate side-chains 118 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 1.341 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1046 time to fit residues: 4.5739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.8326 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 10770 Z= 0.199 Angle : 0.513 9.125 14654 Z= 0.249 Chirality : 0.042 0.124 1744 Planarity : 0.004 0.055 1812 Dihedral : 3.890 44.838 1476 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 0.53 % 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: 1.39 (0.24), residues: 1352 helix: 1.65 (0.18), residues: 890 sheet: 1.95 (0.70), residues: 52 loop : -0.82 (0.32), residues: 410 *********************** 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 117 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.308 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 116 average time/residue: 0.1898 time to fit residues: 33.9808 Evaluate side-chains 107 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0932 time to fit residues: 2.0591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 77 optimal weight: 0.2980 chunk 32 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 126 optimal weight: 40.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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** B 539 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10770 Z= 0.220 Angle : 0.530 9.499 14654 Z= 0.255 Chirality : 0.042 0.125 1744 Planarity : 0.004 0.056 1812 Dihedral : 3.895 44.176 1476 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 1.32 % 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: 1.38 (0.24), residues: 1352 helix: 1.66 (0.18), residues: 890 sheet: 1.92 (0.70), residues: 52 loop : -0.85 (0.32), residues: 410 *********************** 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 120 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 115 average time/residue: 0.1851 time to fit residues: 32.9022 Evaluate side-chains 115 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0990 time to fit residues: 4.0112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 96 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 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: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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: 0.8347 moved from start: 0.1710 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= 0.238 Angle : 0.540 8.364 14654 Z= 0.262 Chirality : 0.042 0.132 1744 Planarity : 0.004 0.055 1812 Dihedral : 3.947 43.960 1476 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 0.44 % 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: 1.70 (0.18), residues: 878 sheet: 1.79 (0.70), residues: 52 loop : -0.83 (0.32), residues: 422 *********************** 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 113 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 1.199 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 110 average time/residue: 0.1948 time to fit residues: 32.9784 Evaluate side-chains 106 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1045 time to fit residues: 2.3995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 125 optimal weight: 0.0980 chunk 114 optimal weight: 10.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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 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: 0.8348 moved from start: 0.1811 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= 0.232 Angle : 0.536 8.815 14654 Z= 0.261 Chirality : 0.042 0.125 1744 Planarity : 0.004 0.055 1812 Dihedral : 3.988 44.064 1476 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.24), residues: 1352 helix: 1.72 (0.18), residues: 878 sheet: 1.73 (0.70), residues: 52 loop : -0.82 (0.31), residues: 422 *********************** 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 112 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 1.356 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 107 average time/residue: 0.1901 time to fit residues: 31.4418 Evaluate side-chains 106 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.215 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0980 time to fit residues: 2.0330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.4096 > 50: distance: 30 - 36: 16.874 distance: 36 - 37: 14.411 distance: 37 - 38: 20.425 distance: 37 - 40: 11.145 distance: 38 - 39: 18.512 distance: 38 - 47: 16.357 distance: 40 - 41: 4.537 distance: 41 - 42: 5.456 distance: 41 - 43: 4.712 distance: 42 - 44: 6.175 distance: 43 - 45: 3.708 distance: 45 - 46: 3.078 distance: 47 - 48: 19.191 distance: 48 - 49: 15.868 distance: 48 - 51: 17.462 distance: 49 - 50: 9.832 distance: 49 - 56: 9.067 distance: 51 - 52: 13.362 distance: 52 - 53: 12.863 distance: 53 - 54: 4.763 distance: 56 - 57: 13.872 distance: 57 - 58: 10.902 distance: 57 - 60: 14.376 distance: 58 - 59: 19.075 distance: 58 - 65: 6.606 distance: 60 - 61: 13.888 distance: 61 - 62: 4.056 distance: 62 - 63: 6.200 distance: 62 - 64: 12.229 distance: 65 - 66: 15.540 distance: 66 - 67: 9.206 distance: 66 - 69: 13.407 distance: 67 - 68: 23.678 distance: 67 - 74: 7.212 distance: 69 - 70: 11.774 distance: 70 - 71: 13.258 distance: 71 - 72: 16.961 distance: 72 - 73: 7.447 distance: 74 - 75: 23.527 distance: 75 - 76: 15.331 distance: 75 - 78: 29.098 distance: 76 - 77: 19.265 distance: 76 - 82: 13.660 distance: 78 - 79: 29.825 distance: 79 - 80: 17.216 distance: 79 - 81: 26.511 distance: 82 - 83: 21.973 distance: 82 - 88: 27.263 distance: 83 - 84: 17.053 distance: 83 - 86: 12.971 distance: 84 - 85: 5.986 distance: 84 - 89: 21.443 distance: 86 - 87: 11.593 distance: 87 - 88: 17.501 distance: 89 - 90: 8.784 distance: 90 - 91: 13.286 distance: 90 - 93: 6.217 distance: 91 - 92: 19.789 distance: 91 - 94: 17.985 distance: 94 - 95: 28.920 distance: 94 - 100: 22.850 distance: 95 - 96: 23.272 distance: 95 - 98: 10.889 distance: 96 - 97: 26.700 distance: 96 - 101: 17.698 distance: 98 - 99: 9.954 distance: 99 - 100: 16.252 distance: 101 - 102: 11.778 distance: 102 - 103: 27.809 distance: 102 - 105: 19.688 distance: 103 - 104: 53.410 distance: 103 - 109: 28.103 distance: 105 - 106: 14.494 distance: 105 - 107: 8.940 distance: 106 - 108: 6.170 distance: 109 - 110: 6.807 distance: 109 - 115: 7.811 distance: 110 - 111: 10.486 distance: 110 - 113: 20.830 distance: 111 - 112: 7.114 distance: 111 - 116: 18.139 distance: 113 - 114: 10.542 distance: 114 - 115: 3.656