Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 11:41:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/04_2023/7vdf_31916_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/04_2023/7vdf_31916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/04_2023/7vdf_31916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/04_2023/7vdf_31916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/04_2023/7vdf_31916_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdf_31916/04_2023/7vdf_31916_trim.pdb" } resolution = 2.56 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= 0.002 sd= 0.151 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 7251 2.51 5 N 2025 2.21 5 O 2316 1.98 5 H 11043 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 31": "OD1" <-> "OD2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "C ASP 104": "OD1" <-> "OD2" Residue "C ASP 493": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 22692 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7497 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "B" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7497 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 7497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7497 Classifications: {'peptide': 485} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 10.21, per 1000 atoms: 0.45 Number of scatterers: 22692 At special positions: 0 Unit cell: (84.36, 85.88, 144.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 2316 8.00 N 2025 7.00 C 7251 6.00 H 11043 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.04 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 285 " " NAG A 602 " - " ASN A 165 " " NAG A 603 " - " ASN A 81 " " NAG B 601 " - " ASN B 285 " " NAG B 602 " - " ASN B 165 " " NAG B 603 " - " ASN B 81 " " NAG C 603 " - " ASN C 285 " " NAG C 604 " - " ASN C 165 " " NAG C 605 " - " ASN C 81 " Time building additional restraints: 18.22 Conformation dependent library (CDL) restraints added in 1.9 seconds 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 34 sheets defined 26.4% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.907A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 367 through 379 removed outlier: 4.202A pdb=" N GLY A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 455 Processing helix chain 'A' and resid 474 through 483 Processing helix chain 'A' and resid 487 through 501 removed outlier: 4.264A pdb=" N TYR A 491 " --> pdb=" O ASP A 487 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLU A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.940A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL B 78 " --> pdb=" O HIS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 367 through 379 removed outlier: 4.231A pdb=" N GLY B 379 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 455 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 487 through 501 removed outlier: 4.250A pdb=" N TYR B 491 " --> pdb=" O ASP B 487 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASP B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLU B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.853A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 367 through 379 removed outlier: 4.239A pdb=" N GLY C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 455 Processing helix chain 'C' and resid 474 through 483 Processing helix chain 'C' and resid 487 through 501 removed outlier: 4.330A pdb=" N TYR C 491 " --> pdb=" O ASP C 487 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ASP C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLU C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 366 removed outlier: 3.764A pdb=" N ASN A 357 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR A 351 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.838A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.971A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.461A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 removed outlier: 5.493A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.306A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 12 through 17 removed outlier: 4.590A pdb=" N TYR B 351 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 357 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AB6, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'B' and resid 51 through 54 removed outlier: 5.906A pdb=" N ILE B 51 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N CYS B 277 " --> pdb=" O ILE B 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.013A pdb=" N PHE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.909A pdb=" N ASP B 101 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N TRP B 234 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 101 removed outlier: 6.909A pdb=" N ASP B 101 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N TRP B 234 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AC4, first strand: chain 'B' and resid 164 through 169 removed outlier: 5.072A pdb=" N ARG B 201 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 286 through 288 removed outlier: 4.265A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 360 through 366 removed outlier: 3.781A pdb=" N ASN C 357 " --> pdb=" O GLY C 360 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR C 351 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC8, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC9, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.000A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AD3, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.892A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 100 through 101 removed outlier: 6.892A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'C' and resid 164 through 169 removed outlier: 5.050A pdb=" N ARG C 201 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 286 through 287 524 hydrogen bonds defined for protein. 1434 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: 9.47 Time building geometry restraints manager: 19.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11037 1.04 - 1.24: 1448 1.24 - 1.44: 3768 1.44 - 1.64: 6598 1.64 - 1.84: 78 Bond restraints: 22929 Sorted by residual: bond pdb=" N SER A 9 " pdb=" CA SER A 9 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N SER B 9 " pdb=" CA SER B 9 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" N SER C 9 " pdb=" CA SER C 9 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.73e+00 bond pdb=" N SER C 9 " pdb=" H SER C 9 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" N SER B 9 " pdb=" H SER B 9 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 22924 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.07: 464 107.07 - 113.80: 27003 113.80 - 120.53: 7121 120.53 - 127.26: 6469 127.26 - 134.00: 139 Bond angle restraints: 41196 Sorted by residual: angle pdb=" CA CYS B 14 " pdb=" CB CYS B 14 " pdb=" SG CYS B 14 " ideal model delta sigma weight residual 114.40 120.12 -5.72 2.30e+00 1.89e-01 6.18e+00 angle pdb=" C LYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta sigma weight residual 122.56 119.39 3.17 1.50e+00 4.44e-01 4.47e+00 angle pdb=" C PHE C 392 " pdb=" N HIS C 393 " pdb=" CA HIS C 393 " ideal model delta sigma weight residual 122.93 119.88 3.05 1.45e+00 4.76e-01 4.41e+00 angle pdb=" C LEU B 13 " pdb=" N CYS B 14 " pdb=" CA CYS B 14 " ideal model delta sigma weight residual 122.45 118.79 3.66 1.78e+00 3.16e-01 4.22e+00 angle pdb=" N CYS B 14 " pdb=" CA CYS B 14 " pdb=" C CYS B 14 " ideal model delta sigma weight residual 107.88 110.71 -2.83 1.41e+00 5.03e-01 4.03e+00 ... (remaining 41191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 8431 17.58 - 35.15: 586 35.15 - 52.73: 105 52.73 - 70.30: 30 70.30 - 87.88: 16 Dihedral angle restraints: 9168 sinusoidal: 4275 harmonic: 4893 Sorted by residual: dihedral pdb=" CA CYS C 97 " pdb=" CB CYS C 97 " pdb=" SG CYS C 97 " pdb=" SG CYS C 139 " ideal model delta sinusoidal sigma weight residual 79.00 8.95 70.05 1 2.00e+01 2.50e-03 1.58e+01 dihedral pdb=" CA CYS B 14 " pdb=" C CYS B 14 " pdb=" N LEU B 15 " pdb=" CA LEU B 15 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA TRP A 84 " pdb=" C TRP A 84 " pdb=" N ASP A 85 " pdb=" CA ASP A 85 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 9165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1570 0.061 - 0.121: 211 0.121 - 0.181: 27 0.181 - 0.242: 1 0.242 - 0.302: 3 Chirality restraints: 1812 Sorted by residual: chirality pdb=" C5 BMA A 605 " pdb=" C4 BMA A 605 " pdb=" C6 BMA A 605 " pdb=" O5 BMA A 605 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C5 BMA B 605 " pdb=" C4 BMA B 605 " pdb=" C6 BMA B 605 " pdb=" O5 BMA B 605 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C5 BMA C 602 " pdb=" C4 BMA C 602 " pdb=" C6 BMA C 602 " pdb=" O5 BMA C 602 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1809 not shown) Planarity restraints: 3495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 20 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.47e+00 pdb=" N PRO A 21 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 73 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO A 74 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 283 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.07e+00 pdb=" N PRO B 284 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " -0.015 5.00e-02 4.00e+02 ... (remaining 3492 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 935 2.15 - 2.76: 45082 2.76 - 3.37: 68804 3.37 - 3.99: 94764 3.99 - 4.60: 143378 Nonbonded interactions: 352963 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 27 " pdb=" O ARG B 383 " model vdw 1.537 1.850 nonbonded pdb=" HZ2 LYS A 27 " pdb=" O ARG B 383 " model vdw 1.540 1.850 nonbonded pdb=" OD2 ASP A 415 " pdb=" HZ2 LYS B 391 " model vdw 1.569 1.850 nonbonded pdb=" H MET B 462 " pdb=" O CYS B 466 " model vdw 1.575 1.850 nonbonded pdb=" HZ1 LYS A 391 " pdb=" OD2 ASP C 419 " model vdw 1.583 1.850 ... (remaining 352958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 501 or resid 601 or resid 603 through 604)) selection = (chain 'B' and (resid 9 through 501 or resid 601 or resid 603 through 604)) selection = (chain 'C' and (resid 9 through 501 or resid 601 or resid 603 through 604)) } 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: 1.570 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: 0.330 Extract box with map and model: 8.880 Check model and map are aligned: 0.330 Set scattering table: 0.170 Process input model: 72.900 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.100 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:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 11886 Z= 0.234 Angle : 0.548 5.986 16122 Z= 0.275 Chirality : 0.046 0.302 1812 Planarity : 0.003 0.035 2094 Dihedral : 14.002 87.880 4290 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.05 (0.21), residues: 1443 helix: 2.24 (0.26), residues: 339 sheet: -0.79 (0.29), residues: 315 loop : -0.70 (0.21), residues: 789 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.820 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 2.0822 time to fit residues: 425.2237 Evaluate side-chains 148 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 248 ASN B 394 GLN C 173 ASN C 211 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 11886 Z= 0.273 Angle : 0.508 7.773 16122 Z= 0.267 Chirality : 0.043 0.180 1812 Planarity : 0.004 0.051 2094 Dihedral : 4.571 18.751 1569 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.10 (0.21), residues: 1443 helix: 2.15 (0.26), residues: 339 sheet: -0.71 (0.31), residues: 291 loop : -0.77 (0.20), residues: 813 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 159 time to evaluate : 1.793 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 166 average time/residue: 2.0431 time to fit residues: 376.8780 Evaluate side-chains 159 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 1.795 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 2.2606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 11886 Z= 0.351 Angle : 0.540 9.453 16122 Z= 0.283 Chirality : 0.044 0.160 1812 Planarity : 0.005 0.068 2094 Dihedral : 4.749 20.002 1569 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.43 (0.21), residues: 1443 helix: 1.86 (0.26), residues: 342 sheet: -0.53 (0.32), residues: 273 loop : -1.15 (0.19), residues: 828 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 175 average time/residue: 1.9885 time to fit residues: 388.6873 Evaluate side-chains 164 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.3389 time to fit residues: 3.6339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 0.0020 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN B 33 GLN B 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 11886 Z= 0.257 Angle : 0.503 9.136 16122 Z= 0.263 Chirality : 0.042 0.156 1812 Planarity : 0.004 0.052 2094 Dihedral : 4.614 18.946 1569 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.28 (0.21), residues: 1443 helix: 1.95 (0.26), residues: 342 sheet: -0.85 (0.30), residues: 291 loop : -0.87 (0.20), residues: 810 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 169 average time/residue: 1.9700 time to fit residues: 372.2888 Evaluate side-chains 161 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 1.962 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.2528 time to fit residues: 2.8904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 11886 Z= 0.408 Angle : 0.564 10.167 16122 Z= 0.294 Chirality : 0.044 0.151 1812 Planarity : 0.005 0.075 2094 Dihedral : 4.843 20.339 1569 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.56 (0.20), residues: 1443 helix: 1.71 (0.26), residues: 342 sheet: -0.74 (0.31), residues: 279 loop : -1.18 (0.19), residues: 822 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.852 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 164 average time/residue: 1.9608 time to fit residues: 359.3827 Evaluate side-chains 162 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 1.949 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.3031 time to fit residues: 4.0661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 11886 Z= 0.333 Angle : 0.536 10.164 16122 Z= 0.280 Chirality : 0.043 0.147 1812 Planarity : 0.004 0.064 2094 Dihedral : 4.781 19.740 1569 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.38 (0.21), residues: 1443 helix: 1.73 (0.26), residues: 342 sheet: -0.70 (0.34), residues: 249 loop : -0.96 (0.19), residues: 852 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 171 average time/residue: 1.9595 time to fit residues: 377.0742 Evaluate side-chains 164 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 1.891 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.3330 time to fit residues: 4.6547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 11886 Z= 0.259 Angle : 0.509 9.679 16122 Z= 0.266 Chirality : 0.043 0.146 1812 Planarity : 0.004 0.050 2094 Dihedral : 4.653 19.110 1569 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.55 (0.21), residues: 1443 helix: 1.86 (0.26), residues: 342 sheet: -0.93 (0.29), residues: 303 loop : -1.14 (0.19), residues: 798 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 166 average time/residue: 1.8600 time to fit residues: 348.1846 Evaluate side-chains 163 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 1.696 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.2807 time to fit residues: 3.2201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 0.0370 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN B 33 GLN B 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 11886 Z= 0.216 Angle : 0.490 9.174 16122 Z= 0.255 Chirality : 0.042 0.148 1812 Planarity : 0.004 0.040 2094 Dihedral : 4.540 18.724 1569 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.44 (0.21), residues: 1443 helix: 2.15 (0.26), residues: 336 sheet: -0.95 (0.29), residues: 303 loop : -1.10 (0.19), residues: 804 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 168 average time/residue: 1.8319 time to fit residues: 347.1113 Evaluate side-chains 160 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 152 time to evaluate : 1.951 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.3616 time to fit residues: 3.7516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 0.0870 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 11886 Z= 0.269 Angle : 0.510 9.272 16122 Z= 0.266 Chirality : 0.043 0.146 1812 Planarity : 0.004 0.052 2094 Dihedral : 4.587 19.095 1569 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.53 (0.21), residues: 1443 helix: 1.95 (0.25), residues: 342 sheet: -1.04 (0.29), residues: 309 loop : -1.11 (0.19), residues: 792 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 161 average time/residue: 1.7730 time to fit residues: 323.3064 Evaluate side-chains 159 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 1.912 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.3017 time to fit residues: 3.4422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 11886 Z= 0.326 Angle : 0.540 9.826 16122 Z= 0.281 Chirality : 0.043 0.145 1812 Planarity : 0.005 0.061 2094 Dihedral : 4.713 19.387 1569 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.58 (0.21), residues: 1443 helix: 1.84 (0.26), residues: 342 sheet: -1.03 (0.29), residues: 309 loop : -1.12 (0.19), residues: 792 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 156 average time/residue: 1.8975 time to fit residues: 334.2258 Evaluate side-chains 153 residues out of total 1272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 1.862 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.2969 time to fit residues: 3.3356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 117 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.0470 chunk 100 optimal weight: 0.8980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN B 33 GLN B 173 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118782 restraints weight = 34908.305| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.58 r_work: 0.3379 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 0.048 11886 Z= 0.170 Angle : 0.477 8.932 16122 Z= 0.249 Chirality : 0.042 0.149 1812 Planarity : 0.004 0.048 2094 Dihedral : 4.442 18.427 1569 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.41 (0.21), residues: 1443 helix: 2.22 (0.25), residues: 339 sheet: -1.03 (0.28), residues: 321 loop : -1.08 (0.20), residues: 783 =============================================================================== Job complete usr+sys time: 7489.58 seconds wall clock time: 133 minutes 3.39 seconds (7983.39 seconds total)