Starting phenix.real_space_refine on Thu Nov 16 17:29:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfp_27410/11_2023/8dfp_27410.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfp_27410/11_2023/8dfp_27410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfp_27410/11_2023/8dfp_27410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfp_27410/11_2023/8dfp_27410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfp_27410/11_2023/8dfp_27410.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfp_27410/11_2023/8dfp_27410.pdb" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.016 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 37 5.16 5 C 5407 2.51 5 N 1389 2.21 5 O 1588 1.98 5 H 7703 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 16124 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6145 Classifications: {'peptide': 438} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 16, 'GLU:plan': 19, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Chain: "B" Number of atoms: 6141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6141 Classifications: {'peptide': 440} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 419} Chain breaks: 2 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 203 Chain: "C" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1852 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1846 Classifications: {'peptide': 119} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.68, per 1000 atoms: 0.48 Number of scatterers: 16124 At special positions: 0 Unit cell: (75.376, 130.562, 183.056, 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 37 16.00 O 1588 8.00 N 1389 7.00 C 5407 6.00 H 7703 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 97 " distance=2.02 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 186 " distance=2.05 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 428 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 290 " distance=2.02 Simple disulfide: pdb=" SG CYS B 428 " - pdb=" SG CYS B 491 " distance=2.04 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 89 " distance=2.04 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1001 " - " ASN A 283 " " NAG B1001 " - " ASN B 283 " " NAG E 1 " - " ASN A 300 " " NAG F 1 " - " ASN A 293 " " NAG G 1 " - " ASN B 293 " " NAG H 1 " - " ASN B 300 " Time building additional restraints: 13.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 24 sheets defined 18.1% alpha, 43.5% 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 88 through 92 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.851A pdb=" N GLY A 387 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 281 through 285 Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.145A pdb=" N GLY B 387 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 12 removed outlier: 3.841A pdb=" N VAL C 12 " --> pdb=" O THR C 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 9 through 12' Processing helix chain 'C' and resid 13 through 22 removed outlier: 4.485A pdb=" N LYS C 17 " --> pdb=" O LYS C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 62 removed outlier: 4.327A pdb=" N TRP C 44 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 94 removed outlier: 3.584A pdb=" N GLU C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.912A pdb=" N PHE C 126 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 13 removed outlier: 3.629A pdb=" N VAL D 12 " --> pdb=" O THR D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 40 through 63 removed outlier: 3.968A pdb=" N TRP D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N SER D 46 " --> pdb=" O HIS D 42 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLU D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE D 63 " --> pdb=" O LEU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 94 Processing helix chain 'D' and resid 111 through 127 removed outlier: 3.747A pdb=" N PHE D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.803A pdb=" N SER A 38 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 127 removed outlier: 6.866A pdb=" N GLY A 126 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 182 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP A 189 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASN A 145 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 127 removed outlier: 6.866A pdb=" N GLY A 126 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 182 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 216 removed outlier: 3.527A pdb=" N ALA A 273 " --> pdb=" O CYS A 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 224 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 317 Processing sheet with id=AA9, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AB1, first strand: chain 'A' and resid 411 through 420 removed outlier: 5.378A pdb=" N LYS A 412 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE A 433 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 429 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR A 418 " --> pdb=" O GLN A 427 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN A 427 " --> pdb=" O TYR A 418 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 437 through 441 removed outlier: 18.234A pdb=" N LYS A 499 " --> pdb=" O LYS B 499 " (cutoff:3.500A) removed outlier: 15.368A pdb=" N SER B 501 " --> pdb=" O LYS A 499 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N SER A 501 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N TYR B 503 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR A 503 " --> pdb=" O TYR B 503 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N TYR B 505 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR A 505 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASN B 507 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN A 507 " --> pdb=" O ASN B 507 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 488 " --> pdb=" O CYS B 443 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS B 443 " --> pdb=" O THR B 488 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.637A pdb=" N SER B 38 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.608A pdb=" N LEU B 46 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ARG B 112 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 48 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 77 " --> pdb=" O TRP B 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 125 through 127 Processing sheet with id=AB6, first strand: chain 'B' and resid 132 through 134 Processing sheet with id=AB7, first strand: chain 'B' and resid 144 through 150 removed outlier: 5.701A pdb=" N ASN B 145 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP B 189 " --> pdb=" O ASN B 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 144 through 150 removed outlier: 5.701A pdb=" N ASN B 145 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP B 189 " --> pdb=" O ASN B 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 213 through 216 Processing sheet with id=AC1, first strand: chain 'B' and resid 220 through 224 removed outlier: 7.791A pdb=" N TRP B 246 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR B 253 " --> pdb=" O TRP B 246 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 248 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 312 through 317 Processing sheet with id=AC3, first strand: chain 'B' and resid 322 through 326 removed outlier: 6.294A pdb=" N VAL B 323 " --> pdb=" O TYR B 408 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASN B 410 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL B 325 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS B 412 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS B 345 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TRP B 348 " --> pdb=" O PHE B 355 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 322 through 326 removed outlier: 6.294A pdb=" N VAL B 323 " --> pdb=" O TYR B 408 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASN B 410 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL B 325 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS B 412 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N PHE B 433 " --> pdb=" O PRO B 413 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE B 415 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA B 431 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B 417 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AC6, first strand: chain 'D' and resid 28 through 31 409 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 13.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 7701 1.01 - 1.22: 12 1.22 - 1.42: 3585 1.42 - 1.63: 4969 1.63 - 1.83: 48 Bond restraints: 16315 Sorted by residual: bond pdb=" C7 NAG A1001 " pdb=" N2 NAG A1001 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" C7 NAG H 2 " pdb=" N2 NAG H 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C7 NAG G 2 " pdb=" N2 NAG G 2 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C7 NAG E 2 " pdb=" N2 NAG E 2 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C7 NAG E 1 " pdb=" N2 NAG E 1 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.30e+01 ... (remaining 16310 not shown) Histogram of bond angle deviations from ideal: 95.89 - 103.59: 112 103.59 - 111.29: 17205 111.29 - 118.99: 4593 118.99 - 126.69: 7250 126.69 - 134.39: 120 Bond angle restraints: 29280 Sorted by residual: angle pdb=" C2 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" C4 NAG G 1 " ideal model delta sigma weight residual 110.24 95.89 14.35 3.00e+00 1.11e-01 2.29e+01 angle pdb=" C3 NAG H 1 " pdb=" C4 NAG H 1 " pdb=" O4 NAG H 1 " ideal model delta sigma weight residual 107.29 118.68 -11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb="HH11 ARG A 122 " pdb=" NH1 ARG A 122 " pdb="HH12 ARG A 122 " ideal model delta sigma weight residual 120.00 108.66 11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C1 NAG F 1 " pdb=" C2 NAG F 1 " pdb=" N2 NAG F 1 " ideal model delta sigma weight residual 110.79 121.36 -10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" N LYS C 62 " pdb=" CA LYS C 62 " pdb=" C LYS C 62 " ideal model delta sigma weight residual 112.38 116.60 -4.22 1.22e+00 6.72e-01 1.20e+01 ... (remaining 29275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 5994 16.47 - 32.94: 404 32.94 - 49.40: 76 49.40 - 65.87: 135 65.87 - 82.34: 27 Dihedral angle restraints: 6636 sinusoidal: 2733 harmonic: 3903 Sorted by residual: dihedral pdb=" CB CYS A 151 " pdb=" SG CYS A 151 " pdb=" SG CYS A 183 " pdb=" CB CYS A 183 " ideal model delta sinusoidal sigma weight residual -86.00 -166.09 80.09 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CA PHE A 118 " pdb=" C PHE A 118 " pdb=" N LEU A 119 " pdb=" CA LEU A 119 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA THR B 59 " pdb=" C THR B 59 " pdb=" N ASP B 60 " pdb=" CA ASP B 60 " ideal model delta harmonic sigma weight residual 180.00 150.84 29.16 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 6633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1398 0.154 - 0.308: 38 0.308 - 0.462: 0 0.462 - 0.616: 2 0.616 - 0.770: 1 Chirality restraints: 1439 Sorted by residual: chirality pdb=" C2 NAG G 1 " pdb=" C1 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" N2 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.49 -1.72 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C4 NAG H 1 " pdb=" C3 NAG H 1 " pdb=" C5 NAG H 1 " pdb=" O4 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.53 -1.93 -0.60 2.00e-01 2.50e+01 9.12e+00 chirality pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" N2 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.49 -1.91 -0.58 2.00e-01 2.50e+01 8.35e+00 ... (remaining 1436 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 122 " 0.052 9.50e-02 1.11e+02 8.19e-02 1.44e+02 pdb=" NE ARG A 122 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG A 122 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 122 " 0.133 2.00e-02 2.50e+03 pdb=" NH2 ARG A 122 " 0.108 2.00e-02 2.50e+03 pdb="HH11 ARG A 122 " 0.017 2.00e-02 2.50e+03 pdb="HH12 ARG A 122 " -0.144 2.00e-02 2.50e+03 pdb="HH21 ARG A 122 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 122 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 248 " 0.361 9.50e-02 1.11e+02 1.39e-01 1.26e+02 pdb=" NE ARG B 248 " 0.075 2.00e-02 2.50e+03 pdb=" CZ ARG B 248 " -0.072 2.00e-02 2.50e+03 pdb=" NH1 ARG B 248 " -0.106 2.00e-02 2.50e+03 pdb=" NH2 ARG B 248 " -0.085 2.00e-02 2.50e+03 pdb="HH11 ARG B 248 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG B 248 " 0.092 2.00e-02 2.50e+03 pdb="HH21 ARG B 248 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 248 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 372 " 0.256 9.50e-02 1.11e+02 9.76e-02 5.74e+01 pdb=" NE ARG A 372 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG A 372 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 372 " -0.083 2.00e-02 2.50e+03 pdb=" NH2 ARG A 372 " -0.043 2.00e-02 2.50e+03 pdb="HH11 ARG A 372 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 372 " 0.072 2.00e-02 2.50e+03 pdb="HH21 ARG A 372 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 372 " 0.041 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 1422 2.26 - 2.84: 35029 2.84 - 3.43: 39397 3.43 - 4.01: 56418 4.01 - 4.60: 84579 Nonbonded interactions: 216845 Sorted by model distance: nonbonded pdb=" OD1 ASP B 159 " pdb=" HH TYR B 179 " model vdw 1.670 1.850 nonbonded pdb=" HG SER D 53 " pdb=" OD1 ASP D 84 " model vdw 1.674 1.850 nonbonded pdb=" O CYS A 491 " pdb=" HG SER A 501 " model vdw 1.692 1.850 nonbonded pdb=" OD1 ASP C 25 " pdb=" HH TYR D 26 " model vdw 1.724 1.850 nonbonded pdb="HD21 ASN A 293 " pdb=" O7 NAG F 1 " model vdw 1.738 1.850 ... (remaining 216840 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 35 through 44 or (resid 45 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 46 through 126 or (resid \ 127 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 128 through 143 or (resid 144 through 145 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 146 through 164 or \ (resid 165 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 166 through 217 or (resid 218 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 219 through 227 or (resid \ 228 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 229 through 248 or (resid 249 through 250 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 251 through 265 or \ (resid 266 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 267 through 351 or (resid 352 through 353 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 354 through 3 \ 69 or (resid 370 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 371 through 375 or (resid 376 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 377 through 478 or \ resid 488 through 507 or (resid 508 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 1001)) selection = (chain 'B' and (resid 35 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 92 through 112 or (resid \ 113 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 114 through 120 or (resid 121 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 122 through 128 or (resid 129 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 130 through 153 or (resid 154 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 155 through 188 or (resid 189 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 190 through 226 or (resid 227 through 228 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 229 through 317 or (resid 318 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 319 through 328 or (resid 329 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 330 through 355 or (resid 356 through \ 358 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 359 through 438 or (resid 439 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 440 through 441 or resid 471 th \ rough 478 or resid 488 through 498 or (resid 499 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 500 through 508 or resid \ 1001)) } ncs_group { reference = (chain 'C' and (resid 3 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 93 through 95 or resid 10 \ 5 through 130)) selection = (chain 'D' and (resid 3 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 7 through 60 or (resid 61 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 62 through 87 or (resid 88 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 89 through 130)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 5.560 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: 0.240 Extract box with map and model: 19.650 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 52.360 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.008 0.117 8612 Z= 0.514 Angle : 1.128 14.345 11790 Z= 0.625 Chirality : 0.071 0.770 1439 Planarity : 0.010 0.118 1478 Dihedral : 12.183 82.341 2839 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: -0.93 (0.23), residues: 1098 helix: -1.24 (0.37), residues: 121 sheet: 0.55 (0.23), residues: 453 loop : -1.53 (0.23), residues: 524 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3795 time to fit residues: 36.2255 Evaluate side-chains 44 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN C 51 GLN C 65 ASN D 21 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8612 Z= 0.277 Angle : 0.700 8.581 11790 Z= 0.367 Chirality : 0.048 0.226 1439 Planarity : 0.004 0.035 1478 Dihedral : 6.687 27.394 1188 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.35 % Allowed : 4.73 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 0.03 (0.24), residues: 1098 helix: 0.51 (0.40), residues: 124 sheet: 0.93 (0.24), residues: 442 loop : -0.90 (0.25), residues: 532 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 1.434 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 47 average time/residue: 0.2855 time to fit residues: 22.3137 Evaluate side-chains 39 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 0.2980 chunk 27 optimal weight: 0.1980 chunk 100 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS A 427 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8612 Z= 0.239 Angle : 0.601 6.407 11790 Z= 0.317 Chirality : 0.046 0.208 1439 Planarity : 0.003 0.032 1478 Dihedral : 5.797 24.372 1188 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.71 % Allowed : 4.37 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 0.24 (0.24), residues: 1098 helix: 1.48 (0.44), residues: 124 sheet: 0.70 (0.24), residues: 447 loop : -0.61 (0.25), residues: 527 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 45 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 0.2729 time to fit residues: 20.0790 Evaluate side-chains 41 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 1.493 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1947 time to fit residues: 2.7534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8612 Z= 0.279 Angle : 0.570 5.587 11790 Z= 0.299 Chirality : 0.045 0.223 1439 Planarity : 0.003 0.031 1478 Dihedral : 5.380 22.438 1188 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.59 % Allowed : 4.73 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 0.36 (0.25), residues: 1098 helix: 1.84 (0.45), residues: 124 sheet: 0.54 (0.24), residues: 448 loop : -0.35 (0.26), residues: 526 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 47 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 1.368 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 47 average time/residue: 0.2830 time to fit residues: 22.9168 Evaluate side-chains 38 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 1.479 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1830 time to fit residues: 2.1238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 0.0770 chunk 1 optimal weight: 0.0000 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 overall best weight: 0.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 347 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8612 Z= 0.166 Angle : 0.534 8.062 11790 Z= 0.278 Chirality : 0.045 0.221 1439 Planarity : 0.003 0.029 1478 Dihedral : 5.086 21.232 1188 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.59 % Allowed : 4.61 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 0.52 (0.25), residues: 1098 helix: 2.23 (0.45), residues: 124 sheet: 0.58 (0.24), residues: 437 loop : -0.24 (0.26), residues: 537 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 44 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 44 average time/residue: 0.2743 time to fit residues: 20.7848 Evaluate side-chains 39 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.424 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 0.0870 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 88 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8612 Z= 0.236 Angle : 0.540 10.391 11790 Z= 0.280 Chirality : 0.044 0.225 1439 Planarity : 0.003 0.033 1478 Dihedral : 4.985 21.263 1188 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.12 % Allowed : 5.20 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 0.52 (0.25), residues: 1098 helix: 2.28 (0.46), residues: 124 sheet: 0.55 (0.24), residues: 438 loop : -0.23 (0.26), residues: 536 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 40 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.3174 time to fit residues: 23.8610 Evaluate side-chains 39 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 1.650 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2195 time to fit residues: 2.2055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8612 Z= 0.265 Angle : 0.537 8.215 11790 Z= 0.281 Chirality : 0.044 0.232 1439 Planarity : 0.003 0.037 1478 Dihedral : 4.911 21.161 1188 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.24 % Allowed : 5.67 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 0.42 (0.25), residues: 1098 helix: 2.21 (0.46), residues: 125 sheet: 0.42 (0.24), residues: 441 loop : -0.23 (0.27), residues: 532 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 40 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.2717 time to fit residues: 18.9912 Evaluate side-chains 39 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1716 time to fit residues: 1.9867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.1980 chunk 92 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8612 Z= 0.341 Angle : 0.559 8.466 11790 Z= 0.294 Chirality : 0.044 0.244 1439 Planarity : 0.003 0.041 1478 Dihedral : 4.964 22.053 1188 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.12 % Allowed : 6.38 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 0.23 (0.25), residues: 1098 helix: 1.99 (0.46), residues: 125 sheet: 0.24 (0.24), residues: 443 loop : -0.29 (0.26), residues: 530 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 38 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.2848 time to fit residues: 18.9922 Evaluate side-chains 38 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1776 time to fit residues: 2.0830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 59 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 0.1980 chunk 93 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8612 Z= 0.214 Angle : 0.516 7.598 11790 Z= 0.271 Chirality : 0.044 0.233 1439 Planarity : 0.003 0.036 1478 Dihedral : 4.814 21.221 1188 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 0.36 (0.25), residues: 1098 helix: 2.21 (0.46), residues: 125 sheet: 0.30 (0.24), residues: 443 loop : -0.20 (0.26), residues: 530 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 38 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.2911 time to fit residues: 18.6471 Evaluate side-chains 37 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 0.0980 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8612 Z= 0.269 Angle : 0.528 7.547 11790 Z= 0.278 Chirality : 0.044 0.243 1439 Planarity : 0.003 0.036 1478 Dihedral : 4.799 21.561 1188 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 0.32 (0.25), residues: 1098 helix: 2.13 (0.46), residues: 125 sheet: 0.25 (0.24), residues: 442 loop : -0.20 (0.26), residues: 531 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue MET 318 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue THR 356 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 499 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LEU 57 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 100 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 144 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 193 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LYS 254 is missing expected H atoms. Skipping. Residue LYS 258 is missing expected H atoms. Skipping. Residue LYS 310 is missing expected H atoms. Skipping. Residue LYS 342 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 383 is missing expected H atoms. Skipping. Residue LYS 412 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue VAL 422 is missing expected H atoms. Skipping. Residue MET 425 is missing expected H atoms. Skipping. Residue LYS 471 is missing expected H atoms. Skipping. Residue LEU 472 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 96 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Evaluate side-chains 36 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2916 time to fit residues: 18.4138 Evaluate side-chains 36 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.070599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.058097 restraints weight = 77991.896| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.16 r_work: 0.3000 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8612 Z= 0.196 Angle : 0.504 7.417 11790 Z= 0.265 Chirality : 0.044 0.234 1439 Planarity : 0.003 0.036 1478 Dihedral : 4.706 21.084 1188 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 0.46 (0.25), residues: 1098 helix: 2.23 (0.46), residues: 128 sheet: 0.32 (0.23), residues: 442 loop : -0.09 (0.27), residues: 528 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3852.43 seconds wall clock time: 69 minutes 11.96 seconds (4151.96 seconds total)