Starting phenix.real_space_refine on Wed Sep 25 04:26:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsv_30847/09_2024/7dsv_30847_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsv_30847/09_2024/7dsv_30847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsv_30847/09_2024/7dsv_30847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsv_30847/09_2024/7dsv_30847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsv_30847/09_2024/7dsv_30847_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsv_30847/09_2024/7dsv_30847_neut.cif" } resolution = 3.4 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 6194 2.51 5 N 1522 2.21 5 O 1596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9340 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3672 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 15, 'TRANS': 447} Chain breaks: 1 Chain: "B" Number of atoms: 3672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3672 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 15, 'TRANS': 447} Chain breaks: 1 Chain: "C" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 915 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 612 Unresolved non-hydrogen angles: 771 Unresolved non-hydrogen dihedrals: 499 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 17, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 4, 'PHE:plan': 13, 'GLU:plan': 20, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 372 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 83 Unusual residues: {'LBN': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'LBN:plan-2': 8, 'LBN:plan-3': 5, 'LBN:plan-1': 8} Unresolved non-hydrogen planarities: 76 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 83 Unusual residues: {'LBN': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'LBN:plan-2': 8, 'LBN:plan-3': 5, 'LBN:plan-1': 8} Unresolved non-hydrogen planarities: 76 Restraints were copied for chains: D Residues with excluded nonbonded symmetry interactions: 16 residue: pdb=" C10 LBN A 601 " occ=0.00 ... (8 atoms not shown) pdb=" C7 LBN A 601 " occ=0.00 residue: pdb=" C11 LBN A 602 " occ=0.00 ... (13 atoms not shown) pdb=" C8 LBN A 602 " occ=0.00 residue: pdb=" C11 LBN A 603 " occ=0.00 ... (10 atoms not shown) pdb=" C8 LBN A 603 " occ=0.00 residue: pdb=" C11 LBN A 604 " occ=0.00 ... (10 atoms not shown) pdb=" C8 LBN A 604 " occ=0.00 residue: pdb=" C11 LBN A 605 " occ=0.00 ... (6 atoms not shown) pdb=" C8 LBN A 605 " occ=0.00 residue: pdb=" C11 LBN A 606 " occ=0.00 ... (6 atoms not shown) pdb=" C8 LBN A 606 " occ=0.00 residue: pdb=" C11 LBN A 607 " occ=0.00 ... (6 atoms not shown) pdb=" C8 LBN A 607 " occ=0.00 residue: pdb=" C34 LBN A 608 " occ=0.00 ... (8 atoms not shown) pdb=" C5 LBN A 608 " occ=0.00 residue: pdb=" C34 LBN B 801 " occ=0.00 ... (8 atoms not shown) pdb=" C5 LBN B 801 " occ=0.00 residue: pdb=" C10 LBN B 802 " occ=0.00 ... (8 atoms not shown) pdb=" C7 LBN B 802 " occ=0.00 residue: pdb=" C11 LBN B 803 " occ=0.00 ... (13 atoms not shown) pdb=" C8 LBN B 803 " occ=0.00 residue: pdb=" C11 LBN B 804 " occ=0.00 ... (10 atoms not shown) pdb=" C8 LBN B 804 " occ=0.00 ... (remaining 4 not shown) Time building chain proxies: 5.86, per 1000 atoms: 0.63 Number of scatterers: 9340 At special positions: 0 Unit cell: (143, 73, 101, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1596 8.00 N 1522 7.00 C 6194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 0 sheets defined 74.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 100 through 117 Processing helix chain 'A' and resid 130 through 150 removed outlier: 3.678A pdb=" N LEU A 134 " --> pdb=" O PRO A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 165 through 176 removed outlier: 4.064A pdb=" N ILE A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 removed outlier: 3.504A pdb=" N ASN A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 214 removed outlier: 3.547A pdb=" N ILE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 235 removed outlier: 3.549A pdb=" N PHE A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 252 through 281 removed outlier: 3.644A pdb=" N ILE A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 320 removed outlier: 3.745A pdb=" N PHE A 299 " --> pdb=" O PHE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 348 removed outlier: 3.586A pdb=" N VAL A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 367 Proline residue: A 365 - end of helix Processing helix chain 'A' and resid 372 through 404 Processing helix chain 'A' and resid 410 through 438 removed outlier: 3.997A pdb=" N LYS A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 454 Processing helix chain 'A' and resid 461 through 468 Processing helix chain 'A' and resid 476 through 494 Processing helix chain 'A' and resid 499 through 504 removed outlier: 3.592A pdb=" N ASP A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 539 Processing helix chain 'A' and resid 543 through 558 Processing helix chain 'B' and resid 100 through 117 Processing helix chain 'B' and resid 130 through 150 removed outlier: 3.679A pdb=" N LEU B 134 " --> pdb=" O PRO B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 165 through 176 removed outlier: 4.064A pdb=" N ILE B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 185 removed outlier: 3.504A pdb=" N ASN B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 214 removed outlier: 3.546A pdb=" N ILE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 235 removed outlier: 3.549A pdb=" N PHE B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 252 through 281 removed outlier: 3.644A pdb=" N ILE B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 320 removed outlier: 3.745A pdb=" N PHE B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 348 removed outlier: 3.587A pdb=" N VAL B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 367 Proline residue: B 365 - end of helix Processing helix chain 'B' and resid 372 through 404 Processing helix chain 'B' and resid 410 through 438 removed outlier: 3.997A pdb=" N LYS B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 454 Processing helix chain 'B' and resid 461 through 468 Processing helix chain 'B' and resid 476 through 494 Processing helix chain 'B' and resid 499 through 504 removed outlier: 3.592A pdb=" N ASP B 504 " --> pdb=" O ARG B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 539 Processing helix chain 'B' and resid 543 through 558 Processing helix chain 'D' and resid 16 through 21 Processing helix chain 'D' and resid 24 through 40 removed outlier: 4.114A pdb=" N LYS D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 53 Processing helix chain 'D' and resid 62 through 71 removed outlier: 4.307A pdb=" N PHE D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 89 removed outlier: 4.196A pdb=" N HIS D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 110 through 123 removed outlier: 3.743A pdb=" N LEU D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 148 through 164 Processing helix chain 'D' and resid 172 through 182 removed outlier: 3.645A pdb=" N LYS D 178 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 removed outlier: 3.592A pdb=" N LYS D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 24 through 40 removed outlier: 4.114A pdb=" N LYS C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 62 through 71 removed outlier: 4.307A pdb=" N PHE C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 4.195A pdb=" N HIS C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 100 Processing helix chain 'C' and resid 110 through 123 removed outlier: 3.743A pdb=" N LEU C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 148 through 164 Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.644A pdb=" N LYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.591A pdb=" N LYS C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1470 1.31 - 1.44: 2546 1.44 - 1.56: 5446 1.56 - 1.69: 22 1.69 - 1.81: 44 Bond restraints: 9528 Sorted by residual: bond pdb=" C GLU D 16 " pdb=" O GLU D 16 " ideal model delta sigma weight residual 1.237 1.186 0.050 1.19e-02 7.06e+03 1.79e+01 bond pdb=" C GLU C 16 " pdb=" O GLU C 16 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.19e-02 7.06e+03 1.77e+01 bond pdb=" N ASP C 95 " pdb=" CA ASP C 95 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.29e+01 bond pdb=" N ASP D 95 " pdb=" CA ASP D 95 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.28e+01 bond pdb=" C5 LBN B 805 " pdb=" C8 LBN B 805 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 9523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 12197 2.15 - 4.31: 642 4.31 - 6.46: 92 6.46 - 8.62: 25 8.62 - 10.77: 4 Bond angle restraints: 12960 Sorted by residual: angle pdb=" CA LYS C 98 " pdb=" C LYS C 98 " pdb=" N SER C 99 " ideal model delta sigma weight residual 118.38 108.99 9.39 1.30e+00 5.92e-01 5.22e+01 angle pdb=" CA LYS D 98 " pdb=" C LYS D 98 " pdb=" N SER D 99 " ideal model delta sigma weight residual 118.38 109.05 9.33 1.30e+00 5.92e-01 5.15e+01 angle pdb=" C LYS D 98 " pdb=" N SER D 99 " pdb=" CA SER D 99 " ideal model delta sigma weight residual 122.09 132.86 -10.77 1.79e+00 3.12e-01 3.62e+01 angle pdb=" C LYS C 98 " pdb=" N SER C 99 " pdb=" CA SER C 99 " ideal model delta sigma weight residual 122.09 132.82 -10.73 1.79e+00 3.12e-01 3.59e+01 angle pdb=" O LYS C 98 " pdb=" C LYS C 98 " pdb=" N SER C 99 " ideal model delta sigma weight residual 122.42 130.08 -7.66 1.31e+00 5.83e-01 3.42e+01 ... (remaining 12955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 4795 14.30 - 28.61: 464 28.61 - 42.91: 155 42.91 - 57.21: 32 57.21 - 71.52: 12 Dihedral angle restraints: 5458 sinusoidal: 1734 harmonic: 3724 Sorted by residual: dihedral pdb=" CA ALA D 171 " pdb=" C ALA D 171 " pdb=" N SER D 172 " pdb=" CA SER D 172 " ideal model delta harmonic sigma weight residual -180.00 -152.32 -27.68 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA ALA C 171 " pdb=" C ALA C 171 " pdb=" N SER C 172 " pdb=" CA SER C 172 " ideal model delta harmonic sigma weight residual -180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA LYS D 129 " pdb=" C LYS D 129 " pdb=" N ILE D 130 " pdb=" CA ILE D 130 " ideal model delta harmonic sigma weight residual 180.00 155.02 24.98 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 5455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1216 0.064 - 0.127: 292 0.127 - 0.191: 45 0.191 - 0.254: 11 0.254 - 0.318: 8 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA GLU C 20 " pdb=" N GLU C 20 " pdb=" C GLU C 20 " pdb=" CB GLU C 20 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA GLU D 20 " pdb=" N GLU D 20 " pdb=" C GLU D 20 " pdb=" CB GLU D 20 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA ASN C 109 " pdb=" N ASN C 109 " pdb=" C ASN C 109 " pdb=" CB ASN C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1569 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 99 " 0.037 2.00e-02 2.50e+03 7.16e-02 5.13e+01 pdb=" C SER D 99 " -0.124 2.00e-02 2.50e+03 pdb=" O SER D 99 " 0.044 2.00e-02 2.50e+03 pdb=" N LYS D 100 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 99 " 0.037 2.00e-02 2.50e+03 7.16e-02 5.12e+01 pdb=" C SER C 99 " -0.124 2.00e-02 2.50e+03 pdb=" O SER C 99 " 0.044 2.00e-02 2.50e+03 pdb=" N LYS C 100 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 96 " 0.017 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C ASN D 96 " -0.062 2.00e-02 2.50e+03 pdb=" O ASN D 96 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU D 97 " 0.021 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 604 2.72 - 3.27: 10053 3.27 - 3.81: 15305 3.81 - 4.36: 18162 4.36 - 4.90: 31162 Nonbonded interactions: 75286 Sorted by model distance: nonbonded pdb=" O VAL B 367 " pdb=" CG GLU B 368 " model vdw 2.180 3.440 nonbonded pdb=" O VAL A 367 " pdb=" CG GLU A 368 " model vdw 2.181 3.440 nonbonded pdb=" O SER A 375 " pdb=" OG1 THR A 378 " model vdw 2.274 3.040 nonbonded pdb=" O SER B 375 " pdb=" OG1 THR B 378 " model vdw 2.275 3.040 nonbonded pdb=" O PHE B 162 " pdb=" OH TYR B 342 " model vdw 2.305 3.040 ... (remaining 75281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 87 through 558 or resid 601 or resid 603 through 607)) selection = (chain 'B' and (resid 87 through 558 or resid 801 or (resid 803 through 804 and \ (name C11 or name C14 or name C17 or name C20 or name C22 or name C23 or name C2 \ 4 or name C40 or name C41 or name C42 or name C5 or name C8 )) or (resid 805 thr \ ough 807 and (name C11 or name C14 or name C17 or name C20 or name C22 or name C \ 23 or name C24 or name C8 )))) } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.250 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 0.070 9528 Z= 0.564 Angle : 1.061 10.769 12960 Z= 0.658 Chirality : 0.061 0.318 1572 Planarity : 0.006 0.072 1620 Dihedral : 13.922 71.516 3054 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.75 % Allowed : 1.37 % Favored : 96.88 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.22), residues: 1284 helix: -0.25 (0.16), residues: 920 sheet: None (None), residues: 0 loop : -2.20 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 386 HIS 0.003 0.001 HIS A 545 PHE 0.018 0.002 PHE A 119 TYR 0.012 0.001 TYR A 283 ARG 0.012 0.001 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ILE cc_start: 0.8509 (tt) cc_final: 0.8269 (tt) REVERT: A 419 LEU cc_start: 0.8807 (tt) cc_final: 0.8520 (tt) REVERT: A 546 TRP cc_start: 0.3155 (OUTLIER) cc_final: 0.2616 (m100) REVERT: B 125 ILE cc_start: 0.8493 (tt) cc_final: 0.8228 (tt) REVERT: B 546 TRP cc_start: 0.2826 (OUTLIER) cc_final: 0.2393 (m100) outliers start: 14 outliers final: 7 residues processed: 118 average time/residue: 0.1805 time to fit residues: 31.5624 Evaluate side-chains 97 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 545 HIS Chi-restraints excluded: chain B residue 546 TRP Chi-restraints excluded: chain B residue 549 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 30.0000 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS A 544 HIS A 545 HIS B 250 HIS B 519 ASN B 544 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9528 Z= 0.231 Angle : 0.557 6.554 12960 Z= 0.298 Chirality : 0.043 0.205 1572 Planarity : 0.004 0.056 1620 Dihedral : 7.796 63.660 1474 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.00 % Allowed : 8.73 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.24), residues: 1284 helix: 1.03 (0.17), residues: 902 sheet: None (None), residues: 0 loop : -1.69 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 386 HIS 0.005 0.001 HIS A 545 PHE 0.015 0.001 PHE B 382 TYR 0.010 0.001 TYR A 274 ARG 0.006 0.001 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.884 Fit side-chains REVERT: A 125 ILE cc_start: 0.8540 (tt) cc_final: 0.8329 (tt) REVERT: A 364 ARG cc_start: 0.8144 (ttt90) cc_final: 0.7845 (ttt180) REVERT: A 419 LEU cc_start: 0.8854 (tt) cc_final: 0.8630 (tt) REVERT: B 125 ILE cc_start: 0.8516 (tt) cc_final: 0.8299 (tt) outliers start: 8 outliers final: 4 residues processed: 101 average time/residue: 0.1582 time to fit residues: 24.6679 Evaluate side-chains 96 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 96 optimal weight: 40.0000 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 40.0000 chunk 125 optimal weight: 30.0000 chunk 103 optimal weight: 40.0000 chunk 115 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 50.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS B 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9528 Z= 0.322 Angle : 0.591 7.383 12960 Z= 0.308 Chirality : 0.045 0.216 1572 Planarity : 0.005 0.058 1620 Dihedral : 7.848 65.778 1454 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.37 % Allowed : 10.60 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.24), residues: 1284 helix: 1.13 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -1.57 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 386 HIS 0.004 0.001 HIS B 545 PHE 0.014 0.001 PHE A 463 TYR 0.010 0.001 TYR A 274 ARG 0.004 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 1.027 Fit side-chains REVERT: A 87 LYS cc_start: 0.6850 (tttt) cc_final: 0.6376 (tttp) REVERT: A 125 ILE cc_start: 0.8591 (tt) cc_final: 0.8353 (tt) REVERT: A 346 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7123 (mm-30) REVERT: B 125 ILE cc_start: 0.8629 (tt) cc_final: 0.8387 (tt) REVERT: B 346 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7039 (mm-30) outliers start: 19 outliers final: 11 residues processed: 105 average time/residue: 0.1716 time to fit residues: 27.0472 Evaluate side-chains 107 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 328 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 50.0000 chunk 33 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS B 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9528 Z= 0.274 Angle : 0.538 6.596 12960 Z= 0.284 Chirality : 0.043 0.201 1572 Planarity : 0.004 0.055 1620 Dihedral : 7.554 67.621 1454 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.99 % Allowed : 11.97 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.24), residues: 1284 helix: 1.36 (0.17), residues: 908 sheet: None (None), residues: 0 loop : -1.53 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 386 HIS 0.003 0.001 HIS B 545 PHE 0.016 0.001 PHE B 382 TYR 0.010 0.001 TYR A 274 ARG 0.002 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 0.960 Fit side-chains REVERT: A 125 ILE cc_start: 0.8615 (tt) cc_final: 0.8357 (tt) REVERT: A 346 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6992 (mm-30) REVERT: A 432 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8183 (mt) REVERT: B 125 ILE cc_start: 0.8692 (tt) cc_final: 0.8446 (tt) REVERT: B 346 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6977 (mm-30) outliers start: 24 outliers final: 16 residues processed: 107 average time/residue: 0.1630 time to fit residues: 26.8500 Evaluate side-chains 111 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 457 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 40.0000 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 92 optimal weight: 40.0000 chunk 51 optimal weight: 0.8980 chunk 105 optimal weight: 50.0000 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 40.0000 chunk 31 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 HIS B 519 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9528 Z= 0.251 Angle : 0.529 7.686 12960 Z= 0.278 Chirality : 0.042 0.200 1572 Planarity : 0.004 0.055 1620 Dihedral : 7.279 68.882 1454 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.49 % Allowed : 12.59 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1284 helix: 1.53 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -1.47 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 386 HIS 0.003 0.001 HIS A 540 PHE 0.013 0.001 PHE B 119 TYR 0.009 0.001 TYR A 274 ARG 0.003 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 0.922 Fit side-chains REVERT: A 346 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6993 (mm-30) REVERT: B 125 ILE cc_start: 0.8704 (tt) cc_final: 0.8457 (tt) REVERT: B 346 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7007 (mm-30) outliers start: 28 outliers final: 19 residues processed: 114 average time/residue: 0.1554 time to fit residues: 27.4732 Evaluate side-chains 118 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 473 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 40.0000 chunk 24 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 123 optimal weight: 50.0000 chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS B 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9528 Z= 0.233 Angle : 0.521 7.067 12960 Z= 0.274 Chirality : 0.042 0.185 1572 Planarity : 0.004 0.055 1620 Dihedral : 7.099 68.473 1454 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.87 % Allowed : 13.84 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1284 helix: 1.61 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -1.39 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 386 HIS 0.003 0.001 HIS B 545 PHE 0.013 0.001 PHE B 119 TYR 0.009 0.001 TYR A 274 ARG 0.002 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 0.999 Fit side-chains REVERT: A 432 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8150 (mt) REVERT: B 125 ILE cc_start: 0.8711 (tt) cc_final: 0.8471 (tt) REVERT: B 346 GLU cc_start: 0.7273 (mm-30) cc_final: 0.7009 (mm-30) outliers start: 23 outliers final: 18 residues processed: 112 average time/residue: 0.1708 time to fit residues: 29.7499 Evaluate side-chains 116 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 473 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 40.0000 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 90 optimal weight: 0.0770 chunk 104 optimal weight: 50.0000 chunk 69 optimal weight: 0.0970 chunk 123 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN B 325 HIS B 495 GLN B 545 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 9528 Z= 0.158 Angle : 0.489 7.312 12960 Z= 0.257 Chirality : 0.040 0.166 1572 Planarity : 0.004 0.053 1620 Dihedral : 6.332 68.670 1454 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.37 % Allowed : 16.71 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1284 helix: 1.88 (0.18), residues: 914 sheet: None (None), residues: 0 loop : -1.29 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 386 HIS 0.001 0.000 HIS B 544 PHE 0.012 0.001 PHE B 382 TYR 0.008 0.001 TYR B 274 ARG 0.002 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.987 Fit side-chains REVERT: A 346 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6968 (mm-30) REVERT: A 422 LEU cc_start: 0.8584 (tp) cc_final: 0.8334 (tp) REVERT: A 432 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8108 (mt) REVERT: B 346 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7006 (mm-30) outliers start: 11 outliers final: 9 residues processed: 115 average time/residue: 0.1523 time to fit residues: 27.6984 Evaluate side-chains 108 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 473 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 50.0000 chunk 112 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN B 495 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9528 Z= 0.322 Angle : 0.577 8.067 12960 Z= 0.300 Chirality : 0.044 0.156 1572 Planarity : 0.004 0.057 1620 Dihedral : 7.220 66.707 1454 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.49 % Allowed : 16.46 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1284 helix: 1.68 (0.17), residues: 902 sheet: None (None), residues: 0 loop : -1.56 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 386 HIS 0.003 0.001 HIS A 540 PHE 0.015 0.001 PHE A 463 TYR 0.010 0.001 TYR B 274 ARG 0.002 0.001 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 0.914 Fit side-chains REVERT: B 346 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7069 (mm-30) outliers start: 20 outliers final: 12 residues processed: 111 average time/residue: 0.1541 time to fit residues: 26.7424 Evaluate side-chains 106 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 473 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 0.9990 chunk 107 optimal weight: 50.0000 chunk 114 optimal weight: 40.0000 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 108 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 121 optimal weight: 40.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9528 Z= 0.214 Angle : 0.532 8.315 12960 Z= 0.276 Chirality : 0.041 0.151 1572 Planarity : 0.004 0.056 1620 Dihedral : 6.658 66.515 1454 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.87 % Allowed : 17.21 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1284 helix: 1.87 (0.17), residues: 902 sheet: None (None), residues: 0 loop : -1.51 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 386 HIS 0.002 0.001 HIS A 98 PHE 0.014 0.001 PHE A 119 TYR 0.009 0.001 TYR B 274 ARG 0.002 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.986 Fit side-chains REVERT: A 432 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8152 (mt) REVERT: B 346 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6983 (mm-30) outliers start: 15 outliers final: 13 residues processed: 108 average time/residue: 0.1568 time to fit residues: 26.8439 Evaluate side-chains 115 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 473 HIS Chi-restraints excluded: chain B residue 502 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 127 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 101 optimal weight: 50.0000 chunk 10 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9528 Z= 0.300 Angle : 0.575 8.772 12960 Z= 0.296 Chirality : 0.043 0.159 1572 Planarity : 0.004 0.057 1620 Dihedral : 7.029 65.142 1454 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.87 % Allowed : 17.33 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.24), residues: 1284 helix: 1.73 (0.17), residues: 902 sheet: None (None), residues: 0 loop : -1.49 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 386 HIS 0.002 0.001 HIS A 98 PHE 0.014 0.001 PHE A 119 TYR 0.010 0.001 TYR B 274 ARG 0.002 0.000 ARG A 440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.012 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 107 average time/residue: 0.1592 time to fit residues: 26.6741 Evaluate side-chains 112 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 473 HIS Chi-restraints excluded: chain B residue 502 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 40.0000 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 50.0000 chunk 42 optimal weight: 3.9990 chunk 104 optimal weight: 50.0000 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.191534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.176429 restraints weight = 8813.976| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 0.60 r_work: 0.3669 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9528 Z= 0.267 Angle : 0.556 8.534 12960 Z= 0.287 Chirality : 0.042 0.153 1572 Planarity : 0.004 0.057 1620 Dihedral : 6.871 64.625 1454 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.87 % Allowed : 17.58 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.24), residues: 1284 helix: 1.79 (0.17), residues: 902 sheet: None (None), residues: 0 loop : -1.48 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 386 HIS 0.002 0.001 HIS A 98 PHE 0.014 0.001 PHE A 119 TYR 0.009 0.001 TYR B 274 ARG 0.002 0.000 ARG A 425 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1725.52 seconds wall clock time: 31 minutes 40.19 seconds (1900.19 seconds total)