Starting phenix.real_space_refine on Fri Dec 8 15:38:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avb_7008/12_2023/6avb_7008_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avb_7008/12_2023/6avb_7008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avb_7008/12_2023/6avb_7008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avb_7008/12_2023/6avb_7008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avb_7008/12_2023/6avb_7008_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6avb_7008/12_2023/6avb_7008_updated.pdb" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 60 5.16 5 C 5469 2.51 5 N 1458 2.21 5 O 1680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8673 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2864 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'SME:plan-1': 2, 'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2864 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'SME:plan-1': 2, 'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2864 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'SME:plan-1': 2, 'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.07, per 1000 atoms: 0.58 Number of scatterers: 8673 At special positions: 0 Unit cell: (86.403, 89.526, 135.33, 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 60 16.00 P 6 15.00 O 1680 8.00 N 1458 7.00 C 5469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.7 seconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2034 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 12 sheets defined 33.5% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.670A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP C 86 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 122 removed outlier: 3.633A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N THR C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 193 removed outlier: 3.551A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 removed outlier: 4.213A pdb=" N ARG C 210 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 231 Processing helix chain 'C' and resid 254 through 261 Proline residue: C 258 - end of helix removed outlier: 4.623A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 254 through 261' Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.672A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.530A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 319 removed outlier: 3.732A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 removed outlier: 4.070A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 367 through 370 Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 80 through 90 removed outlier: 3.670A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.633A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 193 removed outlier: 3.552A pdb=" N TYR A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 removed outlier: 4.213A pdb=" N ARG A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 254 through 261 Proline residue: A 258 - end of helix removed outlier: 4.623A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 261' Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.671A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.529A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.732A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 removed outlier: 4.069A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 367 through 370 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.670A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP B 86 " --> pdb=" O MET B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.633A pdb=" N MET B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N THR B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.552A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 4.213A pdb=" N ARG B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 254 through 261 Proline residue: B 258 - end of helix removed outlier: 4.623A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 254 through 261' Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.672A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.530A pdb=" N TYR B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 319 removed outlier: 3.733A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 removed outlier: 4.070A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 355 No H-bonds generated for 'chain 'B' and resid 353 through 355' Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 367 through 370 Processing sheet with id= A, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.926A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= C, first strand: chain 'C' and resid 160 through 162 Processing sheet with id= D, first strand: chain 'C' and resid 240 through 242 removed outlier: 3.631A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.927A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 18 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= G, first strand: chain 'A' and resid 160 through 162 Processing sheet with id= H, first strand: chain 'A' and resid 240 through 242 removed outlier: 3.630A pdb=" N LEU A 242 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.927A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 18 " --> pdb=" O ASP B 11 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= K, first strand: chain 'B' and resid 160 through 162 Processing sheet with id= L, first strand: chain 'B' and resid 240 through 242 removed outlier: 3.632A pdb=" N LEU B 242 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) 189 hydrogen bonds defined for protein. 450 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: 2.30 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1452 1.30 - 1.42: 2208 1.42 - 1.55: 5086 1.55 - 1.68: 11 1.68 - 1.81: 108 Bond restraints: 8865 Sorted by residual: bond pdb=" CG HIC C 73 " pdb=" CD2 HIC C 73 " ideal model delta sigma weight residual 1.369 1.307 0.062 2.00e-02 2.50e+03 9.66e+00 bond pdb=" CG HIC A 73 " pdb=" CD2 HIC A 73 " ideal model delta sigma weight residual 1.369 1.307 0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" CG HIC B 73 " pdb=" CD2 HIC B 73 " ideal model delta sigma weight residual 1.369 1.307 0.062 2.00e-02 2.50e+03 9.55e+00 bond pdb=" C HIC B 73 " pdb=" O HIC B 73 " ideal model delta sigma weight residual 1.231 1.169 0.062 2.00e-02 2.50e+03 9.54e+00 bond pdb=" C HIC C 73 " pdb=" O HIC C 73 " ideal model delta sigma weight residual 1.231 1.169 0.062 2.00e-02 2.50e+03 9.54e+00 ... (remaining 8860 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.44: 276 105.44 - 112.94: 4825 112.94 - 120.45: 3668 120.45 - 127.95: 3183 127.95 - 135.45: 90 Bond angle restraints: 12042 Sorted by residual: angle pdb=" C CYS C 217 " pdb=" N TYR C 218 " pdb=" CA TYR C 218 " ideal model delta sigma weight residual 121.76 130.12 -8.36 2.19e+00 2.09e-01 1.46e+01 angle pdb=" C CYS A 217 " pdb=" N TYR A 218 " pdb=" CA TYR A 218 " ideal model delta sigma weight residual 121.76 130.11 -8.35 2.19e+00 2.09e-01 1.45e+01 angle pdb=" C CYS B 217 " pdb=" N TYR B 218 " pdb=" CA TYR B 218 " ideal model delta sigma weight residual 121.76 130.11 -8.35 2.19e+00 2.09e-01 1.45e+01 angle pdb=" N GLU A 224 " pdb=" CA GLU A 224 " pdb=" C GLU A 224 " ideal model delta sigma weight residual 110.80 103.60 7.20 2.13e+00 2.20e-01 1.14e+01 angle pdb=" N GLU C 224 " pdb=" CA GLU C 224 " pdb=" C GLU C 224 " ideal model delta sigma weight residual 110.80 103.65 7.15 2.13e+00 2.20e-01 1.13e+01 ... (remaining 12037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 4929 16.21 - 32.42: 309 32.42 - 48.63: 60 48.63 - 64.84: 9 64.84 - 81.04: 9 Dihedral angle restraints: 5316 sinusoidal: 2136 harmonic: 3180 Sorted by residual: dihedral pdb=" CA ARG B 116 " pdb=" C ARG B 116 " pdb=" N GLU B 117 " pdb=" CA GLU B 117 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ARG C 116 " pdb=" C ARG C 116 " pdb=" N GLU C 117 " pdb=" CA GLU C 117 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA ARG A 116 " pdb=" C ARG A 116 " pdb=" N GLU A 117 " pdb=" CA GLU A 117 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 5313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 743 0.044 - 0.088: 406 0.088 - 0.132: 139 0.132 - 0.176: 44 0.176 - 0.220: 9 Chirality restraints: 1341 Sorted by residual: chirality pdb=" CA SME A 47 " pdb=" N SME A 47 " pdb=" C SME A 47 " pdb=" CB SME A 47 " both_signs ideal model delta sigma weight residual False 2.40 2.18 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA SME B 47 " pdb=" N SME B 47 " pdb=" C SME B 47 " pdb=" CB SME B 47 " both_signs ideal model delta sigma weight residual False 2.40 2.18 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA SME C 47 " pdb=" N SME C 47 " pdb=" C SME C 47 " pdb=" CB SME C 47 " both_signs ideal model delta sigma weight residual False 2.40 2.19 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1338 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 101 " -0.041 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO A 102 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 101 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.94e+00 pdb=" N PRO B 102 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 101 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO C 102 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " 0.034 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 295 2.64 - 3.20: 9724 3.20 - 3.77: 13968 3.77 - 4.33: 19668 4.33 - 4.90: 29721 Nonbonded interactions: 73376 Sorted by model distance: nonbonded pdb=" OG1 THR B 358 " pdb=" OE1 GLU B 361 " model vdw 2.072 2.440 nonbonded pdb=" OG1 THR C 358 " pdb=" OE1 GLU C 361 " model vdw 2.072 2.440 nonbonded pdb=" OG1 THR A 358 " pdb=" OE1 GLU A 361 " model vdw 2.072 2.440 nonbonded pdb=" OG SER C 155 " pdb=" OG1 THR C 303 " model vdw 2.073 2.440 nonbonded pdb=" OG SER A 155 " pdb=" OG1 THR A 303 " model vdw 2.073 2.440 ... (remaining 73371 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.94 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 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: 1.440 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.170 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.009 0.062 8865 Z= 0.571 Angle : 1.130 9.701 12042 Z= 0.573 Chirality : 0.061 0.220 1341 Planarity : 0.006 0.061 1536 Dihedral : 11.850 81.044 3282 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 27.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.92 % Favored : 86.80 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.29 % 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: -5.00 (0.19), residues: 1068 helix: -4.19 (0.14), residues: 330 sheet: -1.74 (0.34), residues: 210 loop : -3.41 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 86 HIS 0.009 0.003 HIS A 87 PHE 0.031 0.003 PHE B 262 TYR 0.028 0.003 TYR A 218 ARG 0.009 0.001 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 0.966 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2325 time to fit residues: 77.3792 Evaluate side-chains 148 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 314 GLN ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 314 GLN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8865 Z= 0.310 Angle : 0.939 11.293 12042 Z= 0.456 Chirality : 0.052 0.201 1341 Planarity : 0.006 0.052 1536 Dihedral : 9.340 56.980 1245 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 4.78 % Allowed : 10.42 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.71 (0.22), residues: 1068 helix: -2.65 (0.22), residues: 351 sheet: -1.50 (0.34), residues: 210 loop : -2.70 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 79 HIS 0.008 0.002 HIS A 88 PHE 0.020 0.003 PHE C 352 TYR 0.020 0.002 TYR B 218 ARG 0.005 0.001 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 199 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 25 residues processed: 220 average time/residue: 0.1628 time to fit residues: 52.6654 Evaluate side-chains 181 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0830 time to fit residues: 5.1781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 97 optimal weight: 0.3980 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS B 40 HIS ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8865 Z= 0.204 Angle : 0.812 8.552 12042 Z= 0.389 Chirality : 0.047 0.169 1341 Planarity : 0.005 0.048 1536 Dihedral : 8.235 57.785 1245 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 2.93 % Allowed : 14.01 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.23), residues: 1068 helix: -1.65 (0.26), residues: 348 sheet: -1.34 (0.34), residues: 210 loop : -2.43 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 356 HIS 0.005 0.001 HIS A 88 PHE 0.011 0.002 PHE C 127 TYR 0.015 0.001 TYR B 218 ARG 0.003 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 221 average time/residue: 0.1557 time to fit residues: 51.2774 Evaluate side-chains 164 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1256 time to fit residues: 3.1549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8865 Z= 0.201 Angle : 0.816 9.249 12042 Z= 0.385 Chirality : 0.048 0.193 1341 Planarity : 0.005 0.046 1536 Dihedral : 7.780 59.110 1245 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 3.80 % Allowed : 15.64 % Favored : 80.56 % 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: -2.52 (0.24), residues: 1068 helix: -1.13 (0.27), residues: 351 sheet: -1.17 (0.35), residues: 210 loop : -2.26 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 79 HIS 0.002 0.001 HIS C 371 PHE 0.011 0.002 PHE C 223 TYR 0.016 0.001 TYR C 218 ARG 0.004 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 194 time to evaluate : 1.040 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 217 average time/residue: 0.1625 time to fit residues: 52.8955 Evaluate side-chains 175 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0849 time to fit residues: 4.3350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0970 chunk 59 optimal weight: 30.0000 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8865 Z= 0.170 Angle : 0.803 9.662 12042 Z= 0.372 Chirality : 0.047 0.186 1341 Planarity : 0.004 0.042 1536 Dihedral : 7.270 59.475 1245 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 2.28 % Allowed : 17.59 % Favored : 80.13 % 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: -2.04 (0.25), residues: 1068 helix: -0.67 (0.29), residues: 330 sheet: -0.90 (0.36), residues: 210 loop : -1.98 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 356 HIS 0.003 0.001 HIS B 88 PHE 0.020 0.002 PHE B 31 TYR 0.014 0.001 TYR B 218 ARG 0.003 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 204 average time/residue: 0.1566 time to fit residues: 48.2711 Evaluate side-chains 178 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0846 time to fit residues: 2.7571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 0.4980 chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8865 Z= 0.208 Angle : 0.812 9.543 12042 Z= 0.379 Chirality : 0.048 0.179 1341 Planarity : 0.004 0.043 1536 Dihedral : 7.329 59.208 1245 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 3.37 % Allowed : 20.20 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.25), residues: 1068 helix: -0.59 (0.29), residues: 336 sheet: -0.86 (0.36), residues: 210 loop : -2.08 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 356 HIS 0.004 0.001 HIS B 88 PHE 0.013 0.002 PHE A 200 TYR 0.042 0.002 TYR C 166 ARG 0.003 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 1.040 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 17 residues processed: 177 average time/residue: 0.1621 time to fit residues: 43.0465 Evaluate side-chains 177 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0799 time to fit residues: 3.9295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 0.0970 chunk 87 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 48 optimal weight: 0.0070 chunk 64 optimal weight: 6.9990 overall best weight: 4.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8865 Z= 0.260 Angle : 0.844 10.536 12042 Z= 0.396 Chirality : 0.049 0.231 1341 Planarity : 0.005 0.045 1536 Dihedral : 7.581 58.264 1245 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 2.93 % Allowed : 20.41 % Favored : 76.66 % 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: -2.20 (0.25), residues: 1068 helix: -0.83 (0.28), residues: 357 sheet: -0.85 (0.36), residues: 210 loop : -2.18 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 356 HIS 0.004 0.001 HIS A 88 PHE 0.019 0.002 PHE B 31 TYR 0.028 0.002 TYR C 166 ARG 0.004 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 190 average time/residue: 0.1611 time to fit residues: 45.9557 Evaluate side-chains 173 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0897 time to fit residues: 4.1198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 31 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 overall best weight: 3.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8865 Z= 0.232 Angle : 0.832 10.315 12042 Z= 0.388 Chirality : 0.048 0.227 1341 Planarity : 0.004 0.043 1536 Dihedral : 7.478 59.729 1245 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 1.41 % Allowed : 22.69 % Favored : 75.90 % 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: -2.23 (0.25), residues: 1068 helix: -0.81 (0.28), residues: 357 sheet: -0.88 (0.36), residues: 210 loop : -2.24 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 356 HIS 0.006 0.001 HIS A 88 PHE 0.014 0.002 PHE A 200 TYR 0.025 0.002 TYR C 166 ARG 0.004 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 167 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 171 average time/residue: 0.1529 time to fit residues: 39.8233 Evaluate side-chains 167 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0813 time to fit residues: 3.1182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 9.9990 chunk 97 optimal weight: 0.0040 chunk 99 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 0.0270 chunk 76 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8865 Z= 0.229 Angle : 0.845 15.267 12042 Z= 0.392 Chirality : 0.048 0.203 1341 Planarity : 0.005 0.042 1536 Dihedral : 7.426 58.760 1245 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 0.76 % Allowed : 24.10 % Favored : 75.14 % 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: -2.28 (0.25), residues: 1068 helix: -0.89 (0.28), residues: 348 sheet: -0.95 (0.35), residues: 210 loop : -2.19 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 356 HIS 0.005 0.001 HIS B 88 PHE 0.015 0.002 PHE A 200 TYR 0.022 0.002 TYR C 166 ARG 0.004 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 170 average time/residue: 0.1591 time to fit residues: 41.0028 Evaluate side-chains 166 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 159 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0935 time to fit residues: 2.5916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 HIS ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8865 Z= 0.326 Angle : 0.904 13.232 12042 Z= 0.426 Chirality : 0.051 0.211 1341 Planarity : 0.005 0.044 1536 Dihedral : 7.728 54.483 1245 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 1.41 % Allowed : 24.00 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.25), residues: 1068 helix: -1.03 (0.28), residues: 348 sheet: -1.15 (0.35), residues: 213 loop : -2.22 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP A 79 HIS 0.006 0.001 HIS B 88 PHE 0.017 0.002 PHE B 200 TYR 0.023 0.002 TYR B 218 ARG 0.006 0.001 ARG B 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 158 average time/residue: 0.1556 time to fit residues: 37.4326 Evaluate side-chains 151 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0874 time to fit residues: 2.6281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** 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 = 0.3329 r_free = 0.3329 target = 0.093483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.083478 restraints weight = 24099.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.085523 restraints weight = 12302.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.086875 restraints weight = 7502.129| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8865 Z= 0.215 Angle : 0.865 12.574 12042 Z= 0.401 Chirality : 0.049 0.193 1341 Planarity : 0.005 0.042 1536 Dihedral : 7.469 58.850 1245 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 0.87 % Allowed : 24.32 % Favored : 74.81 % 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: -2.37 (0.25), residues: 1068 helix: -0.92 (0.28), residues: 348 sheet: -1.21 (0.35), residues: 213 loop : -2.18 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 79 HIS 0.005 0.001 HIS B 88 PHE 0.012 0.002 PHE B 200 TYR 0.020 0.001 TYR C 166 ARG 0.003 0.000 ARG C 183 =============================================================================== Job complete usr+sys time: 1777.27 seconds wall clock time: 33 minutes 18.93 seconds (1998.93 seconds total)