Starting phenix.real_space_refine on Tue Jun 25 20:35:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trq_26101/06_2024/7trq_26101_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trq_26101/06_2024/7trq_26101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trq_26101/06_2024/7trq_26101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trq_26101/06_2024/7trq_26101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trq_26101/06_2024/7trq_26101_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trq_26101/06_2024/7trq_26101_updated.pdb" } resolution = 2.5 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 65 5.16 5 C 5558 2.51 5 N 1471 2.21 5 O 1626 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8723 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2597 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 419 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1786 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1764 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'IUI': 1, 'IXO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.26, per 1000 atoms: 0.60 Number of scatterers: 8723 At special positions: 0 Unit cell: (92.13, 121.18, 126.99, 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 65 16.00 F 3 9.00 O 1626 8.00 N 1471 7.00 C 5558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.9 seconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 12 sheets defined 35.0% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'R' and resid 32 through 59 removed outlier: 3.620A pdb=" N ALA R 36 " --> pdb=" O MET R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 63 No H-bonds generated for 'chain 'R' and resid 61 through 63' Processing helix chain 'R' and resid 66 through 83 removed outlier: 4.292A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 Processing helix chain 'R' and resid 103 through 135 Processing helix chain 'R' and resid 140 through 143 No H-bonds generated for 'chain 'R' and resid 140 through 143' Processing helix chain 'R' and resid 146 through 175 Proline residue: R 166 - end of helix removed outlier: 5.189A pdb=" N GLN R 172 " --> pdb=" O ILE R 168 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N PHE R 173 " --> pdb=" O LEU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 190 No H-bonds generated for 'chain 'R' and resid 188 through 190' Processing helix chain 'R' and resid 193 through 203 Processing helix chain 'R' and resid 207 through 222 Processing helix chain 'R' and resid 393 through 425 Proline residue: R 415 - end of helix removed outlier: 3.684A pdb=" N LEU R 421 " --> pdb=" O ASN R 417 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE R 425 " --> pdb=" O LEU R 421 " (cutoff:3.500A) Processing helix chain 'R' and resid 432 through 452 removed outlier: 3.971A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 458 through 468 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.832A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 330 through 350 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.951A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.992A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.621A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.004A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.718A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.542A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.597A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.837A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.373A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 155 through 160 removed outlier: 3.848A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.384A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1179 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: 2.57 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1416 1.32 - 1.45: 2599 1.45 - 1.58: 4797 1.58 - 1.72: 0 1.72 - 1.85: 95 Bond restraints: 8907 Sorted by residual: bond pdb=" C10 IXO R 601 " pdb=" N11 IXO R 601 " ideal model delta sigma weight residual 1.270 1.469 -0.199 2.00e-02 2.50e+03 9.89e+01 bond pdb=" C10 IXO R 601 " pdb=" C14 IXO R 601 " ideal model delta sigma weight residual 1.492 1.324 0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" C13 IXO R 601 " pdb=" O12 IXO R 601 " ideal model delta sigma weight residual 1.439 1.546 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C05 IXO R 601 " pdb=" C06 IXO R 601 " ideal model delta sigma weight residual 1.450 1.529 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C07 IXO R 601 " pdb=" C08 IXO R 601 " ideal model delta sigma weight residual 1.454 1.528 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 8902 not shown) Histogram of bond angle deviations from ideal: 90.86 - 108.68: 495 108.68 - 126.51: 11465 126.51 - 144.33: 140 144.33 - 162.15: 0 162.15 - 179.98: 2 Bond angle restraints: 12102 Sorted by residual: angle pdb=" CA TYR B 105 " pdb=" CB TYR B 105 " pdb=" CG TYR B 105 " ideal model delta sigma weight residual 113.90 119.30 -5.40 1.80e+00 3.09e-01 9.00e+00 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.80e+00 angle pdb=" CA TRP B 82 " pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 113.60 119.19 -5.59 1.90e+00 2.77e-01 8.66e+00 angle pdb=" CA TYR R 439 " pdb=" CB TYR R 439 " pdb=" CG TYR R 439 " ideal model delta sigma weight residual 113.90 119.20 -5.30 1.80e+00 3.09e-01 8.66e+00 angle pdb=" CA LEU B 318 " pdb=" CB LEU B 318 " pdb=" CG LEU B 318 " ideal model delta sigma weight residual 116.30 126.55 -10.25 3.50e+00 8.16e-02 8.58e+00 ... (remaining 12097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4888 16.94 - 33.88: 299 33.88 - 50.82: 69 50.82 - 67.75: 8 67.75 - 84.69: 3 Dihedral angle restraints: 5267 sinusoidal: 1986 harmonic: 3281 Sorted by residual: dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PHE A 196 " pdb=" C PHE A 196 " pdb=" N LYS A 197 " pdb=" CA LYS A 197 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE H 32 " pdb=" C PHE H 32 " pdb=" N GLY H 33 " pdb=" CA GLY H 33 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1139 0.067 - 0.134: 206 0.134 - 0.201: 40 0.201 - 0.268: 3 0.268 - 0.335: 1 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CB VAL R 444 " pdb=" CA VAL R 444 " pdb=" CG1 VAL R 444 " pdb=" CG2 VAL R 444 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA TYR B 105 " pdb=" N TYR B 105 " pdb=" C TYR B 105 " pdb=" CB TYR B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1386 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N IUI R 602 " -0.005 2.00e-02 2.50e+03 3.15e-02 3.23e+01 pdb=" C IUI R 602 " -0.044 2.00e-02 2.50e+03 pdb=" C1 IUI R 602 " -0.011 2.00e-02 2.50e+03 pdb=" C16 IUI R 602 " 0.077 2.00e-02 2.50e+03 pdb=" C2 IUI R 602 " 0.005 2.00e-02 2.50e+03 pdb=" C3 IUI R 602 " -0.022 2.00e-02 2.50e+03 pdb=" C4 IUI R 602 " -0.020 2.00e-02 2.50e+03 pdb=" C5 IUI R 602 " -0.006 2.00e-02 2.50e+03 pdb=" C6 IUI R 602 " -0.000 2.00e-02 2.50e+03 pdb=" C7 IUI R 602 " 0.058 2.00e-02 2.50e+03 pdb=" N1 IUI R 602 " -0.021 2.00e-02 2.50e+03 pdb=" N3 IUI R 602 " 0.000 2.00e-02 2.50e+03 pdb=" S IUI R 602 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O IUI R 602 " -0.007 2.00e-02 2.50e+03 4.03e-02 2.03e+01 pdb=" C6 IUI R 602 " 0.039 2.00e-02 2.50e+03 pdb=" C7 IUI R 602 " -0.018 2.00e-02 2.50e+03 pdb=" C8 IUI R 602 " 0.049 2.00e-02 2.50e+03 pdb=" N2 IUI R 602 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO B 194 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.044 5.00e-02 4.00e+02 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2478 2.82 - 3.34: 7702 3.34 - 3.86: 14781 3.86 - 4.38: 17789 4.38 - 4.90: 30443 Nonbonded interactions: 73193 Sorted by model distance: nonbonded pdb=" O ASN R 87 " pdb=" OG1 THR R 90 " model vdw 2.295 2.440 nonbonded pdb=" OE1 GLU B 130 " pdb=" NH1 ARG B 134 " model vdw 2.345 2.520 nonbonded pdb=" O GLU R 395 " pdb=" OG1 THR R 399 " model vdw 2.350 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.359 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.364 2.440 ... (remaining 73188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.010 Extract box with map and model: 3.760 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.890 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 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 : 0.006 0.199 8907 Z= 0.396 Angle : 0.831 10.254 12102 Z= 0.467 Chirality : 0.056 0.335 1389 Planarity : 0.007 0.079 1520 Dihedral : 11.802 84.693 3137 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.50 (0.23), residues: 1113 helix: -0.01 (0.23), residues: 394 sheet: 0.20 (0.29), residues: 291 loop : -0.88 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.009 0.002 HIS A 322 PHE 0.029 0.003 PHE B 199 TYR 0.021 0.002 TYR R 439 ARG 0.009 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8133 (t-100) cc_final: 0.7748 (t-100) REVERT: R 148 MET cc_start: 0.7830 (mmt) cc_final: 0.7545 (mmt) REVERT: R 152 MET cc_start: 0.8152 (mtm) cc_final: 0.7825 (mtp) REVERT: R 400 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.7533 (mtm110) REVERT: B 16 ASN cc_start: 0.9207 (m-40) cc_final: 0.8715 (m-40) REVERT: B 17 GLN cc_start: 0.9041 (tt0) cc_final: 0.8678 (tp-100) REVERT: H 73 ASP cc_start: 0.8398 (t0) cc_final: 0.8107 (t0) REVERT: H 87 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8157 (mtt180) REVERT: H 219 LEU cc_start: 0.9253 (tt) cc_final: 0.8919 (tt) REVERT: A 24 ARG cc_start: 0.7696 (ttp-110) cc_final: 0.7296 (mtm-85) REVERT: A 35 LYS cc_start: 0.8542 (mttp) cc_final: 0.8293 (mtpp) REVERT: A 197 LYS cc_start: 0.8841 (mttt) cc_final: 0.8460 (mttm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 1.6922 time to fit residues: 311.3516 Evaluate side-chains 132 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 0.1980 chunk 46 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 117 ASN B 32 GLN B 75 GLN B 340 ASN A 241 ASN A 294 ASN A 304 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8907 Z= 0.154 Angle : 0.496 6.054 12102 Z= 0.266 Chirality : 0.041 0.133 1389 Planarity : 0.004 0.042 1520 Dihedral : 5.151 34.718 1246 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.83 % Allowed : 10.12 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.63 (0.25), residues: 1113 helix: 1.48 (0.26), residues: 398 sheet: 0.49 (0.30), residues: 280 loop : -0.57 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE A 189 TYR 0.012 0.001 TYR R 439 ARG 0.003 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 121 MET cc_start: 0.8661 (mmm) cc_final: 0.8435 (mmp) REVERT: R 148 MET cc_start: 0.7893 (mmt) cc_final: 0.7617 (mmt) REVERT: R 152 MET cc_start: 0.8154 (mtm) cc_final: 0.7836 (mtp) REVERT: R 400 ARG cc_start: 0.7813 (ttp-170) cc_final: 0.7500 (mtm110) REVERT: B 15 LYS cc_start: 0.9225 (mtpp) cc_final: 0.8926 (mtmt) REVERT: B 217 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7781 (pmm) REVERT: G 42 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: H 73 ASP cc_start: 0.8366 (t0) cc_final: 0.8054 (t0) REVERT: H 87 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.8083 (mtt180) REVERT: H 163 LYS cc_start: 0.8301 (tttt) cc_final: 0.8086 (tttt) REVERT: H 219 LEU cc_start: 0.9221 (tt) cc_final: 0.8970 (tt) REVERT: A 24 ARG cc_start: 0.7701 (ttp-110) cc_final: 0.7310 (ttp-170) REVERT: A 35 LYS cc_start: 0.8492 (mttp) cc_final: 0.8248 (mtpp) REVERT: A 197 LYS cc_start: 0.8843 (mttt) cc_final: 0.8479 (mttp) outliers start: 17 outliers final: 5 residues processed: 158 average time/residue: 1.5865 time to fit residues: 262.9126 Evaluate side-chains 144 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain R residue 447 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN A 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8907 Z= 0.290 Angle : 0.534 5.866 12102 Z= 0.287 Chirality : 0.043 0.132 1389 Planarity : 0.004 0.048 1520 Dihedral : 5.185 54.900 1246 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.72 % Allowed : 11.73 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.98 (0.25), residues: 1113 helix: 1.89 (0.26), residues: 398 sheet: 0.59 (0.30), residues: 280 loop : -0.43 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.002 PHE B 199 TYR 0.013 0.001 TYR H 95 ARG 0.006 0.001 ARG R 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 121 MET cc_start: 0.8679 (mmm) cc_final: 0.8454 (mmp) REVERT: R 148 MET cc_start: 0.7877 (mmt) cc_final: 0.7633 (mmt) REVERT: R 152 MET cc_start: 0.8174 (mtm) cc_final: 0.7870 (mtp) REVERT: R 400 ARG cc_start: 0.7861 (ttp-170) cc_final: 0.7524 (mtm110) REVERT: B 15 LYS cc_start: 0.9227 (mtpp) cc_final: 0.8918 (mtmt) REVERT: G 20 LYS cc_start: 0.8995 (tmtt) cc_final: 0.8617 (tptt) REVERT: G 24 ASN cc_start: 0.8571 (m-40) cc_final: 0.7926 (m-40) REVERT: G 42 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: H 223 ASP cc_start: 0.9081 (m-30) cc_final: 0.8707 (m-30) REVERT: A 24 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7285 (ttp-170) REVERT: A 35 LYS cc_start: 0.8540 (mttp) cc_final: 0.8278 (mtpp) REVERT: A 197 LYS cc_start: 0.8846 (mttt) cc_final: 0.8544 (mtmm) outliers start: 16 outliers final: 7 residues processed: 149 average time/residue: 1.6265 time to fit residues: 253.9987 Evaluate side-chains 150 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8907 Z= 0.175 Angle : 0.503 7.017 12102 Z= 0.266 Chirality : 0.041 0.131 1389 Planarity : 0.003 0.040 1520 Dihedral : 4.584 30.018 1246 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.05 % Allowed : 12.16 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1113 helix: 1.98 (0.26), residues: 404 sheet: 0.65 (0.30), residues: 278 loop : -0.36 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS H 35 PHE 0.018 0.001 PHE R 84 TYR 0.012 0.001 TYR H 190 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 121 MET cc_start: 0.8681 (mmm) cc_final: 0.8471 (mmp) REVERT: R 148 MET cc_start: 0.7875 (mmt) cc_final: 0.7547 (mmt) REVERT: R 152 MET cc_start: 0.8164 (mtm) cc_final: 0.7820 (mtp) REVERT: R 400 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7500 (mtm110) REVERT: B 15 LYS cc_start: 0.9234 (mtpp) cc_final: 0.8925 (mtmt) REVERT: G 20 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8503 (tptt) REVERT: G 24 ASN cc_start: 0.8532 (m-40) cc_final: 0.7652 (m-40) REVERT: G 42 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: A 24 ARG cc_start: 0.7754 (ttp-110) cc_final: 0.7278 (ttp-170) REVERT: A 35 LYS cc_start: 0.8505 (mttp) cc_final: 0.8282 (mtpp) REVERT: A 197 LYS cc_start: 0.8832 (mttt) cc_final: 0.8467 (mtmt) outliers start: 19 outliers final: 10 residues processed: 157 average time/residue: 1.6138 time to fit residues: 265.6001 Evaluate side-chains 157 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8907 Z= 0.175 Angle : 0.503 7.017 12102 Z= 0.267 Chirality : 0.041 0.131 1389 Planarity : 0.003 0.040 1520 Dihedral : 4.601 30.018 1246 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.18 % Allowed : 14.42 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1113 helix: 1.98 (0.26), residues: 404 sheet: 0.65 (0.30), residues: 278 loop : -0.36 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS H 35 PHE 0.018 0.001 PHE R 84 TYR 0.012 0.001 TYR H 190 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 121 MET cc_start: 0.8681 (mmm) cc_final: 0.8471 (mmp) REVERT: R 148 MET cc_start: 0.7875 (mmt) cc_final: 0.7547 (mmt) REVERT: R 152 MET cc_start: 0.8164 (mtm) cc_final: 0.7820 (mtp) REVERT: R 400 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7500 (mtm110) REVERT: B 15 LYS cc_start: 0.9236 (mtpp) cc_final: 0.8925 (mtmt) REVERT: G 20 LYS cc_start: 0.8863 (tmtt) cc_final: 0.8503 (tptt) REVERT: G 24 ASN cc_start: 0.8532 (m-40) cc_final: 0.7652 (m-40) REVERT: G 42 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: A 24 ARG cc_start: 0.7754 (ttp-110) cc_final: 0.7278 (ttp-170) REVERT: A 35 LYS cc_start: 0.8505 (mttp) cc_final: 0.8282 (mtpp) REVERT: A 197 LYS cc_start: 0.8833 (mttt) cc_final: 0.8467 (mtmt) outliers start: 11 outliers final: 10 residues processed: 150 average time/residue: 1.6631 time to fit residues: 261.7062 Evaluate side-chains 157 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8907 Z= 0.175 Angle : 0.503 7.018 12102 Z= 0.266 Chirality : 0.041 0.131 1389 Planarity : 0.003 0.040 1520 Dihedral : 4.645 30.018 1246 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.18 % Allowed : 14.42 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1113 helix: 1.98 (0.26), residues: 404 sheet: 0.65 (0.30), residues: 278 loop : -0.36 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS H 35 PHE 0.018 0.001 PHE R 84 TYR 0.012 0.001 TYR H 190 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 121 MET cc_start: 0.8681 (mmm) cc_final: 0.8471 (mmp) REVERT: R 148 MET cc_start: 0.7874 (mmt) cc_final: 0.7547 (mmt) REVERT: R 152 MET cc_start: 0.8164 (mtm) cc_final: 0.7820 (mtp) REVERT: R 400 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7500 (mtm110) REVERT: B 15 LYS cc_start: 0.9236 (mtpp) cc_final: 0.8925 (mtmt) REVERT: G 20 LYS cc_start: 0.8863 (tmtt) cc_final: 0.8503 (tptt) REVERT: G 24 ASN cc_start: 0.8532 (m-40) cc_final: 0.7650 (m-40) REVERT: G 42 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: A 24 ARG cc_start: 0.7754 (ttp-110) cc_final: 0.7278 (ttp-170) REVERT: A 35 LYS cc_start: 0.8505 (mttp) cc_final: 0.8282 (mtpp) REVERT: A 197 LYS cc_start: 0.8833 (mttt) cc_final: 0.8467 (mtmt) outliers start: 11 outliers final: 10 residues processed: 150 average time/residue: 1.6160 time to fit residues: 253.4439 Evaluate side-chains 157 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 0.0040 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8907 Z= 0.182 Angle : 0.501 7.032 12102 Z= 0.266 Chirality : 0.041 0.129 1389 Planarity : 0.003 0.040 1520 Dihedral : 4.705 30.016 1246 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.29 % Allowed : 14.32 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1113 helix: 1.99 (0.26), residues: 404 sheet: 0.65 (0.30), residues: 278 loop : -0.36 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS H 35 PHE 0.017 0.001 PHE R 84 TYR 0.012 0.001 TYR H 190 ARG 0.006 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 121 MET cc_start: 0.8682 (mmm) cc_final: 0.8471 (mmp) REVERT: R 148 MET cc_start: 0.7875 (mmt) cc_final: 0.7547 (mmt) REVERT: R 152 MET cc_start: 0.8164 (mtm) cc_final: 0.7820 (mtp) REVERT: R 400 ARG cc_start: 0.7836 (ttp-170) cc_final: 0.7500 (mtm110) REVERT: B 15 LYS cc_start: 0.9236 (mtpp) cc_final: 0.8925 (mtmt) REVERT: G 20 LYS cc_start: 0.8863 (tmtt) cc_final: 0.8498 (tptt) REVERT: G 24 ASN cc_start: 0.8532 (m-40) cc_final: 0.7644 (m-40) REVERT: G 42 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: A 24 ARG cc_start: 0.7754 (ttp-110) cc_final: 0.7279 (ttp-170) REVERT: A 35 LYS cc_start: 0.8505 (mttp) cc_final: 0.8282 (mtpp) REVERT: A 197 LYS cc_start: 0.8834 (mttt) cc_final: 0.8467 (mtmt) outliers start: 12 outliers final: 11 residues processed: 151 average time/residue: 1.6564 time to fit residues: 262.1152 Evaluate side-chains 158 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 96 optimal weight: 0.1980 chunk 101 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 GLN A 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8907 Z= 0.157 Angle : 0.525 10.520 12102 Z= 0.274 Chirality : 0.041 0.170 1389 Planarity : 0.003 0.039 1520 Dihedral : 4.533 28.891 1246 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.51 % Allowed : 13.78 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.25), residues: 1113 helix: 2.11 (0.26), residues: 400 sheet: 0.68 (0.30), residues: 276 loop : -0.30 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS H 35 PHE 0.027 0.001 PHE R 84 TYR 0.012 0.001 TYR H 190 ARG 0.007 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 148 MET cc_start: 0.7883 (mmt) cc_final: 0.7638 (mmt) REVERT: R 152 MET cc_start: 0.8166 (mtm) cc_final: 0.7808 (mtp) REVERT: R 400 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7497 (mtm110) REVERT: B 15 LYS cc_start: 0.9229 (mtpp) cc_final: 0.8909 (mtmt) REVERT: G 20 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8466 (tptt) REVERT: G 24 ASN cc_start: 0.8534 (m-40) cc_final: 0.7591 (m-40) REVERT: G 42 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: G 58 GLU cc_start: 0.8265 (mp0) cc_final: 0.8044 (pm20) REVERT: A 24 ARG cc_start: 0.7739 (ttp-110) cc_final: 0.7278 (ttp-170) REVERT: A 35 LYS cc_start: 0.8475 (mttp) cc_final: 0.8251 (mtpp) REVERT: A 197 LYS cc_start: 0.8836 (mttt) cc_final: 0.8480 (mtmt) outliers start: 14 outliers final: 10 residues processed: 152 average time/residue: 1.6265 time to fit residues: 259.2224 Evaluate side-chains 157 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8907 Z= 0.157 Angle : 0.525 10.520 12102 Z= 0.274 Chirality : 0.041 0.170 1389 Planarity : 0.003 0.039 1520 Dihedral : 4.533 28.891 1246 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.18 % Allowed : 14.64 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.25), residues: 1113 helix: 2.11 (0.26), residues: 400 sheet: 0.68 (0.30), residues: 276 loop : -0.30 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS H 35 PHE 0.027 0.001 PHE R 84 TYR 0.012 0.001 TYR H 190 ARG 0.007 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 148 MET cc_start: 0.7883 (mmt) cc_final: 0.7638 (mmt) REVERT: R 152 MET cc_start: 0.8166 (mtm) cc_final: 0.7808 (mtp) REVERT: R 400 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7497 (mtm110) REVERT: B 15 LYS cc_start: 0.9227 (mtpp) cc_final: 0.8909 (mtmt) REVERT: G 20 LYS cc_start: 0.8867 (tmtt) cc_final: 0.8466 (tptt) REVERT: G 24 ASN cc_start: 0.8534 (m-40) cc_final: 0.7591 (m-40) REVERT: G 42 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: G 58 GLU cc_start: 0.8265 (mp0) cc_final: 0.8044 (pm20) REVERT: A 24 ARG cc_start: 0.7745 (ttp-110) cc_final: 0.7278 (ttp-170) REVERT: A 35 LYS cc_start: 0.8475 (mttp) cc_final: 0.8251 (mtpp) REVERT: A 197 LYS cc_start: 0.8837 (mttt) cc_final: 0.8480 (mtmt) outliers start: 11 outliers final: 10 residues processed: 150 average time/residue: 1.6579 time to fit residues: 260.5272 Evaluate side-chains 155 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 87 optimal weight: 0.4980 chunk 9 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8907 Z= 0.157 Angle : 0.525 10.520 12102 Z= 0.274 Chirality : 0.041 0.170 1389 Planarity : 0.003 0.039 1520 Dihedral : 4.533 28.891 1246 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.18 % Allowed : 14.64 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.25), residues: 1113 helix: 2.11 (0.26), residues: 400 sheet: 0.68 (0.30), residues: 276 loop : -0.30 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS H 35 PHE 0.027 0.001 PHE R 84 TYR 0.012 0.001 TYR H 190 ARG 0.007 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 148 MET cc_start: 0.7883 (mmt) cc_final: 0.7638 (mmt) REVERT: R 152 MET cc_start: 0.8166 (mtm) cc_final: 0.7808 (mtp) REVERT: R 400 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7497 (mtm110) REVERT: B 15 LYS cc_start: 0.9227 (mtpp) cc_final: 0.8909 (mtmt) REVERT: G 20 LYS cc_start: 0.8867 (tmtt) cc_final: 0.8466 (tptt) REVERT: G 24 ASN cc_start: 0.8534 (m-40) cc_final: 0.7591 (m-40) REVERT: G 42 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: G 58 GLU cc_start: 0.8265 (mp0) cc_final: 0.8044 (pm20) REVERT: A 24 ARG cc_start: 0.7745 (ttp-110) cc_final: 0.7278 (ttp-170) REVERT: A 35 LYS cc_start: 0.8475 (mttp) cc_final: 0.8251 (mtpp) REVERT: A 197 LYS cc_start: 0.8837 (mttt) cc_final: 0.8480 (mtmt) outliers start: 11 outliers final: 10 residues processed: 148 average time/residue: 1.6593 time to fit residues: 256.9102 Evaluate side-chains 155 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 48 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 0.0470 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.095770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.061533 restraints weight = 15304.050| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.39 r_work: 0.2634 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8907 Z= 0.157 Angle : 0.525 10.520 12102 Z= 0.274 Chirality : 0.041 0.170 1389 Planarity : 0.003 0.039 1520 Dihedral : 4.533 28.891 1246 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.18 % Allowed : 14.75 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.25), residues: 1113 helix: 2.11 (0.26), residues: 400 sheet: 0.68 (0.30), residues: 276 loop : -0.30 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS H 35 PHE 0.027 0.001 PHE R 84 TYR 0.012 0.001 TYR H 190 ARG 0.007 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4463.39 seconds wall clock time: 78 minutes 8.28 seconds (4688.28 seconds total)