Starting phenix.real_space_refine on Fri Dec 8 16:01:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trq_26101/12_2023/7trq_26101_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trq_26101/12_2023/7trq_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_26101/12_2023/7trq_26101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trq_26101/12_2023/7trq_26101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trq_26101/12_2023/7trq_26101_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trq_26101/12_2023/7trq_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-1.21rc1-5172/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: 4.86, per 1000 atoms: 0.56 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: 3.08 Conformation dependent library (CDL) restraints added in 1.8 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: 1.64 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: 2.74 Time building geometry restraints manager: 3.35 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: 1.840 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: 4.140 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.580 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.110 ------------------------------------------------------------------------------- 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 : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 1.7043 time to fit residues: 313.7084 Evaluate side-chains 130 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3533 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 117 ASN B 75 GLN B 340 ASN A 241 ASN A 294 ASN A 304 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1518 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= 0.148 Angle : 0.506 8.350 12102 Z= 0.269 Chirality : 0.041 0.133 1389 Planarity : 0.004 0.040 1520 Dihedral : 5.224 35.027 1246 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.94 % Allowed : 10.66 % Favored : 87.41 % 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: 0.61 (0.25), residues: 1113 helix: 1.45 (0.26), residues: 398 sheet: 0.48 (0.30), residues: 280 loop : -0.56 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS H 35 PHE 0.014 0.001 PHE A 189 TYR 0.014 0.001 TYR R 439 ARG 0.006 0.000 ARG R 400 *********************** 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 164 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 5 residues processed: 154 average time/residue: 1.7221 time to fit residues: 277.8359 Evaluate side-chains 139 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 4 average time/residue: 0.5999 time to fit residues: 3.9508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 0.0670 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8907 Z= 0.148 Angle : 0.506 8.351 12102 Z= 0.269 Chirality : 0.041 0.133 1389 Planarity : 0.004 0.040 1520 Dihedral : 5.390 45.172 1246 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.11 % Allowed : 14.42 % Favored : 85.47 % 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: 0.61 (0.25), residues: 1113 helix: 1.45 (0.26), residues: 398 sheet: 0.48 (0.30), residues: 280 loop : -0.56 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS H 35 PHE 0.014 0.001 PHE A 189 TYR 0.014 0.001 TYR R 439 ARG 0.006 0.000 ARG R 400 *********************** 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 135 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 1.7350 time to fit residues: 245.8466 Evaluate side-chains 135 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.5776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8907 Z= 0.148 Angle : 0.506 8.353 12102 Z= 0.269 Chirality : 0.041 0.133 1389 Planarity : 0.004 0.040 1520 Dihedral : 5.563 59.311 1246 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.22 % Allowed : 14.32 % Favored : 85.47 % 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: 0.61 (0.25), residues: 1113 helix: 1.45 (0.26), residues: 398 sheet: 0.48 (0.30), residues: 280 loop : -0.56 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS H 35 PHE 0.014 0.001 PHE A 189 TYR 0.014 0.001 TYR R 439 ARG 0.006 0.000 ARG R 400 *********************** 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 136 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 135 average time/residue: 1.7066 time to fit residues: 241.6760 Evaluate side-chains 136 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.008 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.0787 time to fit residues: 1.4842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 90 optimal weight: 0.2980 chunk 73 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN A 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8907 Z= 0.329 Angle : 0.572 9.972 12102 Z= 0.305 Chirality : 0.044 0.131 1389 Planarity : 0.004 0.040 1520 Dihedral : 4.887 32.314 1246 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.72 % Allowed : 12.70 % Favored : 85.58 % 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: 0.97 (0.25), residues: 1113 helix: 1.81 (0.26), residues: 400 sheet: 0.67 (0.30), residues: 277 loop : -0.43 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS H 35 PHE 0.014 0.002 PHE B 199 TYR 0.014 0.001 TYR R 453 ARG 0.009 0.001 ARG R 400 *********************** 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 152 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 145 average time/residue: 1.6876 time to fit residues: 257.0091 Evaluate side-chains 143 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1601 time to fit residues: 1.9356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 26 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.8576 moved from start: 0.1952 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= 0.158 Angle : 0.512 10.643 12102 Z= 0.269 Chirality : 0.041 0.131 1389 Planarity : 0.003 0.047 1520 Dihedral : 4.514 29.118 1246 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.61 % Allowed : 13.35 % Favored : 85.04 % 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: 1.88 (0.26), residues: 406 sheet: 0.72 (0.30), residues: 276 loop : -0.30 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS A 188 PHE 0.022 0.001 PHE R 84 TYR 0.012 0.001 TYR H 190 ARG 0.010 0.000 ARG R 400 *********************** 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 162 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 153 average time/residue: 1.7450 time to fit residues: 280.1119 Evaluate side-chains 151 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.1465 time to fit residues: 2.1816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 0.0040 chunk 48 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.7794 ------------------------------------------------------------------------------- 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** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8907 Z= 0.163 Angle : 0.513 10.655 12102 Z= 0.269 Chirality : 0.041 0.130 1389 Planarity : 0.003 0.046 1520 Dihedral : 4.660 34.575 1246 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.43 % Allowed : 15.50 % 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: 1.11 (0.25), residues: 1113 helix: 1.88 (0.26), residues: 406 sheet: 0.72 (0.30), residues: 276 loop : -0.30 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS A 188 PHE 0.021 0.001 PHE R 84 TYR 0.012 0.001 TYR H 190 ARG 0.009 0.000 ARG R 400 *********************** 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 148 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 148 average time/residue: 1.8135 time to fit residues: 280.9691 Evaluate side-chains 145 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.2154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8907 Z= 0.198 Angle : 0.542 9.468 12102 Z= 0.283 Chirality : 0.041 0.162 1389 Planarity : 0.004 0.060 1520 Dihedral : 4.507 28.574 1246 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.08 % Allowed : 15.18 % Favored : 83.75 % 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: 1.18 (0.25), residues: 1113 helix: 1.97 (0.26), residues: 406 sheet: 0.70 (0.30), residues: 278 loop : -0.26 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 PHE 0.026 0.001 PHE R 84 TYR 0.011 0.001 TYR H 190 ARG 0.013 0.000 ARG R 400 *********************** 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 156 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 152 average time/residue: 1.7689 time to fit residues: 281.2769 Evaluate side-chains 148 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0817 time to fit residues: 1.5288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 0.3980 chunk 104 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8576 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8907 Z= 0.198 Angle : 0.542 9.468 12102 Z= 0.283 Chirality : 0.041 0.162 1389 Planarity : 0.004 0.060 1520 Dihedral : 4.509 28.574 1246 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.43 % Allowed : 15.82 % Favored : 83.75 % 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: 1.18 (0.25), residues: 1113 helix: 1.97 (0.26), residues: 406 sheet: 0.70 (0.30), residues: 278 loop : -0.26 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 PHE 0.026 0.001 PHE R 84 TYR 0.011 0.001 TYR H 190 ARG 0.013 0.000 ARG R 400 *********************** 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 147 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 147 average time/residue: 1.7467 time to fit residues: 268.7500 Evaluate side-chains 147 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.3431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8578 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8907 Z= 0.198 Angle : 0.542 9.470 12102 Z= 0.283 Chirality : 0.041 0.161 1389 Planarity : 0.004 0.060 1520 Dihedral : 4.520 28.574 1246 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.43 % Allowed : 15.82 % Favored : 83.75 % 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: 1.18 (0.25), residues: 1113 helix: 1.97 (0.26), residues: 406 sheet: 0.70 (0.30), residues: 278 loop : -0.26 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 PHE 0.026 0.001 PHE R 84 TYR 0.011 0.001 TYR H 190 ARG 0.013 0.000 ARG R 400 ********************** 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 147 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 147 average time/residue: 1.7444 time to fit residues: 268.8072 Evaluate side-chains 147 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.1920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 0.0070 chunk 36 optimal weight: 0.0010 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.9808 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.095618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.061655 restraints weight = 15277.327| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.35 r_work: 0.2638 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8907 Z= 0.179 Angle : 0.552 9.800 12102 Z= 0.288 Chirality : 0.041 0.155 1389 Planarity : 0.004 0.067 1520 Dihedral : 4.483 28.304 1246 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.54 % Allowed : 15.61 % Favored : 83.85 % 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: 1.20 (0.25), residues: 1113 helix: 2.00 (0.26), residues: 406 sheet: 0.74 (0.30), residues: 276 loop : -0.27 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.002 0.001 HIS H 35 PHE 0.029 0.001 PHE R 84 TYR 0.011 0.001 TYR H 190 ARG 0.014 0.000 ARG R 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4607.34 seconds wall clock time: 82 minutes 4.00 seconds (4924.00 seconds total)