Starting phenix.real_space_refine on Wed Feb 14 09:36:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/02_2024/7dfl_30665_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/02_2024/7dfl_30665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/02_2024/7dfl_30665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/02_2024/7dfl_30665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/02_2024/7dfl_30665_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/02_2024/7dfl_30665_neut_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5729 2.51 5 N 1535 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 153": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8987 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2273 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "A" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1847 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain breaks: 2 Chain: "C" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1808 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.45, per 1000 atoms: 0.72 Number of scatterers: 8987 At special positions: 0 Unit cell: (90.72, 119.88, 126.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1657 8.00 N 1535 7.00 C 5729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 180 " distance=2.04 Simple disulfide: pdb=" SG CYS R 441 " - pdb=" SG CYS R 444 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 229 " distance=1.95 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: 4.10 Conformation dependent library (CDL) restraints added in 1.9 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 13 sheets defined 33.5% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'R' and resid 29 through 52 Processing helix chain 'R' and resid 61 through 79 removed outlier: 4.084A pdb=" N TYR R 65 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 89 Processing helix chain 'R' and resid 97 through 130 Processing helix chain 'R' and resid 141 through 163 removed outlier: 4.816A pdb=" N TRP R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL R 159 " --> pdb=" O SER R 155 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE R 160 " --> pdb=" O PHE R 156 " (cutoff:3.500A) Proline residue: R 161 - end of helix Processing helix chain 'R' and resid 169 through 171 No H-bonds generated for 'chain 'R' and resid 169 through 171' Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 200 through 217 Processing helix chain 'R' and resid 409 through 438 Proline residue: R 430 - end of helix removed outlier: 3.735A pdb=" N PHE R 434 " --> pdb=" O PRO R 430 " (cutoff:3.500A) Processing helix chain 'R' and resid 446 through 466 removed outlier: 3.586A pdb=" N ASN R 460 " --> pdb=" O LEU R 456 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER R 461 " --> pdb=" O GLY R 457 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR R 462 " --> pdb=" O TYR R 458 " (cutoff:3.500A) Proline residue: R 465 - end of helix Processing helix chain 'R' and resid 469 through 471 No H-bonds generated for 'chain 'R' and resid 469 through 471' Processing helix chain 'R' and resid 476 through 481 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'A' and resid 7 through 36 removed outlier: 4.128A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 277 through 283 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 336 through 355 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 53 through 55 No H-bonds generated for 'chain 'C' and resid 53 through 55' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.970A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.099A 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: 7.047A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.078A 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: 6.861A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.862A 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: 6.847A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 240 through 245 removed outlier: 4.086A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 276 through 278 Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.936A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 268 through 274 removed outlier: 4.112A pdb=" N SER A 225 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A 200 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LEU A 42 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG A 202 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU A 44 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 204 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'C' and resid 115 through 117 removed outlier: 5.827A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU C 45 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'C' and resid 146 through 149 removed outlier: 7.459A pdb=" N LYS C 244 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL C 149 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU C 246 " --> pdb=" O VAL C 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 226 through 231 removed outlier: 6.055A pdb=" N LEU C 178 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU C 187 " --> pdb=" O LEU C 178 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1098 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: 2.89 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2897 1.35 - 1.47: 2300 1.47 - 1.59: 3884 1.59 - 1.71: 0 1.71 - 1.84: 100 Bond restraints: 9181 Sorted by residual: bond pdb=" C VAL R 80 " pdb=" O VAL R 80 " ideal model delta sigma weight residual 1.233 1.285 -0.052 1.02e-02 9.61e+03 2.60e+01 bond pdb=" N THR C 118 " pdb=" CA THR C 118 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.23e-02 6.61e+03 1.76e+01 bond pdb=" N PRO C 236 " pdb=" CD PRO C 236 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" N LEU C 187 " pdb=" CA LEU C 187 " ideal model delta sigma weight residual 1.456 1.503 -0.046 1.22e-02 6.72e+03 1.44e+01 bond pdb=" N VAL R 80 " pdb=" CA VAL R 80 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.19e-02 7.06e+03 1.30e+01 ... (remaining 9176 not shown) Histogram of bond angle deviations from ideal: 96.80 - 104.25: 118 104.25 - 111.70: 4235 111.70 - 119.14: 3207 119.14 - 126.59: 4731 126.59 - 134.04: 136 Bond angle restraints: 12427 Sorted by residual: angle pdb=" N ARG R 218 " pdb=" CA ARG R 218 " pdb=" C ARG R 218 " ideal model delta sigma weight residual 110.80 121.85 -11.05 2.13e+00 2.20e-01 2.69e+01 angle pdb=" N SER C 136 " pdb=" CA SER C 136 " pdb=" C SER C 136 " ideal model delta sigma weight residual 110.80 100.47 10.33 2.13e+00 2.20e-01 2.35e+01 angle pdb=" N ARG R 134 " pdb=" CA ARG R 134 " pdb=" C ARG R 134 " ideal model delta sigma weight residual 108.58 99.99 8.59 1.82e+00 3.02e-01 2.23e+01 angle pdb=" N HIS R 406 " pdb=" CA HIS R 406 " pdb=" C HIS R 406 " ideal model delta sigma weight residual 108.02 116.30 -8.28 1.78e+00 3.16e-01 2.16e+01 angle pdb=" N CYS R 445 " pdb=" CA CYS R 445 " pdb=" C CYS R 445 " ideal model delta sigma weight residual 110.80 101.30 9.50 2.13e+00 2.20e-01 1.99e+01 ... (remaining 12422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 5048 16.82 - 33.65: 340 33.65 - 50.47: 54 50.47 - 67.29: 9 67.29 - 84.12: 6 Dihedral angle restraints: 5457 sinusoidal: 2162 harmonic: 3295 Sorted by residual: dihedral pdb=" C SER C 136 " pdb=" N SER C 136 " pdb=" CA SER C 136 " pdb=" CB SER C 136 " ideal model delta harmonic sigma weight residual -122.60 -110.84 -11.76 0 2.50e+00 1.60e-01 2.21e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ARG R 134 " pdb=" C ARG R 134 " pdb=" N TYR R 135 " pdb=" CA TYR R 135 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1233 0.085 - 0.169: 142 0.169 - 0.254: 14 0.254 - 0.339: 2 0.339 - 0.423: 2 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA SER C 136 " pdb=" N SER C 136 " pdb=" C SER C 136 " pdb=" CB SER C 136 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA SER B 67 " pdb=" N SER B 67 " pdb=" C SER B 67 " pdb=" CB SER B 67 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA ARG R 218 " pdb=" N ARG R 218 " pdb=" C ARG R 218 " pdb=" CB ARG R 218 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1390 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 235 " 0.061 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO C 236 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 435 " -0.029 2.00e-02 2.50e+03 2.46e-02 1.06e+01 pdb=" CG PHE R 435 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE R 435 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 435 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE R 435 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 435 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE R 435 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " -0.025 2.00e-02 2.50e+03 2.02e-02 7.15e+00 pdb=" CG PHE B 234 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " -0.004 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 34 2.51 - 3.11: 7019 3.11 - 3.70: 13399 3.70 - 4.30: 19462 4.30 - 4.90: 32443 Nonbonded interactions: 72357 Sorted by model distance: nonbonded pdb=" SD MET A 203 " pdb=" CE MET A 227 " model vdw 1.910 3.820 nonbonded pdb=" O ILE B 43 " pdb=" NH2 ARG B 304 " model vdw 2.129 2.520 nonbonded pdb=" O ILE R 37 " pdb=" OG1 THR R 41 " model vdw 2.165 2.440 nonbonded pdb=" OG SER B 227 " pdb=" OD1 ASP B 247 " model vdw 2.186 2.440 nonbonded pdb=" OD2 ASP B 212 " pdb=" N GLU B 215 " model vdw 2.297 2.520 ... (remaining 72352 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: 1.510 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: 7.720 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 30.340 Find NCS groups from input model: 0.250 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 9181 Z= 0.509 Angle : 0.951 11.046 12427 Z= 0.557 Chirality : 0.057 0.423 1393 Planarity : 0.006 0.089 1568 Dihedral : 11.969 84.118 3319 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.24), residues: 1115 helix: 0.54 (0.27), residues: 363 sheet: -0.92 (0.32), residues: 252 loop : -1.31 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 216 HIS 0.013 0.002 HIS A 327 PHE 0.057 0.003 PHE R 435 TYR 0.025 0.003 TYR R 138 ARG 0.010 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 ILE cc_start: 0.8031 (mt) cc_final: 0.7708 (mt) REVERT: R 179 LYS cc_start: 0.5155 (pttm) cc_final: 0.4651 (mttp) REVERT: R 436 MET cc_start: 0.7342 (mtp) cc_final: 0.7061 (mmp) REVERT: B 32 GLN cc_start: 0.7585 (tt0) cc_final: 0.7350 (tm-30) REVERT: B 118 ASP cc_start: 0.7398 (p0) cc_final: 0.7161 (p0) REVERT: B 255 LEU cc_start: 0.8060 (mt) cc_final: 0.7798 (mt) REVERT: A 311 LYS cc_start: 0.8097 (tptm) cc_final: 0.7812 (tptm) REVERT: C 80 PHE cc_start: 0.6826 (m-10) cc_final: 0.6553 (m-10) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.2444 time to fit residues: 109.5670 Evaluate side-chains 225 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 0.0470 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9181 Z= 0.193 Angle : 0.644 8.132 12427 Z= 0.331 Chirality : 0.044 0.166 1393 Planarity : 0.005 0.061 1568 Dihedral : 5.316 46.378 1239 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.34 % Allowed : 13.02 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1115 helix: 1.11 (0.27), residues: 366 sheet: -0.54 (0.32), residues: 247 loop : -0.93 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.003 0.001 HIS C 35 PHE 0.020 0.002 PHE R 435 TYR 0.019 0.002 TYR R 50 ARG 0.005 0.001 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 263 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7520 (pmm) cc_final: 0.6163 (mpp) REVERT: R 103 TRP cc_start: 0.8031 (t60) cc_final: 0.7606 (t60) REVERT: R 179 LYS cc_start: 0.5111 (pttm) cc_final: 0.4680 (mttp) REVERT: R 436 MET cc_start: 0.7609 (mtp) cc_final: 0.7239 (mmp) REVERT: R 481 ARG cc_start: 0.8115 (mtt90) cc_final: 0.7464 (tpt170) REVERT: B 20 ASP cc_start: 0.8030 (m-30) cc_final: 0.7819 (m-30) REVERT: B 118 ASP cc_start: 0.7171 (p0) cc_final: 0.6954 (p0) REVERT: G 19 LEU cc_start: 0.9274 (mp) cc_final: 0.9032 (mp) REVERT: G 28 ILE cc_start: 0.8315 (tp) cc_final: 0.8067 (tt) REVERT: G 29 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8194 (mptt) REVERT: A 287 HIS cc_start: 0.7299 (m90) cc_final: 0.7041 (m-70) REVERT: A 350 GLN cc_start: 0.7903 (tp40) cc_final: 0.7234 (mm110) REVERT: C 113 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7972 (tm-30) outliers start: 23 outliers final: 16 residues processed: 276 average time/residue: 0.2214 time to fit residues: 82.3077 Evaluate side-chains 235 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 450 HIS Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR 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: 0.0670 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 0.0270 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 GLN C 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9181 Z= 0.188 Angle : 0.626 9.896 12427 Z= 0.322 Chirality : 0.043 0.148 1393 Planarity : 0.004 0.065 1568 Dihedral : 4.943 44.515 1239 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.66 % Allowed : 15.46 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1115 helix: 1.22 (0.27), residues: 361 sheet: -0.44 (0.32), residues: 252 loop : -0.69 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 297 HIS 0.003 0.001 HIS C 35 PHE 0.020 0.002 PHE R 435 TYR 0.027 0.002 TYR A 295 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7009 (pmm) cc_final: 0.6097 (mpp) REVERT: R 103 TRP cc_start: 0.7988 (t60) cc_final: 0.7545 (t60) REVERT: R 133 LEU cc_start: 0.5083 (mp) cc_final: 0.4708 (tp) REVERT: R 179 LYS cc_start: 0.5117 (pttm) cc_final: 0.4611 (mttp) REVERT: R 481 ARG cc_start: 0.8214 (mtt90) cc_final: 0.7628 (tpt170) REVERT: B 20 ASP cc_start: 0.8009 (m-30) cc_final: 0.7796 (m-30) REVERT: B 32 GLN cc_start: 0.7547 (tm-30) cc_final: 0.7230 (tm-30) REVERT: B 51 LEU cc_start: 0.8659 (mt) cc_final: 0.8454 (mt) REVERT: B 118 ASP cc_start: 0.7174 (p0) cc_final: 0.6933 (p0) REVERT: B 217 MET cc_start: 0.7170 (tmm) cc_final: 0.6705 (tmm) REVERT: G 29 LYS cc_start: 0.8409 (mtmm) cc_final: 0.8120 (mptt) REVERT: A 350 GLN cc_start: 0.7940 (tp40) cc_final: 0.7234 (mm110) REVERT: C 113 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7711 (tm-30) REVERT: C 218 ARG cc_start: 0.7812 (tpp-160) cc_final: 0.7576 (ttm-80) outliers start: 36 outliers final: 23 residues processed: 257 average time/residue: 0.2335 time to fit residues: 81.0490 Evaluate side-chains 230 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 207 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 0.0770 chunk 47 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 GLN B 6 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9181 Z= 0.173 Angle : 0.604 9.607 12427 Z= 0.309 Chirality : 0.043 0.162 1393 Planarity : 0.004 0.059 1568 Dihedral : 4.712 40.166 1239 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.76 % Allowed : 16.58 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1115 helix: 1.35 (0.27), residues: 363 sheet: -0.28 (0.32), residues: 242 loop : -0.72 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 297 HIS 0.003 0.001 HIS C 35 PHE 0.019 0.001 PHE R 435 TYR 0.012 0.001 TYR R 50 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 220 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 MET cc_start: 0.7694 (mmm) cc_final: 0.7433 (mmm) REVERT: R 93 TRP cc_start: 0.6190 (t-100) cc_final: 0.5628 (t-100) REVERT: R 133 LEU cc_start: 0.5078 (mp) cc_final: 0.4521 (tp) REVERT: R 158 TRP cc_start: 0.7800 (OUTLIER) cc_final: 0.6313 (t60) REVERT: R 179 LYS cc_start: 0.5222 (pttm) cc_final: 0.4667 (mttp) REVERT: R 481 ARG cc_start: 0.8087 (mtt90) cc_final: 0.7582 (tpt170) REVERT: B 20 ASP cc_start: 0.7946 (m-30) cc_final: 0.7717 (m-30) REVERT: B 118 ASP cc_start: 0.7170 (p0) cc_final: 0.6942 (p0) REVERT: B 247 ASP cc_start: 0.7792 (m-30) cc_final: 0.7559 (t0) REVERT: A 350 GLN cc_start: 0.7880 (tp40) cc_final: 0.7192 (mm110) REVERT: C 113 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7903 (tp40) REVERT: C 230 MET cc_start: 0.7323 (ttt) cc_final: 0.7000 (ttm) outliers start: 37 outliers final: 29 residues processed: 238 average time/residue: 0.2074 time to fit residues: 68.0600 Evaluate side-chains 235 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 450 HIS Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain R residue 462 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9181 Z= 0.287 Angle : 0.652 9.217 12427 Z= 0.339 Chirality : 0.044 0.141 1393 Planarity : 0.004 0.067 1568 Dihedral : 4.792 36.576 1239 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.88 % Allowed : 15.77 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1115 helix: 1.42 (0.27), residues: 363 sheet: -0.50 (0.32), residues: 248 loop : -0.77 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 297 HIS 0.004 0.001 HIS C 232 PHE 0.031 0.002 PHE R 435 TYR 0.026 0.002 TYR A 295 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 210 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7947 (pmm) cc_final: 0.6453 (mpp) REVERT: R 47 LEU cc_start: 0.8488 (tt) cc_final: 0.8188 (tp) REVERT: R 83 MET cc_start: 0.7861 (mmm) cc_final: 0.7510 (mmm) REVERT: R 158 TRP cc_start: 0.7712 (OUTLIER) cc_final: 0.6227 (t60) REVERT: R 179 LYS cc_start: 0.5323 (pttm) cc_final: 0.4662 (mttp) REVERT: R 426 LEU cc_start: 0.8609 (tt) cc_final: 0.8060 (mt) REVERT: R 481 ARG cc_start: 0.8038 (mtt90) cc_final: 0.7499 (tpt90) REVERT: B 32 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7454 (tm-30) REVERT: B 118 ASP cc_start: 0.7378 (p0) cc_final: 0.7126 (p0) REVERT: G 28 ILE cc_start: 0.8162 (tp) cc_final: 0.7957 (tt) REVERT: A 350 GLN cc_start: 0.7837 (tp40) cc_final: 0.7170 (mm110) REVERT: C 73 ASP cc_start: 0.6577 (t0) cc_final: 0.6273 (t0) REVERT: C 113 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8089 (tp40) outliers start: 48 outliers final: 36 residues processed: 241 average time/residue: 0.2131 time to fit residues: 70.9482 Evaluate side-chains 239 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 202 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9181 Z= 0.201 Angle : 0.620 10.079 12427 Z= 0.321 Chirality : 0.043 0.150 1393 Planarity : 0.004 0.059 1568 Dihedral : 4.632 32.287 1239 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.58 % Allowed : 16.58 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1115 helix: 1.53 (0.27), residues: 362 sheet: -0.50 (0.31), residues: 254 loop : -0.71 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 297 HIS 0.002 0.001 HIS A 287 PHE 0.022 0.002 PHE R 435 TYR 0.013 0.001 TYR A 235 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 221 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7743 (pmm) cc_final: 0.6258 (mpp) REVERT: R 47 LEU cc_start: 0.8420 (tt) cc_final: 0.8174 (tp) REVERT: R 83 MET cc_start: 0.7757 (mmm) cc_final: 0.7341 (mmm) REVERT: R 158 TRP cc_start: 0.7737 (OUTLIER) cc_final: 0.6273 (t60) REVERT: R 179 LYS cc_start: 0.5414 (pttm) cc_final: 0.4152 (mttp) REVERT: R 426 LEU cc_start: 0.8513 (tt) cc_final: 0.8047 (mt) REVERT: R 481 ARG cc_start: 0.7972 (mtt90) cc_final: 0.7507 (tpt90) REVERT: B 32 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7240 (tm-30) REVERT: B 118 ASP cc_start: 0.7327 (p0) cc_final: 0.7067 (p0) REVERT: A 315 ASP cc_start: 0.8318 (m-30) cc_final: 0.7997 (m-30) REVERT: A 350 GLN cc_start: 0.7774 (tp40) cc_final: 0.7131 (mm110) REVERT: C 34 MET cc_start: 0.7526 (mmm) cc_final: 0.7266 (mtt) REVERT: C 113 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7976 (tp40) outliers start: 45 outliers final: 34 residues processed: 245 average time/residue: 0.2110 time to fit residues: 70.9826 Evaluate side-chains 242 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 207 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 429 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 450 HIS Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain R residue 463 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 0.0770 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 416 GLN ** R 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9181 Z= 0.195 Angle : 0.638 11.100 12427 Z= 0.326 Chirality : 0.043 0.246 1393 Planarity : 0.004 0.065 1568 Dihedral : 4.575 27.217 1239 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.07 % Allowed : 18.11 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1115 helix: 1.51 (0.27), residues: 364 sheet: -0.45 (0.31), residues: 253 loop : -0.68 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 297 HIS 0.003 0.001 HIS C 35 PHE 0.019 0.002 PHE B 241 TYR 0.012 0.001 TYR A 235 ARG 0.003 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 215 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7462 (pmm) cc_final: 0.6150 (mpp) REVERT: R 37 ILE cc_start: 0.7994 (mt) cc_final: 0.7703 (mt) REVERT: R 47 LEU cc_start: 0.8423 (tt) cc_final: 0.8185 (tp) REVERT: R 83 MET cc_start: 0.7562 (mmm) cc_final: 0.7243 (mmm) REVERT: R 158 TRP cc_start: 0.7720 (OUTLIER) cc_final: 0.6311 (t60) REVERT: R 179 LYS cc_start: 0.5838 (pttm) cc_final: 0.4994 (mttp) REVERT: R 426 LEU cc_start: 0.8442 (tt) cc_final: 0.8049 (mp) REVERT: R 481 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7326 (tpt90) REVERT: B 32 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7229 (tm-30) REVERT: B 118 ASP cc_start: 0.7318 (p0) cc_final: 0.7031 (p0) REVERT: B 209 LYS cc_start: 0.8663 (mttt) cc_final: 0.8441 (mmmt) REVERT: B 234 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: A 350 GLN cc_start: 0.7717 (tp40) cc_final: 0.7091 (mm110) REVERT: C 113 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7980 (tp40) outliers start: 40 outliers final: 30 residues processed: 236 average time/residue: 0.2181 time to fit residues: 69.9607 Evaluate side-chains 237 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 429 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 450 HIS Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 472 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9181 Z= 0.213 Angle : 0.654 13.254 12427 Z= 0.335 Chirality : 0.043 0.178 1393 Planarity : 0.004 0.064 1568 Dihedral : 4.529 19.969 1239 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.76 % Allowed : 19.02 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1115 helix: 1.50 (0.27), residues: 365 sheet: -0.47 (0.31), residues: 252 loop : -0.71 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 297 HIS 0.003 0.001 HIS A 287 PHE 0.020 0.001 PHE B 241 TYR 0.019 0.001 TYR C 103 ARG 0.008 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 209 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 28 MET cc_start: 0.7256 (pmm) cc_final: 0.6120 (mpp) REVERT: R 37 ILE cc_start: 0.8001 (mt) cc_final: 0.7757 (mt) REVERT: R 47 LEU cc_start: 0.8427 (tt) cc_final: 0.8190 (tp) REVERT: R 93 TRP cc_start: 0.5987 (t-100) cc_final: 0.5393 (t-100) REVERT: R 158 TRP cc_start: 0.7585 (OUTLIER) cc_final: 0.6212 (t60) REVERT: R 179 LYS cc_start: 0.5849 (pttm) cc_final: 0.5108 (mttp) REVERT: R 426 LEU cc_start: 0.8404 (tt) cc_final: 0.8046 (mp) REVERT: R 481 ARG cc_start: 0.7946 (mtt90) cc_final: 0.7350 (tpt90) REVERT: B 32 GLN cc_start: 0.7613 (tm-30) cc_final: 0.7203 (tm-30) REVERT: B 118 ASP cc_start: 0.7357 (p0) cc_final: 0.7148 (p0) REVERT: B 234 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: A 311 LYS cc_start: 0.7997 (tptm) cc_final: 0.7610 (tptt) REVERT: A 315 ASP cc_start: 0.8280 (m-30) cc_final: 0.7889 (m-30) REVERT: A 350 GLN cc_start: 0.7716 (tp40) cc_final: 0.7106 (mm110) REVERT: C 113 GLN cc_start: 0.8243 (tm-30) cc_final: 0.8009 (tp40) REVERT: C 230 MET cc_start: 0.7471 (ttt) cc_final: 0.7207 (ttm) outliers start: 37 outliers final: 32 residues processed: 231 average time/residue: 0.2198 time to fit residues: 69.2917 Evaluate side-chains 236 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 202 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 429 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 450 HIS Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 0.2980 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.0270 chunk 104 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9181 Z= 0.184 Angle : 0.644 12.697 12427 Z= 0.325 Chirality : 0.043 0.209 1393 Planarity : 0.004 0.063 1568 Dihedral : 4.431 19.398 1239 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.95 % Allowed : 19.94 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1115 helix: 1.48 (0.27), residues: 363 sheet: -0.49 (0.32), residues: 241 loop : -0.70 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 297 HIS 0.003 0.000 HIS C 35 PHE 0.017 0.001 PHE B 241 TYR 0.026 0.001 TYR A 295 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 213 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 ILE cc_start: 0.7996 (mt) cc_final: 0.7689 (mt) REVERT: R 47 LEU cc_start: 0.8373 (tt) cc_final: 0.8157 (tp) REVERT: R 93 TRP cc_start: 0.5878 (t-100) cc_final: 0.5550 (t-100) REVERT: R 124 ASP cc_start: 0.8781 (t70) cc_final: 0.8552 (t0) REVERT: R 130 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7735 (tm-30) REVERT: R 158 TRP cc_start: 0.7515 (OUTLIER) cc_final: 0.6261 (t60) REVERT: R 179 LYS cc_start: 0.5846 (pttm) cc_final: 0.5185 (mttp) REVERT: R 426 LEU cc_start: 0.8372 (tt) cc_final: 0.8023 (mp) REVERT: R 481 ARG cc_start: 0.8006 (mtt90) cc_final: 0.7386 (tpt90) REVERT: B 32 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7151 (tm-30) REVERT: B 118 ASP cc_start: 0.7312 (p0) cc_final: 0.7096 (p0) REVERT: B 209 LYS cc_start: 0.8612 (mttt) cc_final: 0.8362 (mmmt) REVERT: B 234 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7811 (m-10) REVERT: A 350 GLN cc_start: 0.7677 (tp40) cc_final: 0.7112 (mm110) REVERT: C 73 ASP cc_start: 0.6295 (t0) cc_final: 0.5998 (t0) REVERT: C 113 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7818 (tp40) outliers start: 29 outliers final: 27 residues processed: 230 average time/residue: 0.2142 time to fit residues: 67.4161 Evaluate side-chains 224 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 429 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 438 ILE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 222 GLU Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9181 Z= 0.341 Angle : 0.729 12.765 12427 Z= 0.371 Chirality : 0.046 0.273 1393 Planarity : 0.005 0.068 1568 Dihedral : 4.770 19.862 1239 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.66 % Allowed : 19.74 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1115 helix: 1.30 (0.27), residues: 365 sheet: -0.86 (0.31), residues: 245 loop : -0.83 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP B 297 HIS 0.005 0.001 HIS C 232 PHE 0.024 0.002 PHE B 241 TYR 0.016 0.002 TYR C 103 ARG 0.006 0.001 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 204 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 37 ILE cc_start: 0.8108 (mt) cc_final: 0.7846 (mt) REVERT: R 93 TRP cc_start: 0.6498 (t-100) cc_final: 0.5763 (t-100) REVERT: R 130 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7719 (tm-30) REVERT: R 158 TRP cc_start: 0.7856 (OUTLIER) cc_final: 0.6474 (t60) REVERT: R 179 LYS cc_start: 0.5983 (pttm) cc_final: 0.5253 (mttp) REVERT: R 426 LEU cc_start: 0.8468 (tt) cc_final: 0.8068 (mp) REVERT: R 481 ARG cc_start: 0.8003 (mtt90) cc_final: 0.7338 (tpt90) REVERT: B 32 GLN cc_start: 0.7665 (tm-30) cc_final: 0.7244 (tm-30) REVERT: B 234 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8300 (m-80) REVERT: A 311 LYS cc_start: 0.8048 (tptm) cc_final: 0.7617 (tptt) REVERT: A 315 ASP cc_start: 0.8273 (m-30) cc_final: 0.7891 (m-30) REVERT: A 350 GLN cc_start: 0.7840 (tp40) cc_final: 0.7168 (mm110) REVERT: C 73 ASP cc_start: 0.6459 (t0) cc_final: 0.6192 (t0) outliers start: 36 outliers final: 31 residues processed: 224 average time/residue: 0.2190 time to fit residues: 66.9125 Evaluate side-chains 234 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 169 MET Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 429 ILE Chi-restraints excluded: chain R residue 435 PHE Chi-restraints excluded: chain R residue 449 LEU Chi-restraints excluded: chain R residue 451 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.0070 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.147714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.111419 restraints weight = 14720.314| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.89 r_work: 0.3373 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9181 Z= 0.206 Angle : 0.676 12.356 12427 Z= 0.342 Chirality : 0.044 0.191 1393 Planarity : 0.004 0.061 1568 Dihedral : 4.550 18.172 1239 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.15 % Allowed : 20.45 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1115 helix: 1.41 (0.27), residues: 363 sheet: -0.74 (0.31), residues: 242 loop : -0.79 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 82 HIS 0.003 0.001 HIS C 35 PHE 0.020 0.002 PHE R 435 TYR 0.016 0.001 TYR C 103 ARG 0.007 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2391.98 seconds wall clock time: 44 minutes 4.77 seconds (2644.77 seconds total)