Starting phenix.real_space_refine on Mon Mar 11 05:41:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8inr_35601/03_2024/8inr_35601.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8inr_35601/03_2024/8inr_35601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8inr_35601/03_2024/8inr_35601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8inr_35601/03_2024/8inr_35601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8inr_35601/03_2024/8inr_35601.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8inr_35601/03_2024/8inr_35601.pdb" } resolution = 2.73 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= 0.064 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 Ca 1 9.91 5 S 62 5.16 5 C 4582 2.51 5 N 1255 2.21 5 O 1319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 53": "OE1" <-> "OE2" Residue "L GLU 5": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7219 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2137 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 5, 'TRANS': 265} Chain breaks: 1 Chain: "L" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 114 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2607 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 410 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.21, per 1000 atoms: 0.58 Number of scatterers: 7219 At special positions: 0 Unit cell: (82.467, 96.39, 126.378, 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) Ca 1 19.99 S 62 16.00 O 1319 8.00 N 1255 7.00 C 4582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 264 " - pdb=" SG CYS R 270 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1732 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 46.6% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'R' and resid 39 through 63 removed outlier: 3.712A pdb=" N PHE R 43 " --> pdb=" O ALA R 39 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU R 46 " --> pdb=" O VAL R 42 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY R 47 " --> pdb=" O PHE R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 100 Processing helix chain 'R' and resid 107 through 146 Processing helix chain 'R' and resid 147 through 153 removed outlier: 3.805A pdb=" N TYR R 150 " --> pdb=" O ALA R 147 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS R 151 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 180 Processing helix chain 'R' and resid 183 through 221 removed outlier: 4.065A pdb=" N ILE R 187 " --> pdb=" O SER R 183 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU R 201 " --> pdb=" O MET R 197 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS R 207 " --> pdb=" O SER R 203 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET R 208 " --> pdb=" O LEU R 204 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR R 214 " --> pdb=" O LEU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 264 removed outlier: 4.067A pdb=" N GLY R 236 " --> pdb=" O THR R 232 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL R 246 " --> pdb=" O MET R 242 " (cutoff:3.500A) Proline residue: R 253 - end of helix Processing helix chain 'R' and resid 267 through 275 Processing helix chain 'R' and resid 276 through 296 removed outlier: 3.748A pdb=" N LEU R 283 " --> pdb=" O MET R 279 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER R 288 " --> pdb=" O ILE R 284 " (cutoff:3.500A) Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 311 Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.712A pdb=" N LYS A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.710A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.615A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.631A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.958A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.526A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 31 through 35' Processing helix chain 'G' and resid 11 through 24 removed outlier: 3.827A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 40 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.859A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.156A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 52 removed outlier: 5.800A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.765A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.599A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.757A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.261A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.267A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.355A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1092 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: 2.06 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2246 1.33 - 1.45: 1253 1.45 - 1.57: 3771 1.57 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 7363 Sorted by residual: bond pdb=" CA GLU R 92 " pdb=" C GLU R 92 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.26e-02 6.30e+03 1.48e+01 bond pdb=" C GLU R 92 " pdb=" N THR R 93 " ideal model delta sigma weight residual 1.335 1.297 0.038 1.31e-02 5.83e+03 8.49e+00 bond pdb=" CB LYS A 53 " pdb=" CG LYS A 53 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.82e+00 bond pdb=" CG1 ILE R 144 " pdb=" CD1 ILE R 144 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.60e+00 bond pdb=" CA GLU L 5 " pdb=" CB GLU L 5 " ideal model delta sigma weight residual 1.533 1.499 0.034 1.65e-02 3.67e+03 4.30e+00 ... (remaining 7358 not shown) Histogram of bond angle deviations from ideal: 98.24 - 105.41: 102 105.41 - 112.58: 3868 112.58 - 119.74: 2452 119.74 - 126.91: 3454 126.91 - 134.08: 84 Bond angle restraints: 9960 Sorted by residual: angle pdb=" N GLU R 92 " pdb=" CA GLU R 92 " pdb=" C GLU R 92 " ideal model delta sigma weight residual 111.14 104.28 6.86 1.08e+00 8.57e-01 4.03e+01 angle pdb=" C GLU L 5 " pdb=" CA GLU L 5 " pdb=" CB GLU L 5 " ideal model delta sigma weight residual 110.62 99.29 11.33 1.86e+00 2.89e-01 3.71e+01 angle pdb=" N ALA B 305 " pdb=" CA ALA B 305 " pdb=" C ALA B 305 " ideal model delta sigma weight residual 114.75 109.39 5.36 1.26e+00 6.30e-01 1.81e+01 angle pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta sigma weight residual 121.80 131.63 -9.83 2.44e+00 1.68e-01 1.62e+01 angle pdb=" N HIS L 6 " pdb=" CA HIS L 6 " pdb=" C HIS L 6 " ideal model delta sigma weight residual 110.64 116.24 -5.60 1.48e+00 4.57e-01 1.43e+01 ... (remaining 9955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 3957 17.26 - 34.53: 360 34.53 - 51.79: 64 51.79 - 69.06: 11 69.06 - 86.32: 6 Dihedral angle restraints: 4398 sinusoidal: 1731 harmonic: 2667 Sorted by residual: dihedral pdb=" C GLU L 5 " pdb=" N GLU L 5 " pdb=" CA GLU L 5 " pdb=" CB GLU L 5 " ideal model delta harmonic sigma weight residual -122.60 -110.14 -12.46 0 2.50e+00 1.60e-01 2.48e+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 180.00 155.65 24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLU A 392 " pdb=" C GLU A 392 " pdb=" N LEU A 393 " pdb=" CA LEU A 393 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 4395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 602 0.040 - 0.081: 350 0.081 - 0.121: 137 0.121 - 0.162: 31 0.162 - 0.202: 12 Chirality restraints: 1132 Sorted by residual: chirality pdb=" CG LEU B 255 " pdb=" CB LEU B 255 " pdb=" CD1 LEU B 255 " pdb=" CD2 LEU B 255 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU R 134 " pdb=" N LEU R 134 " pdb=" C LEU R 134 " pdb=" CB LEU R 134 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" CA PHE B 234 " pdb=" N PHE B 234 " pdb=" C PHE B 234 " pdb=" CB PHE B 234 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.31e-01 ... (remaining 1129 not shown) Planarity restraints: 1260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 222 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.57e+00 pdb=" N PRO R 223 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO R 223 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 223 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU L 5 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C GLU L 5 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU L 5 " 0.014 2.00e-02 2.50e+03 pdb=" N HIS L 6 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 194 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.027 5.00e-02 4.00e+02 ... (remaining 1257 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 338 2.70 - 3.25: 7264 3.25 - 3.80: 12006 3.80 - 4.35: 14793 4.35 - 4.90: 25596 Nonbonded interactions: 59997 Sorted by model distance: nonbonded pdb=" O PHE L 7 " pdb="CA CA R 501 " model vdw 2.153 2.510 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.168 2.440 nonbonded pdb=" ND2 ASN B 237 " pdb=" OD1 ASP G 36 " model vdw 2.177 2.520 nonbonded pdb=" O TYR R 97 " pdb=" ND2 ASN R 101 " model vdw 2.198 2.520 nonbonded pdb=" O ASP B 228 " pdb=" OG SER B 245 " model vdw 2.277 2.440 ... (remaining 59992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.360 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:14.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 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 : 0.012 0.084 7363 Z= 0.750 Angle : 0.883 11.334 9960 Z= 0.502 Chirality : 0.058 0.202 1132 Planarity : 0.005 0.053 1260 Dihedral : 13.812 86.324 2663 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.27), residues: 898 helix: 0.26 (0.25), residues: 396 sheet: -1.48 (0.36), residues: 181 loop : -1.61 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 63 HIS 0.015 0.003 HIS B 91 PHE 0.031 0.003 PHE B 151 TYR 0.031 0.002 TYR B 105 ARG 0.013 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: R 152 HIS cc_start: 0.7071 (m170) cc_final: 0.6828 (m-70) REVERT: R 153 ILE cc_start: 0.7774 (mt) cc_final: 0.7429 (mt) REVERT: R 279 MET cc_start: 0.6807 (mmm) cc_final: 0.6517 (mmm) REVERT: R 302 MET cc_start: 0.7347 (ttm) cc_final: 0.7086 (ttt) REVERT: A 216 LYS cc_start: 0.7497 (mtmm) cc_final: 0.7206 (mtpp) REVERT: A 271 ASN cc_start: 0.7191 (m110) cc_final: 0.6973 (m-40) REVERT: A 335 THR cc_start: 0.7705 (t) cc_final: 0.7458 (m) REVERT: A 347 ARG cc_start: 0.6586 (ttm-80) cc_final: 0.6091 (ttm-80) REVERT: A 373 ARG cc_start: 0.7637 (tpp-160) cc_final: 0.7075 (tpp-160) REVERT: A 378 ASP cc_start: 0.7121 (m-30) cc_final: 0.6907 (m-30) REVERT: A 390 GLN cc_start: 0.7416 (pt0) cc_final: 0.7206 (pt0) REVERT: B 43 ILE cc_start: 0.7343 (mp) cc_final: 0.7122 (mm) REVERT: B 188 MET cc_start: 0.7984 (mmm) cc_final: 0.7298 (mmm) REVERT: B 239 ASN cc_start: 0.7596 (m-40) cc_final: 0.7371 (m-40) REVERT: B 298 ASP cc_start: 0.7463 (m-30) cc_final: 0.7230 (m-30) REVERT: B 314 ARG cc_start: 0.7121 (ttp-170) cc_final: 0.6813 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 1.3592 time to fit residues: 208.7627 Evaluate side-chains 92 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 HIS A 31 GLN A 213 GLN A 236 GLN A 279 ASN A 292 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7363 Z= 0.207 Angle : 0.562 7.018 9960 Z= 0.305 Chirality : 0.043 0.174 1132 Planarity : 0.004 0.042 1260 Dihedral : 5.197 64.105 994 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.66 % Allowed : 10.41 % Favored : 86.93 % 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: -0.19 (0.28), residues: 898 helix: 1.42 (0.26), residues: 386 sheet: -1.07 (0.38), residues: 175 loop : -1.39 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 167 HIS 0.008 0.002 HIS A 220 PHE 0.019 0.002 PHE A 222 TYR 0.017 0.001 TYR R 72 ARG 0.005 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.746 Fit side-chains REVERT: R 234 MET cc_start: 0.5556 (tpp) cc_final: 0.5136 (tpt) REVERT: R 279 MET cc_start: 0.6653 (mmm) cc_final: 0.6332 (mmm) REVERT: R 285 MET cc_start: 0.6751 (mtp) cc_final: 0.6548 (mtp) REVERT: A 347 ARG cc_start: 0.6780 (ttm-80) cc_final: 0.6225 (ttm-80) REVERT: A 373 ARG cc_start: 0.7911 (tpp-160) cc_final: 0.7548 (tpp-160) REVERT: A 378 ASP cc_start: 0.7372 (m-30) cc_final: 0.7164 (m-30) REVERT: B 59 TYR cc_start: 0.7063 (OUTLIER) cc_final: 0.6331 (m-80) REVERT: B 221 THR cc_start: 0.7462 (m) cc_final: 0.7200 (m) REVERT: B 239 ASN cc_start: 0.7326 (m-40) cc_final: 0.7088 (m-40) REVERT: G 38 MET cc_start: 0.5604 (OUTLIER) cc_final: 0.4975 (tmm) REVERT: G 47 GLU cc_start: 0.6634 (tt0) cc_final: 0.6256 (tt0) outliers start: 21 outliers final: 7 residues processed: 118 average time/residue: 1.1895 time to fit residues: 148.7652 Evaluate side-chains 97 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 HIS A 213 GLN A 236 GLN A 267 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7363 Z= 0.208 Angle : 0.520 6.551 9960 Z= 0.284 Chirality : 0.042 0.152 1132 Planarity : 0.004 0.041 1260 Dihedral : 4.918 65.237 994 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.81 % Allowed : 12.82 % Favored : 83.38 % 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: 0.16 (0.28), residues: 898 helix: 1.82 (0.27), residues: 388 sheet: -1.06 (0.37), residues: 179 loop : -1.27 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 91 HIS 0.005 0.001 HIS B 62 PHE 0.018 0.002 PHE A 222 TYR 0.011 0.001 TYR R 72 ARG 0.002 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: R 234 MET cc_start: 0.5589 (tpp) cc_final: 0.5128 (tpt) REVERT: R 274 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7163 (mtp) REVERT: R 279 MET cc_start: 0.6734 (mmm) cc_final: 0.6388 (mmm) REVERT: R 285 MET cc_start: 0.6818 (mtp) cc_final: 0.6611 (mtp) REVERT: R 297 PHE cc_start: 0.6772 (m-80) cc_final: 0.5844 (t80) REVERT: A 216 LYS cc_start: 0.7795 (mtmm) cc_final: 0.7428 (mttm) REVERT: A 373 ARG cc_start: 0.7830 (tpp-160) cc_final: 0.7422 (tpp-160) REVERT: A 378 ASP cc_start: 0.7487 (m-30) cc_final: 0.7267 (m-30) REVERT: B 59 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.6459 (m-80) REVERT: B 195 ASP cc_start: 0.7314 (p0) cc_final: 0.6958 (p0) REVERT: B 239 ASN cc_start: 0.7470 (m-40) cc_final: 0.7186 (m-40) REVERT: G 38 MET cc_start: 0.5794 (OUTLIER) cc_final: 0.5289 (tmm) outliers start: 30 outliers final: 9 residues processed: 111 average time/residue: 1.0099 time to fit residues: 119.8772 Evaluate side-chains 99 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.4980 chunk 42 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 HIS ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 267 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7363 Z= 0.264 Angle : 0.558 6.750 9960 Z= 0.303 Chirality : 0.044 0.141 1132 Planarity : 0.004 0.042 1260 Dihedral : 5.037 66.796 994 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.81 % Allowed : 15.36 % Favored : 80.84 % 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: 0.19 (0.28), residues: 898 helix: 1.76 (0.27), residues: 388 sheet: -1.01 (0.38), residues: 180 loop : -1.17 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 91 HIS 0.013 0.002 HIS A 220 PHE 0.017 0.002 PHE B 151 TYR 0.011 0.002 TYR R 295 ARG 0.003 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: R 43 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.5442 (t80) REVERT: R 217 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6496 (mtmp) REVERT: R 279 MET cc_start: 0.6688 (mmm) cc_final: 0.6396 (mmm) REVERT: R 285 MET cc_start: 0.6915 (mtp) cc_final: 0.6663 (mtp) REVERT: R 297 PHE cc_start: 0.6816 (m-80) cc_final: 0.5868 (t80) REVERT: A 373 ARG cc_start: 0.7826 (tpp-160) cc_final: 0.7424 (tpp-160) REVERT: B 59 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6507 (m-80) REVERT: B 124 TYR cc_start: 0.8471 (m-80) cc_final: 0.8095 (m-80) REVERT: B 195 ASP cc_start: 0.7386 (p0) cc_final: 0.7024 (p0) REVERT: G 47 GLU cc_start: 0.6466 (tt0) cc_final: 0.6196 (tt0) outliers start: 30 outliers final: 13 residues processed: 109 average time/residue: 1.0759 time to fit residues: 124.8022 Evaluate side-chains 102 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 334 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 215 HIS L 6 HIS ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS A 267 GLN A 390 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7363 Z= 0.214 Angle : 0.507 5.893 9960 Z= 0.278 Chirality : 0.042 0.141 1132 Planarity : 0.004 0.042 1260 Dihedral : 4.868 68.407 994 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.81 % Allowed : 16.37 % Favored : 79.82 % 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: 0.37 (0.29), residues: 898 helix: 1.96 (0.27), residues: 390 sheet: -0.97 (0.37), residues: 181 loop : -1.12 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS B 91 PHE 0.021 0.002 PHE R 169 TYR 0.010 0.001 TYR B 289 ARG 0.002 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 89 time to evaluate : 0.794 Fit side-chains REVERT: R 43 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.5348 (t80) REVERT: R 65 LYS cc_start: 0.7863 (mptt) cc_final: 0.7500 (mptt) REVERT: R 279 MET cc_start: 0.6696 (mmm) cc_final: 0.6427 (mmm) REVERT: R 285 MET cc_start: 0.6926 (mtp) cc_final: 0.6680 (mtp) REVERT: R 297 PHE cc_start: 0.6861 (m-80) cc_final: 0.5898 (t80) REVERT: L 11 LYS cc_start: 0.5943 (mppt) cc_final: 0.5589 (mmmt) REVERT: A 29 GLN cc_start: 0.7156 (mm-40) cc_final: 0.6393 (tp-100) REVERT: A 221 MET cc_start: 0.8604 (ttm) cc_final: 0.8362 (ttp) REVERT: A 356 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6953 (mmp80) REVERT: A 373 ARG cc_start: 0.7834 (tpp-160) cc_final: 0.7452 (tpp-160) REVERT: B 59 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6424 (m-80) REVERT: B 124 TYR cc_start: 0.8425 (m-80) cc_final: 0.8081 (m-80) REVERT: B 219 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6711 (mmm-85) outliers start: 30 outliers final: 16 residues processed: 106 average time/residue: 1.0617 time to fit residues: 119.7644 Evaluate side-chains 108 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 334 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 40 optimal weight: 0.0870 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 HIS ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 390 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7363 Z= 0.257 Angle : 0.533 6.592 9960 Z= 0.292 Chirality : 0.043 0.140 1132 Planarity : 0.004 0.043 1260 Dihedral : 4.937 67.932 994 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.81 % Allowed : 16.88 % Favored : 79.31 % 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: 0.35 (0.28), residues: 898 helix: 1.90 (0.26), residues: 390 sheet: -0.98 (0.37), residues: 180 loop : -1.05 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.005 0.001 HIS B 62 PHE 0.017 0.002 PHE B 151 TYR 0.010 0.002 TYR R 295 ARG 0.002 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 0.842 Fit side-chains REVERT: R 43 PHE cc_start: 0.6956 (OUTLIER) cc_final: 0.5399 (t80) REVERT: R 65 LYS cc_start: 0.7893 (mptt) cc_final: 0.7542 (mptt) REVERT: R 152 HIS cc_start: 0.7203 (OUTLIER) cc_final: 0.6922 (m90) REVERT: R 217 LYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6445 (mtmp) REVERT: R 279 MET cc_start: 0.6785 (mmm) cc_final: 0.6487 (mmm) REVERT: R 285 MET cc_start: 0.6910 (mtp) cc_final: 0.6667 (mtp) REVERT: R 297 PHE cc_start: 0.6841 (m-80) cc_final: 0.5933 (t80) REVERT: L 11 LYS cc_start: 0.6075 (mppt) cc_final: 0.5719 (mmmt) REVERT: A 356 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7017 (mmp80) REVERT: A 373 ARG cc_start: 0.7854 (tpp-160) cc_final: 0.7469 (tpp-160) REVERT: B 124 TYR cc_start: 0.8486 (m-80) cc_final: 0.8116 (m-80) REVERT: B 219 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6712 (mmm-85) outliers start: 30 outliers final: 16 residues processed: 109 average time/residue: 1.0911 time to fit residues: 126.4699 Evaluate side-chains 108 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 HIS ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 16 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7363 Z= 0.214 Angle : 0.503 6.581 9960 Z= 0.277 Chirality : 0.042 0.140 1132 Planarity : 0.004 0.042 1260 Dihedral : 4.816 69.194 994 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.31 % Allowed : 16.62 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.29), residues: 898 helix: 2.05 (0.26), residues: 390 sheet: -0.91 (0.38), residues: 179 loop : -1.03 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS B 91 PHE 0.015 0.002 PHE B 151 TYR 0.012 0.001 TYR R 72 ARG 0.002 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 92 time to evaluate : 0.812 Fit side-chains REVERT: R 43 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.5308 (t80) REVERT: R 65 LYS cc_start: 0.7881 (mptt) cc_final: 0.7531 (mptt) REVERT: R 217 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6418 (mtmp) REVERT: R 279 MET cc_start: 0.6729 (mmm) cc_final: 0.6416 (mmm) REVERT: R 285 MET cc_start: 0.6920 (mtp) cc_final: 0.6675 (mtp) REVERT: R 297 PHE cc_start: 0.6790 (m-80) cc_final: 0.5914 (t80) REVERT: L 11 LYS cc_start: 0.5936 (OUTLIER) cc_final: 0.5651 (mmmt) REVERT: A 29 GLN cc_start: 0.7161 (mm-40) cc_final: 0.6309 (tp-100) REVERT: A 323 ASP cc_start: 0.6857 (p0) cc_final: 0.6593 (p0) REVERT: A 356 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6930 (mmp80) REVERT: A 373 ARG cc_start: 0.7840 (tpp-160) cc_final: 0.7482 (tpp-160) REVERT: B 124 TYR cc_start: 0.8440 (m-80) cc_final: 0.8103 (m-80) REVERT: B 219 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6689 (mmm-85) outliers start: 34 outliers final: 18 residues processed: 112 average time/residue: 1.0331 time to fit residues: 123.2436 Evaluate side-chains 112 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 HIS ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7363 Z= 0.198 Angle : 0.509 8.010 9960 Z= 0.276 Chirality : 0.042 0.153 1132 Planarity : 0.004 0.042 1260 Dihedral : 4.797 69.656 994 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.55 % Allowed : 17.39 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.29), residues: 898 helix: 2.15 (0.26), residues: 390 sheet: -0.86 (0.37), residues: 179 loop : -0.96 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS B 91 PHE 0.014 0.002 PHE B 151 TYR 0.012 0.001 TYR R 72 ARG 0.002 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 86 time to evaluate : 0.808 Fit side-chains REVERT: R 43 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.5249 (t80) REVERT: R 65 LYS cc_start: 0.7868 (mptt) cc_final: 0.7538 (mptt) REVERT: R 234 MET cc_start: 0.5664 (tpp) cc_final: 0.5206 (tpt) REVERT: R 279 MET cc_start: 0.6724 (mmm) cc_final: 0.6434 (mmm) REVERT: R 285 MET cc_start: 0.6912 (mtp) cc_final: 0.6673 (mtp) REVERT: R 297 PHE cc_start: 0.6802 (m-80) cc_final: 0.5928 (t80) REVERT: L 11 LYS cc_start: 0.5909 (OUTLIER) cc_final: 0.5665 (mmmt) REVERT: A 323 ASP cc_start: 0.6905 (p0) cc_final: 0.6614 (p0) REVERT: A 373 ARG cc_start: 0.7825 (tpp-160) cc_final: 0.7440 (tpp-160) REVERT: B 124 TYR cc_start: 0.8425 (m-80) cc_final: 0.8047 (m-80) REVERT: B 219 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6708 (mmm-85) outliers start: 28 outliers final: 16 residues processed: 102 average time/residue: 1.1045 time to fit residues: 119.8834 Evaluate side-chains 106 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 HIS ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7363 Z= 0.266 Angle : 0.543 8.115 9960 Z= 0.297 Chirality : 0.043 0.159 1132 Planarity : 0.004 0.042 1260 Dihedral : 4.898 67.733 994 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.55 % Allowed : 18.02 % Favored : 78.43 % 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: 0.50 (0.28), residues: 898 helix: 2.04 (0.26), residues: 389 sheet: -0.92 (0.37), residues: 180 loop : -0.98 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.023 0.002 PHE R 169 TYR 0.016 0.002 TYR R 72 ARG 0.002 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 0.808 Fit side-chains REVERT: R 43 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.5372 (t80) REVERT: R 65 LYS cc_start: 0.7881 (mptt) cc_final: 0.7550 (mptt) REVERT: R 152 HIS cc_start: 0.7202 (OUTLIER) cc_final: 0.6891 (m90) REVERT: R 217 LYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6442 (mtmp) REVERT: R 279 MET cc_start: 0.6781 (mmm) cc_final: 0.6506 (mmm) REVERT: R 285 MET cc_start: 0.6955 (mtp) cc_final: 0.6710 (mtp) REVERT: R 297 PHE cc_start: 0.6872 (m-80) cc_final: 0.5966 (t80) REVERT: L 11 LYS cc_start: 0.6000 (OUTLIER) cc_final: 0.5726 (mmmt) REVERT: A 29 GLN cc_start: 0.7164 (mm-40) cc_final: 0.6299 (tp-100) REVERT: A 323 ASP cc_start: 0.6955 (p0) cc_final: 0.6662 (p0) REVERT: A 373 ARG cc_start: 0.7831 (tpp-160) cc_final: 0.7482 (tpp-160) REVERT: B 123 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7757 (mp) REVERT: B 124 TYR cc_start: 0.8556 (m-80) cc_final: 0.8177 (m-80) REVERT: B 219 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6761 (mmm-85) outliers start: 28 outliers final: 17 residues processed: 108 average time/residue: 1.1345 time to fit residues: 130.0655 Evaluate side-chains 112 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 242 MET Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 HIS ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 390 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7363 Z= 0.220 Angle : 0.518 8.637 9960 Z= 0.283 Chirality : 0.042 0.173 1132 Planarity : 0.004 0.042 1260 Dihedral : 4.844 69.287 994 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.92 % Allowed : 18.91 % Favored : 78.17 % 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: 0.61 (0.29), residues: 898 helix: 2.13 (0.26), residues: 390 sheet: -0.79 (0.38), residues: 176 loop : -0.98 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS B 91 PHE 0.016 0.002 PHE B 151 TYR 0.017 0.001 TYR R 72 ARG 0.003 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 0.804 Fit side-chains REVERT: R 43 PHE cc_start: 0.6882 (OUTLIER) cc_final: 0.5303 (t80) REVERT: R 65 LYS cc_start: 0.7878 (mptt) cc_final: 0.7518 (mptt) REVERT: R 152 HIS cc_start: 0.7174 (OUTLIER) cc_final: 0.6885 (m90) REVERT: R 217 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6412 (mtmp) REVERT: R 279 MET cc_start: 0.6748 (mmm) cc_final: 0.6456 (mmm) REVERT: R 285 MET cc_start: 0.6993 (mtp) cc_final: 0.6784 (mtp) REVERT: R 297 PHE cc_start: 0.6888 (m-80) cc_final: 0.5958 (t80) REVERT: L 11 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5694 (mmmt) REVERT: A 29 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6319 (tp-100) REVERT: A 323 ASP cc_start: 0.6944 (p0) cc_final: 0.6659 (p0) REVERT: A 373 ARG cc_start: 0.7825 (tpp-160) cc_final: 0.7490 (tpp-160) REVERT: B 123 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7751 (mp) REVERT: B 124 TYR cc_start: 0.8443 (m-80) cc_final: 0.8087 (m-80) REVERT: B 219 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6693 (mmm-85) outliers start: 23 outliers final: 16 residues processed: 101 average time/residue: 1.1609 time to fit residues: 124.4523 Evaluate side-chains 108 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 152 HIS Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 HIS ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS A 390 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.205973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.165208 restraints weight = 7333.999| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.56 r_work: 0.3732 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7363 Z= 0.209 Angle : 0.510 9.293 9960 Z= 0.279 Chirality : 0.042 0.180 1132 Planarity : 0.004 0.042 1260 Dihedral : 4.784 69.324 994 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.92 % Allowed : 18.65 % Favored : 78.43 % 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: 0.66 (0.29), residues: 898 helix: 2.18 (0.26), residues: 391 sheet: -0.83 (0.38), residues: 180 loop : -0.93 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS B 91 PHE 0.016 0.002 PHE R 169 TYR 0.017 0.001 TYR R 72 ARG 0.003 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2880.64 seconds wall clock time: 52 minutes 14.12 seconds (3134.12 seconds total)