Starting phenix.real_space_refine on Fri Jul 19 15:09:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxe_40849/07_2024/8sxe_40849.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxe_40849/07_2024/8sxe_40849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxe_40849/07_2024/8sxe_40849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxe_40849/07_2024/8sxe_40849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxe_40849/07_2024/8sxe_40849.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxe_40849/07_2024/8sxe_40849.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.051 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 11 5.16 5 C 5193 2.51 5 N 1457 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8285 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2680 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 19, 'TRANS': 338} Chain breaks: 1 Chain: "B" Number of atoms: 2708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2708 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 20, 'TRANS': 340} Chain breaks: 1 Chain: "C" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1100 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1619 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 10, 'TRANS': 205} Chain breaks: 2 Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 143 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Time building chain proxies: 4.81, per 1000 atoms: 0.58 Number of scatterers: 8285 At special positions: 0 Unit cell: (86.94, 132.894, 144.072, 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 11 16.00 O 1624 8.00 N 1457 7.00 C 5193 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.7 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1996 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 14 sheets defined 42.7% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 42 through 60 Processing helix chain 'A' and resid 65 through 80 removed outlier: 3.547A pdb=" N LEU A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 127 through 133 removed outlier: 4.097A pdb=" N ALA A 132 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 214 through 230 removed outlier: 3.686A pdb=" N ASN A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 259 removed outlier: 3.539A pdb=" N ALA A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 removed outlier: 3.515A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 435 Processing helix chain 'B' and resid 42 through 59 Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.538A pdb=" N GLU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 214 through 230 Processing helix chain 'B' and resid 248 through 259 removed outlier: 3.632A pdb=" N PHE B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 removed outlier: 4.276A pdb=" N GLU B 276 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 314 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 417 through 434 Processing helix chain 'C' and resid 49 through 65 Processing helix chain 'C' and resid 67 through 83 removed outlier: 3.630A pdb=" N ALA C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 99 removed outlier: 3.511A pdb=" N SER C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 118 through 132 removed outlier: 3.621A pdb=" N ALA C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 148 removed outlier: 4.195A pdb=" N GLY C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'E' and resid 214 through 230 removed outlier: 4.284A pdb=" N VAL E 220 " --> pdb=" O GLY E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 260 Processing helix chain 'E' and resid 302 through 315 removed outlier: 3.778A pdb=" N LEU E 311 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 417 Processing helix chain 'E' and resid 417 through 434 Processing helix chain 'F' and resid 419 through 435 removed outlier: 3.521A pdb=" N LEU F 430 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER F 431 " --> pdb=" O LEU F 427 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 removed outlier: 5.502A pdb=" N LYS A 343 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 334 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N THR A 345 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR A 332 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 106 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 114 removed outlier: 6.830A pdb=" N GLU A 110 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 200 removed outlier: 5.523A pdb=" N SER A 196 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG A 207 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL A 198 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR A 205 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 200 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA A 204 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASP A 240 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 206 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 237 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU A 295 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU A 239 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 296 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AA8, first strand: chain 'B' and resid 86 through 88 removed outlier: 4.520A pdb=" N VAL B 266 " --> pdb=" O PHE B 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 86 through 88 removed outlier: 5.675A pdb=" N LYS B 343 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 334 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N THR B 345 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR B 332 " --> pdb=" O THR B 345 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 112 removed outlier: 6.770A pdb=" N GLU B 110 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE B 118 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 110 through 112 removed outlier: 6.770A pdb=" N GLU B 110 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE B 118 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE B 140 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 173 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 142 " --> pdb=" O THR B 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 194 through 200 removed outlier: 5.365A pdb=" N SER B 196 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ARG B 207 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL B 198 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR B 205 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 200 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ALA B 204 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ASP B 240 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 206 " --> pdb=" O ASP B 240 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU B 295 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU B 239 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 198 through 200 removed outlier: 6.566A pdb=" N TYR E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 237 through 239 removed outlier: 6.901A pdb=" N LEU E 237 " --> pdb=" O VAL E 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 391 hydrogen bonds defined for protein. 1101 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: 2.31 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2846 1.34 - 1.46: 1105 1.46 - 1.57: 4421 1.57 - 1.69: 0 1.69 - 1.80: 22 Bond restraints: 8394 Sorted by residual: bond pdb=" CA ILE B 118 " pdb=" CB ILE B 118 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 6.31e-01 bond pdb=" C ARG C 83 " pdb=" N ASP C 84 " ideal model delta sigma weight residual 1.330 1.340 -0.010 1.47e-02 4.63e+03 4.64e-01 bond pdb=" CA ARG C 67 " pdb=" C ARG C 67 " ideal model delta sigma weight residual 1.530 1.522 0.007 1.10e-02 8.26e+03 4.44e-01 bond pdb=" CG PRO B 123 " pdb=" CD PRO B 123 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.25e-01 bond pdb=" CA ARG C 67 " pdb=" CB ARG C 67 " ideal model delta sigma weight residual 1.522 1.530 -0.008 1.32e-02 5.74e+03 3.80e-01 ... (remaining 8389 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.11: 238 107.11 - 113.79: 4719 113.79 - 120.47: 3148 120.47 - 127.15: 3188 127.15 - 133.83: 60 Bond angle restraints: 11353 Sorted by residual: angle pdb=" CA TYR A 349 " pdb=" CB TYR A 349 " pdb=" CG TYR A 349 " ideal model delta sigma weight residual 113.90 117.05 -3.15 1.80e+00 3.09e-01 3.05e+00 angle pdb=" N ALA A 59 " pdb=" CA ALA A 59 " pdb=" C ALA A 59 " ideal model delta sigma weight residual 114.04 112.01 2.03 1.24e+00 6.50e-01 2.67e+00 angle pdb=" CA ARG C 67 " pdb=" C ARG C 67 " pdb=" N PHE C 68 " ideal model delta sigma weight residual 114.76 116.54 -1.78 1.14e+00 7.69e-01 2.43e+00 angle pdb=" CA ARG C 67 " pdb=" C ARG C 67 " pdb=" O ARG C 67 " ideal model delta sigma weight residual 122.64 120.75 1.89 1.25e+00 6.40e-01 2.28e+00 angle pdb=" N ALA A 302 " pdb=" CA ALA A 302 " pdb=" C ALA A 302 " ideal model delta sigma weight residual 111.02 112.77 -1.75 1.22e+00 6.72e-01 2.05e+00 ... (remaining 11348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 4584 17.80 - 35.60: 477 35.60 - 53.40: 67 53.40 - 71.20: 8 71.20 - 89.00: 13 Dihedral angle restraints: 5149 sinusoidal: 2032 harmonic: 3117 Sorted by residual: dihedral pdb=" CA PHE C 48 " pdb=" C PHE C 48 " pdb=" N SER C 49 " pdb=" CA SER C 49 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASP E 323 " pdb=" CB ASP E 323 " pdb=" CG ASP E 323 " pdb=" OD1 ASP E 323 " ideal model delta sinusoidal sigma weight residual -30.00 -88.92 58.92 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CB GLU A 218 " pdb=" CG GLU A 218 " pdb=" CD GLU A 218 " pdb=" OE1 GLU A 218 " ideal model delta sinusoidal sigma weight residual 0.00 87.69 -87.69 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 5146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 822 0.026 - 0.052: 298 0.052 - 0.079: 87 0.079 - 0.105: 70 0.105 - 0.131: 40 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CA VAL B 363 " pdb=" N VAL B 363 " pdb=" C VAL B 363 " pdb=" CB VAL B 363 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE B 318 " pdb=" N ILE B 318 " pdb=" C ILE B 318 " pdb=" CB ILE B 318 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE E 366 " pdb=" N ILE E 366 " pdb=" C ILE E 366 " pdb=" CB ILE E 366 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1314 not shown) Planarity restraints: 1501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 285 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 286 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 286 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 286 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 222 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ALA A 222 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA A 222 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 223 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 166 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO B 167 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " 0.018 5.00e-02 4.00e+02 ... (remaining 1498 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 151 2.65 - 3.21: 8324 3.21 - 3.78: 12562 3.78 - 4.34: 16938 4.34 - 4.90: 28377 Nonbonded interactions: 66352 Sorted by model distance: nonbonded pdb=" OG1 THR E 351 " pdb=" O ARG E 355 " model vdw 2.089 2.440 nonbonded pdb=" O ARG C 83 " pdb=" OG SER C 114 " model vdw 2.123 2.440 nonbonded pdb=" O LEU F 430 " pdb=" OG1 THR F 433 " model vdw 2.163 2.440 nonbonded pdb=" O MET B 160 " pdb=" NH1 ARG B 186 " model vdw 2.209 2.520 nonbonded pdb=" OD1 ASP A 257 " pdb=" N ASP A 282 " model vdw 2.255 2.520 ... (remaining 66347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 38 through 373 or resid 416 through 436)) selection = (chain 'B' and (resid 38 through 373 or resid 416 through 436)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.130 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.002 0.028 8394 Z= 0.132 Angle : 0.468 4.108 11353 Z= 0.240 Chirality : 0.040 0.131 1317 Planarity : 0.003 0.037 1501 Dihedral : 14.582 89.003 3153 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % 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: 0.44 (0.27), residues: 1076 helix: 1.76 (0.26), residues: 432 sheet: -1.22 (0.42), residues: 170 loop : -0.43 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 111 HIS 0.002 0.001 HIS A 84 PHE 0.010 0.001 PHE C 48 TYR 0.014 0.001 TYR A 349 ARG 0.002 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 GLN cc_start: 0.7760 (mt0) cc_final: 0.7426 (mt0) REVERT: B 149 LYS cc_start: 0.8107 (mttp) cc_final: 0.7340 (tptt) REVERT: B 153 MET cc_start: 0.7844 (ttp) cc_final: 0.7588 (ttt) REVERT: B 237 LEU cc_start: 0.8707 (tt) cc_final: 0.8462 (tt) REVERT: B 266 VAL cc_start: 0.8564 (p) cc_final: 0.8350 (p) REVERT: C 134 ARG cc_start: 0.6130 (mpp80) cc_final: 0.5483 (mmm160) REVERT: C 139 MET cc_start: 0.8181 (ttm) cc_final: 0.7835 (ttp) REVERT: E 320 MET cc_start: 0.8513 (ttm) cc_final: 0.8228 (ttm) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2311 time to fit residues: 39.3024 Evaluate side-chains 80 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 0.0170 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 0.0070 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8394 Z= 0.238 Angle : 0.573 7.891 11353 Z= 0.296 Chirality : 0.042 0.140 1317 Planarity : 0.004 0.034 1501 Dihedral : 3.988 18.572 1182 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.82 % Allowed : 11.46 % Favored : 86.72 % 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: 0.49 (0.26), residues: 1076 helix: 1.78 (0.25), residues: 439 sheet: -0.90 (0.44), residues: 158 loop : -0.57 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 111 HIS 0.002 0.000 HIS A 84 PHE 0.011 0.001 PHE C 48 TYR 0.014 0.002 TYR A 349 ARG 0.003 0.000 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LEU cc_start: 0.8589 (tp) cc_final: 0.8367 (tp) REVERT: C 68 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.7095 (t80) REVERT: C 72 LEU cc_start: 0.8498 (tp) cc_final: 0.8209 (tp) REVERT: C 134 ARG cc_start: 0.6244 (mpp80) cc_final: 0.5525 (mmm160) REVERT: C 143 GLU cc_start: 0.7463 (tp30) cc_final: 0.7243 (tp30) outliers start: 16 outliers final: 12 residues processed: 102 average time/residue: 0.1848 time to fit residues: 26.8676 Evaluate side-chains 85 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 305 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 0.1980 chunk 96 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8394 Z= 0.233 Angle : 0.548 6.111 11353 Z= 0.282 Chirality : 0.041 0.147 1317 Planarity : 0.004 0.038 1501 Dihedral : 3.958 19.597 1182 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.27 % Allowed : 14.30 % Favored : 83.43 % 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: 0.42 (0.26), residues: 1076 helix: 1.75 (0.25), residues: 441 sheet: -1.09 (0.43), residues: 155 loop : -0.59 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP C 111 HIS 0.002 0.000 HIS A 84 PHE 0.013 0.001 PHE A 104 TYR 0.015 0.001 TYR A 349 ARG 0.003 0.000 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.8193 (mttp) cc_final: 0.7473 (tptt) REVERT: C 68 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.7017 (t80) REVERT: C 72 LEU cc_start: 0.8507 (tp) cc_final: 0.8261 (tp) REVERT: C 134 ARG cc_start: 0.6233 (mpp80) cc_final: 0.5501 (mmm160) REVERT: C 143 GLU cc_start: 0.7728 (tp30) cc_final: 0.7444 (tp30) outliers start: 20 outliers final: 13 residues processed: 97 average time/residue: 0.2338 time to fit residues: 32.6734 Evaluate side-chains 89 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 433 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 103 optimal weight: 0.0770 chunk 51 optimal weight: 0.2980 chunk 92 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8394 Z= 0.157 Angle : 0.509 6.093 11353 Z= 0.262 Chirality : 0.041 0.141 1317 Planarity : 0.004 0.042 1501 Dihedral : 3.761 18.187 1182 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.16 % Allowed : 15.10 % Favored : 82.75 % 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: 0.59 (0.26), residues: 1076 helix: 1.97 (0.25), residues: 438 sheet: -1.05 (0.42), residues: 161 loop : -0.53 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 111 HIS 0.001 0.000 HIS A 84 PHE 0.009 0.001 PHE E 380 TYR 0.015 0.001 TYR A 349 ARG 0.003 0.000 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LEU cc_start: 0.8534 (tp) cc_final: 0.8300 (tp) REVERT: B 348 LEU cc_start: 0.7639 (pt) cc_final: 0.7418 (pt) REVERT: C 68 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6945 (t80) REVERT: C 72 LEU cc_start: 0.8317 (tp) cc_final: 0.8042 (tp) REVERT: C 134 ARG cc_start: 0.6133 (mpp80) cc_final: 0.5333 (mmm160) REVERT: C 143 GLU cc_start: 0.7816 (tp30) cc_final: 0.7613 (tp30) outliers start: 19 outliers final: 12 residues processed: 99 average time/residue: 0.1988 time to fit residues: 27.9707 Evaluate side-chains 88 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 430 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 92 optimal weight: 0.0050 chunk 26 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8394 Z= 0.211 Angle : 0.540 9.321 11353 Z= 0.274 Chirality : 0.041 0.139 1317 Planarity : 0.004 0.044 1501 Dihedral : 3.802 17.985 1182 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.61 % Allowed : 15.89 % Favored : 81.50 % 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: 0.62 (0.26), residues: 1076 helix: 2.01 (0.25), residues: 434 sheet: -1.14 (0.41), residues: 164 loop : -0.47 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 111 HIS 0.002 0.000 HIS A 84 PHE 0.007 0.001 PHE C 156 TYR 0.016 0.001 TYR A 349 ARG 0.003 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 LEU cc_start: 0.8568 (tp) cc_final: 0.8345 (tp) REVERT: B 340 ARG cc_start: 0.7689 (mpp-170) cc_final: 0.7314 (mtt90) REVERT: C 68 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7163 (t80) REVERT: C 72 LEU cc_start: 0.8410 (tp) cc_final: 0.8150 (tp) REVERT: C 134 ARG cc_start: 0.6193 (mpp80) cc_final: 0.5350 (mmm160) REVERT: C 143 GLU cc_start: 0.7847 (tp30) cc_final: 0.7640 (tp30) outliers start: 23 outliers final: 17 residues processed: 98 average time/residue: 0.2050 time to fit residues: 28.3092 Evaluate side-chains 91 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 433 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 25 optimal weight: 0.0870 chunk 103 optimal weight: 0.0010 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8394 Z= 0.175 Angle : 0.515 8.287 11353 Z= 0.261 Chirality : 0.041 0.140 1317 Planarity : 0.004 0.044 1501 Dihedral : 3.703 17.647 1182 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.38 % Allowed : 17.14 % Favored : 80.48 % 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: 0.63 (0.26), residues: 1076 helix: 2.06 (0.25), residues: 439 sheet: -1.11 (0.42), residues: 159 loop : -0.56 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 111 HIS 0.001 0.000 HIS A 84 PHE 0.009 0.001 PHE E 380 TYR 0.015 0.001 TYR A 349 ARG 0.003 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 LEU cc_start: 0.8529 (tp) cc_final: 0.8327 (tp) REVERT: B 110 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: B 305 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7562 (mt-10) REVERT: C 68 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7056 (t80) REVERT: C 72 LEU cc_start: 0.8414 (tp) cc_final: 0.8144 (tp) REVERT: C 134 ARG cc_start: 0.6046 (mpp80) cc_final: 0.5288 (mmm160) REVERT: E 380 PHE cc_start: 0.6359 (p90) cc_final: 0.6060 (p90) outliers start: 21 outliers final: 13 residues processed: 99 average time/residue: 0.1967 time to fit residues: 27.5216 Evaluate side-chains 89 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 430 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8394 Z= 0.238 Angle : 0.544 7.637 11353 Z= 0.277 Chirality : 0.041 0.132 1317 Planarity : 0.004 0.046 1501 Dihedral : 3.837 17.460 1182 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.72 % Allowed : 18.16 % Favored : 79.11 % 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: 0.53 (0.26), residues: 1076 helix: 1.93 (0.25), residues: 441 sheet: -1.17 (0.43), residues: 155 loop : -0.57 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP C 111 HIS 0.002 0.001 HIS A 84 PHE 0.009 0.001 PHE C 48 TYR 0.015 0.001 TYR A 349 ARG 0.002 0.000 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6887 (mt-10) REVERT: B 110 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: B 149 LYS cc_start: 0.8289 (mptt) cc_final: 0.8072 (mptt) REVERT: B 305 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7539 (mt-10) REVERT: C 68 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.7239 (t80) REVERT: C 72 LEU cc_start: 0.8435 (tp) cc_final: 0.8213 (tp) REVERT: C 134 ARG cc_start: 0.6205 (mpp80) cc_final: 0.5320 (mmm160) outliers start: 24 outliers final: 17 residues processed: 96 average time/residue: 0.1837 time to fit residues: 25.5384 Evaluate side-chains 94 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 320 MET Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 433 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.0870 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 0.0470 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8394 Z= 0.162 Angle : 0.511 6.762 11353 Z= 0.261 Chirality : 0.040 0.130 1317 Planarity : 0.004 0.045 1501 Dihedral : 3.663 17.523 1182 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.59 % Allowed : 19.07 % Favored : 79.34 % 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 (0.26), residues: 1076 helix: 2.12 (0.25), residues: 434 sheet: -1.23 (0.41), residues: 164 loop : -0.48 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP C 111 HIS 0.002 0.000 HIS A 84 PHE 0.011 0.001 PHE E 380 TYR 0.014 0.001 TYR A 349 ARG 0.002 0.000 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 VAL cc_start: 0.8428 (p) cc_final: 0.8184 (m) REVERT: B 71 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6871 (mt-10) REVERT: B 110 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: B 305 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7563 (mt-10) REVERT: C 68 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7017 (t80) REVERT: C 72 LEU cc_start: 0.8421 (tp) cc_final: 0.8149 (tp) REVERT: C 134 ARG cc_start: 0.5962 (mpp80) cc_final: 0.5115 (mmm160) outliers start: 14 outliers final: 12 residues processed: 92 average time/residue: 0.1893 time to fit residues: 24.7764 Evaluate side-chains 93 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 430 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8394 Z= 0.229 Angle : 0.541 6.596 11353 Z= 0.274 Chirality : 0.041 0.131 1317 Planarity : 0.004 0.048 1501 Dihedral : 3.766 17.264 1182 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.04 % Allowed : 19.52 % 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: 0.57 (0.26), residues: 1076 helix: 1.99 (0.25), residues: 439 sheet: -1.12 (0.43), residues: 155 loop : -0.58 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP C 111 HIS 0.002 0.000 HIS A 84 PHE 0.012 0.001 PHE E 380 TYR 0.015 0.001 TYR A 349 ARG 0.002 0.000 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6927 (mt-10) REVERT: B 110 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: B 149 LYS cc_start: 0.8215 (mptt) cc_final: 0.7825 (mmtm) REVERT: B 305 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7550 (mt-10) REVERT: C 68 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7228 (t80) REVERT: C 72 LEU cc_start: 0.8455 (tp) cc_final: 0.8217 (tp) REVERT: C 134 ARG cc_start: 0.6101 (mpp80) cc_final: 0.5265 (mmm160) REVERT: F 428 LYS cc_start: 0.6185 (mmmt) cc_final: 0.5342 (mptt) outliers start: 18 outliers final: 16 residues processed: 97 average time/residue: 0.1969 time to fit residues: 27.0921 Evaluate side-chains 99 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 433 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 0.0570 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.0050 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 overall best weight: 0.5512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8394 Z= 0.208 Angle : 0.543 8.992 11353 Z= 0.274 Chirality : 0.041 0.131 1317 Planarity : 0.004 0.050 1501 Dihedral : 3.736 17.196 1182 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.16 % Allowed : 19.52 % Favored : 78.32 % 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: 0.62 (0.26), residues: 1076 helix: 1.96 (0.25), residues: 440 sheet: -1.05 (0.45), residues: 143 loop : -0.53 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP C 111 HIS 0.002 0.000 HIS A 84 PHE 0.014 0.001 PHE E 380 TYR 0.015 0.001 TYR A 349 ARG 0.002 0.000 ARG E 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6904 (mt-10) REVERT: B 110 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: B 149 LYS cc_start: 0.8109 (mptt) cc_final: 0.7732 (mmtm) REVERT: B 305 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7533 (mt-10) REVERT: C 68 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7137 (t80) REVERT: C 72 LEU cc_start: 0.8420 (tp) cc_final: 0.8155 (tp) REVERT: C 134 ARG cc_start: 0.5958 (mpp80) cc_final: 0.5016 (mmm160) REVERT: F 428 LYS cc_start: 0.6054 (mmmt) cc_final: 0.5252 (mptt) outliers start: 19 outliers final: 16 residues processed: 95 average time/residue: 0.1962 time to fit residues: 26.5403 Evaluate side-chains 97 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 433 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.168156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.139187 restraints weight = 13859.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.142091 restraints weight = 10882.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.142877 restraints weight = 7847.317| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8394 Z= 0.238 Angle : 0.556 8.796 11353 Z= 0.281 Chirality : 0.041 0.133 1317 Planarity : 0.004 0.052 1501 Dihedral : 3.811 17.235 1182 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.27 % Allowed : 19.64 % Favored : 78.09 % 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: 0.57 (0.26), residues: 1076 helix: 1.92 (0.25), residues: 440 sheet: -1.14 (0.44), residues: 148 loop : -0.52 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.004 TRP C 111 HIS 0.002 0.000 HIS A 84 PHE 0.014 0.001 PHE E 380 TYR 0.016 0.001 TYR A 349 ARG 0.003 0.000 ARG C 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1799.83 seconds wall clock time: 33 minutes 2.70 seconds (1982.70 seconds total)