Starting phenix.real_space_refine on Fri Nov 15 04:52:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxe_40849/11_2024/8sxe_40849.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxe_40849/11_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_40849/11_2024/8sxe_40849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxe_40849/11_2024/8sxe_40849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxe_40849/11_2024/8sxe_40849.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxe_40849/11_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. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 5.41, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 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: 2.30 Conformation dependent library (CDL) restraints added in 1.1 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: 0.97 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: 2.35 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: 1.23 - 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: 0.00 - 0.82: 10666 0.82 - 1.64: 542 1.64 - 2.46: 81 2.46 - 3.29: 34 3.29 - 4.11: 30 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 3.040 nonbonded pdb=" O ARG C 83 " pdb=" OG SER C 114 " model vdw 2.123 3.040 nonbonded pdb=" O LEU F 430 " pdb=" OG1 THR F 433 " model vdw 2.163 3.040 nonbonded pdb=" O MET B 160 " pdb=" NH1 ARG B 186 " model vdw 2.209 3.120 nonbonded pdb=" OD1 ASP A 257 " pdb=" N ASP A 282 " model vdw 2.255 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 1.770 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.470 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.910 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.006 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: 0.2407 time to fit residues: 41.0328 Evaluate side-chains 80 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 0.0870 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8394 Z= 0.220 Angle : 0.573 7.703 11353 Z= 0.299 Chirality : 0.043 0.150 1317 Planarity : 0.004 0.043 1501 Dihedral : 3.972 18.286 1182 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.02 % Allowed : 11.12 % Favored : 87.85 % 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: 0.47 (0.26), residues: 1076 helix: 1.84 (0.25), residues: 437 sheet: -1.09 (0.41), residues: 172 loop : -0.55 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 111 HIS 0.002 0.000 HIS A 84 PHE 0.011 0.001 PHE C 48 TYR 0.014 0.001 TYR C 54 ARG 0.005 0.000 ARG B 186 *********************** 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 105 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7472 (ttt) REVERT: B 142 GLN cc_start: 0.7713 (mt0) cc_final: 0.7506 (mt0) REVERT: C 68 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6984 (t80) REVERT: C 72 LEU cc_start: 0.8450 (tp) cc_final: 0.8195 (tp) REVERT: C 113 ARG cc_start: 0.7875 (tpt90) cc_final: 0.7619 (tpt90) REVERT: C 134 ARG cc_start: 0.6234 (mpp80) cc_final: 0.5512 (mmm160) REVERT: C 143 GLU cc_start: 0.7576 (tp30) cc_final: 0.7351 (tp30) outliers start: 9 outliers final: 4 residues processed: 102 average time/residue: 0.2122 time to fit residues: 30.2809 Evaluate side-chains 77 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 196 SER Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 260 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 96 optimal weight: 0.3980 chunk 33 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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** F 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1786 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= 0.237 Angle : 0.560 6.561 11353 Z= 0.291 Chirality : 0.042 0.140 1317 Planarity : 0.004 0.041 1501 Dihedral : 3.990 18.084 1182 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.48 % Allowed : 13.96 % Favored : 84.56 % 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: 0.41 (0.26), residues: 1076 helix: 1.80 (0.25), residues: 440 sheet: -1.28 (0.41), residues: 167 loop : -0.56 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 111 HIS 0.002 0.000 HIS A 84 PHE 0.012 0.001 PHE A 104 TYR 0.015 0.001 TYR A 349 ARG 0.004 0.000 ARG B 186 *********************** 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 95 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.7009 (t80) REVERT: C 72 LEU cc_start: 0.8509 (tp) cc_final: 0.8260 (tp) REVERT: C 113 ARG cc_start: 0.7845 (tpt90) cc_final: 0.7551 (tpt90) REVERT: C 134 ARG cc_start: 0.6228 (mpp80) cc_final: 0.5379 (mmm160) REVERT: C 143 GLU cc_start: 0.7779 (tp30) cc_final: 0.7435 (tp30) outliers start: 13 outliers final: 8 residues processed: 90 average time/residue: 0.2048 time to fit residues: 26.0517 Evaluate side-chains 81 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 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 E residue 219 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 320 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7421 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8394 Z= 0.270 Angle : 0.575 6.652 11353 Z= 0.297 Chirality : 0.043 0.145 1317 Planarity : 0.004 0.045 1501 Dihedral : 4.080 18.494 1182 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.16 % Allowed : 14.98 % Favored : 82.86 % 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 (0.26), residues: 1076 helix: 1.72 (0.25), residues: 440 sheet: -1.18 (0.43), residues: 153 loop : -0.64 (0.27), residues: 483 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 0.009 0.001 PHE C 156 TYR 0.015 0.002 TYR A 349 ARG 0.003 0.000 ARG E 355 *********************** 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 101 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7032 (t80) REVERT: C 72 LEU cc_start: 0.8532 (tp) cc_final: 0.8316 (tp) REVERT: C 84 ASP cc_start: 0.7424 (t0) cc_final: 0.7100 (t0) REVERT: C 113 ARG cc_start: 0.7908 (tpt90) cc_final: 0.7671 (tpt90) REVERT: C 134 ARG cc_start: 0.6245 (mpp80) cc_final: 0.5380 (mmm160) REVERT: C 143 GLU cc_start: 0.7707 (tp30) cc_final: 0.7400 (tp30) outliers start: 19 outliers final: 14 residues processed: 96 average time/residue: 0.1947 time to fit residues: 26.4638 Evaluate side-chains 88 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 B residue 261 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 68 PHE 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 E residue 351 THR Chi-restraints excluded: chain E residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 71 optimal weight: 0.0970 chunk 0 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8394 Z= 0.222 Angle : 0.562 8.617 11353 Z= 0.289 Chirality : 0.042 0.144 1317 Planarity : 0.004 0.048 1501 Dihedral : 3.956 18.324 1182 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.38 % Allowed : 16.23 % Favored : 81.38 % 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: 0.37 (0.26), residues: 1076 helix: 1.82 (0.25), residues: 438 sheet: -1.31 (0.41), residues: 166 loop : -0.61 (0.27), residues: 472 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 108 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7142 (t80) REVERT: C 72 LEU cc_start: 0.8515 (tp) cc_final: 0.8299 (tp) REVERT: C 134 ARG cc_start: 0.6203 (mpp80) cc_final: 0.5430 (mmm160) REVERT: C 143 GLU cc_start: 0.7742 (tp30) cc_final: 0.7505 (tp30) REVERT: E 422 GLN cc_start: 0.8685 (mm110) cc_final: 0.8317 (tp40) outliers start: 21 outliers final: 17 residues processed: 103 average time/residue: 0.1879 time to fit residues: 27.8860 Evaluate side-chains 90 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 41 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 257 ASP Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 68 PHE 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 E residue 351 THR Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 430 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8394 Z= 0.227 Angle : 0.563 8.160 11353 Z= 0.287 Chirality : 0.042 0.147 1317 Planarity : 0.004 0.044 1501 Dihedral : 3.949 17.937 1182 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.95 % Allowed : 17.48 % Favored : 79.57 % 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: 0.38 (0.26), residues: 1076 helix: 1.83 (0.25), residues: 436 sheet: -1.38 (0.42), residues: 160 loop : -0.59 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 111 HIS 0.002 0.000 HIS A 84 PHE 0.010 0.001 PHE E 380 TYR 0.015 0.001 TYR A 349 ARG 0.004 0.000 ARG C 113 *********************** 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 107 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6955 (mt-10) REVERT: B 110 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: B 228 LYS cc_start: 0.6688 (tptp) cc_final: 0.6061 (pttp) REVERT: C 68 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.7145 (t80) REVERT: C 72 LEU cc_start: 0.8513 (tp) cc_final: 0.8283 (tp) REVERT: C 134 ARG cc_start: 0.6174 (mpp80) cc_final: 0.5391 (mmm160) REVERT: C 143 GLU cc_start: 0.7630 (tp30) cc_final: 0.7364 (tp30) REVERT: E 422 GLN cc_start: 0.8682 (mm110) cc_final: 0.8326 (tp40) outliers start: 26 outliers final: 18 residues processed: 101 average time/residue: 0.1922 time to fit residues: 27.6815 Evaluate side-chains 96 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 363 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 41 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 257 ASP Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 68 PHE 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 351 THR Chi-restraints excluded: chain E residue 356 SER 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: 9.9990 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8394 Z= 0.249 Angle : 0.570 7.907 11353 Z= 0.291 Chirality : 0.042 0.145 1317 Planarity : 0.004 0.046 1501 Dihedral : 3.989 17.971 1182 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.06 % Allowed : 17.59 % 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: 0.37 (0.26), residues: 1076 helix: 1.77 (0.25), residues: 440 sheet: -1.31 (0.44), residues: 146 loop : -0.62 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP C 111 HIS 0.002 0.000 HIS A 84 PHE 0.009 0.001 PHE E 380 TYR 0.016 0.001 TYR A 349 ARG 0.006 0.000 ARG C 113 *********************** 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 111 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6870 (mt-10) REVERT: B 110 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: C 68 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.7174 (t80) REVERT: C 72 LEU cc_start: 0.8536 (tp) cc_final: 0.8325 (tp) REVERT: C 134 ARG cc_start: 0.6188 (mpp80) cc_final: 0.5383 (mmm160) REVERT: C 143 GLU cc_start: 0.7685 (tp30) cc_final: 0.7427 (tp30) REVERT: E 422 GLN cc_start: 0.8709 (mm110) cc_final: 0.8350 (tp40) outliers start: 27 outliers final: 16 residues processed: 103 average time/residue: 0.2043 time to fit residues: 29.6279 Evaluate side-chains 95 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 363 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 41 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 B residue 348 LEU Chi-restraints excluded: chain C residue 68 PHE 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 351 THR Chi-restraints excluded: chain F residue 430 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.0570 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.0370 chunk 81 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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: 0.7379 moved from start: 0.2409 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= 0.201 Angle : 0.560 7.739 11353 Z= 0.286 Chirality : 0.042 0.140 1317 Planarity : 0.004 0.048 1501 Dihedral : 3.877 17.894 1182 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.50 % Allowed : 18.50 % Favored : 79.00 % 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: 0.43 (0.26), residues: 1076 helix: 1.85 (0.25), residues: 439 sheet: -1.21 (0.45), residues: 143 loop : -0.65 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 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 0.005 0.000 ARG C 113 *********************** 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 104 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6883 (mt-10) REVERT: B 110 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: B 228 LYS cc_start: 0.6423 (tptt) cc_final: 0.5968 (pttp) REVERT: C 68 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.7084 (t80) REVERT: C 72 LEU cc_start: 0.8486 (tp) cc_final: 0.8250 (tp) REVERT: C 134 ARG cc_start: 0.6193 (mpp80) cc_final: 0.5354 (mmm160) REVERT: C 143 GLU cc_start: 0.7848 (tp30) cc_final: 0.7633 (tp30) REVERT: E 422 GLN cc_start: 0.8685 (mm110) cc_final: 0.8344 (tp40) outliers start: 22 outliers final: 17 residues processed: 97 average time/residue: 0.2065 time to fit residues: 28.4868 Evaluate side-chains 94 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 363 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 41 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 248 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 146 LEU 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 351 THR 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: 0.7980 chunk 96 optimal weight: 0.6980 chunk 98 optimal weight: 0.0670 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 101 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8394 Z= 0.201 Angle : 0.556 7.470 11353 Z= 0.284 Chirality : 0.041 0.140 1317 Planarity : 0.004 0.051 1501 Dihedral : 3.832 17.751 1182 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.50 % Allowed : 18.62 % Favored : 78.89 % 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: 1.97 (0.25), residues: 433 sheet: -1.24 (0.45), residues: 143 loop : -0.58 (0.27), residues: 500 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 0.013 0.001 PHE E 380 TYR 0.014 0.001 TYR A 349 ARG 0.007 0.000 ARG C 113 *********************** 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 102 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6881 (mt-10) REVERT: B 110 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: B 228 LYS cc_start: 0.6494 (tptt) cc_final: 0.6082 (pttp) REVERT: B 305 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7547 (mt-10) REVERT: C 68 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.7099 (t80) REVERT: C 72 LEU cc_start: 0.8417 (tp) cc_final: 0.8158 (tp) REVERT: C 134 ARG cc_start: 0.6202 (mpp80) cc_final: 0.5345 (mmm160) REVERT: E 422 GLN cc_start: 0.8678 (mm110) cc_final: 0.8344 (tp40) REVERT: F 428 LYS cc_start: 0.6136 (mmmt) cc_final: 0.5415 (mptt) outliers start: 22 outliers final: 18 residues processed: 98 average time/residue: 0.2021 time to fit residues: 28.2929 Evaluate side-chains 96 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 363 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 41 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 248 VAL Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 146 LEU 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 351 THR Chi-restraints excluded: chain F residue 430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.0980 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 84 optimal weight: 0.0050 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2588 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= 0.204 Angle : 0.567 8.840 11353 Z= 0.287 Chirality : 0.042 0.140 1317 Planarity : 0.004 0.051 1501 Dihedral : 3.790 17.718 1182 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.16 % Allowed : 18.96 % Favored : 78.89 % 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: 0.55 (0.26), residues: 1076 helix: 1.99 (0.25), residues: 434 sheet: -1.25 (0.45), residues: 143 loop : -0.57 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP C 111 HIS 0.002 0.000 HIS A 84 PHE 0.013 0.001 PHE E 380 TYR 0.014 0.001 TYR A 349 ARG 0.007 0.000 ARG C 113 ********************** 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 97 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6917 (mt-10) REVERT: B 110 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: B 228 LYS cc_start: 0.6734 (tptt) cc_final: 0.6299 (pttp) REVERT: B 305 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7555 (mt-10) REVERT: C 68 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.7101 (t80) REVERT: C 72 LEU cc_start: 0.8470 (tp) cc_final: 0.8252 (tp) REVERT: C 134 ARG cc_start: 0.6218 (mpp80) cc_final: 0.5310 (mmm160) REVERT: E 422 GLN cc_start: 0.8679 (mm110) cc_final: 0.8353 (tp40) REVERT: F 428 LYS cc_start: 0.6067 (mmmt) cc_final: 0.5374 (mptt) outliers start: 19 outliers final: 16 residues processed: 93 average time/residue: 0.1918 time to fit residues: 26.2432 Evaluate side-chains 95 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 363 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 41 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 248 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 146 LEU 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 351 THR Chi-restraints excluded: chain F residue 430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.165063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.136149 restraints weight = 14192.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.137102 restraints weight = 14214.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.138473 restraints weight = 10644.581| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2580 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= 0.230 Angle : 0.574 9.133 11353 Z= 0.292 Chirality : 0.042 0.142 1317 Planarity : 0.004 0.051 1501 Dihedral : 3.853 17.644 1182 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.61 % Allowed : 18.96 % 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: 0.51 (0.26), residues: 1076 helix: 1.95 (0.25), residues: 434 sheet: -1.32 (0.44), residues: 148 loop : -0.54 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.005 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 0.006 0.000 ARG C 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1802.47 seconds wall clock time: 33 minutes 40.55 seconds (2020.55 seconds total)