Starting phenix.real_space_refine on Sat Aug 23 14:00:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8chf_16660/08_2025/8chf_16660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8chf_16660/08_2025/8chf_16660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8chf_16660/08_2025/8chf_16660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8chf_16660/08_2025/8chf_16660.map" model { file = "/net/cci-nas-00/data/ceres_data/8chf_16660/08_2025/8chf_16660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8chf_16660/08_2025/8chf_16660.cif" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 76 5.16 5 C 8044 2.51 5 N 2150 2.21 5 O 2356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12628 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2253 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 1 Chain: "B" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2253 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 1 Chain: "C" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1842 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Chain: "D" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1842 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Chain: "E" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2194 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 16, 'TRANS': 261} Chain breaks: 2 Chain: "F" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2194 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 16, 'TRANS': 261} Chain breaks: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'29L': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'29L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.02, per 1000 atoms: 0.24 Number of scatterers: 12628 At special positions: 0 Unit cell: (132.481, 121.517, 105.985, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 2 15.00 O 2356 8.00 N 2150 7.00 C 8044 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: 1.10 Conformation dependent library (CDL) restraints added in 527.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2984 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 8 sheets defined 61.3% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 383 through 399 Processing helix chain 'A' and resid 428 through 435 Processing helix chain 'A' and resid 441 through 462 Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 526 through 542 Processing helix chain 'A' and resid 553 through 563 removed outlier: 3.545A pdb=" N PHE A 559 " --> pdb=" O ASP A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 Processing helix chain 'A' and resid 578 through 589 Processing helix chain 'A' and resid 592 through 596 removed outlier: 3.568A pdb=" N GLU A 595 " --> pdb=" O VAL A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 612 Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 428 through 435 Processing helix chain 'B' and resid 441 through 462 Processing helix chain 'B' and resid 513 through 519 Processing helix chain 'B' and resid 526 through 542 Processing helix chain 'B' and resid 553 through 563 removed outlier: 3.546A pdb=" N PHE B 559 " --> pdb=" O ASP B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 573 Processing helix chain 'B' and resid 578 through 589 Processing helix chain 'B' and resid 592 through 596 removed outlier: 3.567A pdb=" N GLU B 595 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 612 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 22 through 36 removed outlier: 4.049A pdb=" N GLY C 36 " --> pdb=" O VAL C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 72 removed outlier: 4.244A pdb=" N ARG C 58 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 111 Processing helix chain 'C' and resid 117 through 139 removed outlier: 3.830A pdb=" N VAL C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 166 Processing helix chain 'C' and resid 170 through 187 Processing helix chain 'C' and resid 190 through 208 removed outlier: 3.616A pdb=" N GLU C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 212 removed outlier: 4.091A pdb=" N LEU C 212 " --> pdb=" O LEU C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 209 through 212' Processing helix chain 'C' and resid 213 through 236 removed outlier: 4.274A pdb=" N ASP C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 18 Processing helix chain 'D' and resid 22 through 36 removed outlier: 4.050A pdb=" N GLY D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 72 removed outlier: 4.244A pdb=" N ARG D 58 " --> pdb=" O VAL D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 111 Processing helix chain 'D' and resid 117 through 139 removed outlier: 3.830A pdb=" N VAL D 138 " --> pdb=" O TYR D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 166 Processing helix chain 'D' and resid 170 through 187 Processing helix chain 'D' and resid 190 through 208 removed outlier: 3.616A pdb=" N GLU D 208 " --> pdb=" O ASP D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 212 removed outlier: 4.091A pdb=" N LEU D 212 " --> pdb=" O LEU D 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 209 through 212' Processing helix chain 'D' and resid 213 through 236 removed outlier: 4.274A pdb=" N ASP D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 110 through 120 removed outlier: 4.211A pdb=" N GLU E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 159 removed outlier: 4.016A pdb=" N VAL E 154 " --> pdb=" O SER E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 184 Processing helix chain 'E' and resid 192 through 196 Processing helix chain 'E' and resid 212 through 221 removed outlier: 4.143A pdb=" N ASN E 221 " --> pdb=" O ASP E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 237 Processing helix chain 'E' and resid 241 through 259 removed outlier: 3.776A pdb=" N ASP E 245 " --> pdb=" O SER E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 273 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 331 through 342 Processing helix chain 'E' and resid 345 through 349 Processing helix chain 'E' and resid 351 through 358 removed outlier: 3.584A pdb=" N HIS E 358 " --> pdb=" O GLN E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 367 Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'F' and resid 104 through 109 Processing helix chain 'F' and resid 110 through 120 removed outlier: 4.211A pdb=" N GLU F 114 " --> pdb=" O GLN F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 159 removed outlier: 4.016A pdb=" N VAL F 154 " --> pdb=" O SER F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 184 Processing helix chain 'F' and resid 192 through 196 Processing helix chain 'F' and resid 212 through 221 removed outlier: 4.142A pdb=" N ASN F 221 " --> pdb=" O ASP F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 237 Processing helix chain 'F' and resid 241 through 259 removed outlier: 3.776A pdb=" N ASP F 245 " --> pdb=" O SER F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 273 Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 331 through 342 Processing helix chain 'F' and resid 345 through 349 Processing helix chain 'F' and resid 351 through 358 removed outlier: 3.585A pdb=" N HIS F 358 " --> pdb=" O GLN F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 367 Processing helix chain 'F' and resid 370 through 379 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.892A pdb=" N GLY A 356 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN A 422 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE A 408 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.893A pdb=" N GLY B 356 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN B 422 " --> pdb=" O PHE B 408 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE B 408 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 464 through 465 Processing sheet with id=AA5, first strand: chain 'E' and resid 68 through 72 removed outlier: 7.022A pdb=" N LYS E 84 " --> pdb=" O ILE E 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 94 through 96 removed outlier: 3.786A pdb=" N PHE E 133 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N CYS E 142 " --> pdb=" O GLY E 131 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY E 131 " --> pdb=" O CYS E 142 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU E 144 " --> pdb=" O PHE E 129 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE E 129 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 68 through 72 removed outlier: 7.023A pdb=" N LYS F 84 " --> pdb=" O ILE F 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 94 through 96 removed outlier: 3.785A pdb=" N PHE F 133 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N CYS F 142 " --> pdb=" O GLY F 131 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY F 131 " --> pdb=" O CYS F 142 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU F 144 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N PHE F 129 " --> pdb=" O GLU F 144 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 2070 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: 1.76 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4015 1.34 - 1.46: 1818 1.46 - 1.57: 6909 1.57 - 1.69: 2 1.69 - 1.81: 132 Bond restraints: 12876 Sorted by residual: bond pdb=" O3P SEP B 621 " pdb=" P SEP B 621 " ideal model delta sigma weight residual 1.610 1.517 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" O3P SEP A 621 " pdb=" P SEP A 621 " ideal model delta sigma weight residual 1.610 1.517 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" O1P SEP A 621 " pdb=" P SEP A 621 " ideal model delta sigma weight residual 1.610 1.517 0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" O1P SEP B 621 " pdb=" P SEP B 621 " ideal model delta sigma weight residual 1.610 1.517 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" O2P SEP B 621 " pdb=" P SEP B 621 " ideal model delta sigma weight residual 1.610 1.517 0.093 2.00e-02 2.50e+03 2.14e+01 ... (remaining 12871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 17011 2.41 - 4.83: 307 4.83 - 7.24: 34 7.24 - 9.65: 8 9.65 - 12.06: 4 Bond angle restraints: 17364 Sorted by residual: angle pdb=" N TRP A 511 " pdb=" CA TRP A 511 " pdb=" C TRP A 511 " ideal model delta sigma weight residual 114.56 108.96 5.60 1.27e+00 6.20e-01 1.94e+01 angle pdb=" N TRP B 511 " pdb=" CA TRP B 511 " pdb=" C TRP B 511 " ideal model delta sigma weight residual 114.56 108.97 5.59 1.27e+00 6.20e-01 1.93e+01 angle pdb=" CB MET C 25 " pdb=" CG MET C 25 " pdb=" SD MET C 25 " ideal model delta sigma weight residual 112.70 124.76 -12.06 3.00e+00 1.11e-01 1.62e+01 angle pdb=" CB MET D 25 " pdb=" CG MET D 25 " pdb=" SD MET D 25 " ideal model delta sigma weight residual 112.70 124.75 -12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" C ASP D 24 " pdb=" N MET D 25 " pdb=" CA MET D 25 " ideal model delta sigma weight residual 121.14 114.13 7.01 1.75e+00 3.27e-01 1.61e+01 ... (remaining 17359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.38: 7460 25.38 - 50.76: 406 50.76 - 76.15: 22 76.15 - 101.53: 10 101.53 - 126.91: 2 Dihedral angle restraints: 7900 sinusoidal: 3298 harmonic: 4602 Sorted by residual: dihedral pdb=" N9 29L A 701 " pdb=" C18 29L A 701 " pdb=" C19 29L A 701 " pdb=" O20 29L A 701 " ideal model delta sinusoidal sigma weight residual 296.81 169.90 126.91 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" N9 29L B 701 " pdb=" C18 29L B 701 " pdb=" C19 29L B 701 " pdb=" O20 29L B 701 " ideal model delta sinusoidal sigma weight residual 296.81 174.97 121.84 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" CA PRO E 262 " pdb=" C PRO E 262 " pdb=" N ILE E 263 " pdb=" CA ILE E 263 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 7897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1326 0.043 - 0.087: 429 0.087 - 0.130: 129 0.130 - 0.174: 24 0.174 - 0.217: 10 Chirality restraints: 1918 Sorted by residual: chirality pdb=" CA VAL A 492 " pdb=" N VAL A 492 " pdb=" C VAL A 492 " pdb=" CB VAL A 492 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA VAL B 492 " pdb=" N VAL B 492 " pdb=" C VAL B 492 " pdb=" CB VAL B 492 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE B 551 " pdb=" N ILE B 551 " pdb=" C ILE B 551 " pdb=" CB ILE B 551 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 1915 not shown) Planarity restraints: 2216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 180 " 0.011 2.00e-02 2.50e+03 1.71e-02 5.14e+00 pdb=" CG PHE D 180 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE D 180 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE D 180 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 180 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE D 180 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE D 180 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 180 " -0.011 2.00e-02 2.50e+03 1.71e-02 5.09e+00 pdb=" CG PHE C 180 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 180 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE C 180 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 180 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE C 180 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 180 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 599 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.01e+00 pdb=" N PRO A 600 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 600 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 600 " 0.028 5.00e-02 4.00e+02 ... (remaining 2213 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 352 2.69 - 3.24: 14086 3.24 - 3.79: 21399 3.79 - 4.35: 27180 4.35 - 4.90: 42136 Nonbonded interactions: 105153 Sorted by model distance: nonbonded pdb=" OD2 ASP E 65 " pdb=" OG SER E 135 " model vdw 2.136 3.040 nonbonded pdb=" OD2 ASP F 65 " pdb=" OG SER F 135 " model vdw 2.137 3.040 nonbonded pdb=" OD2 ASP B 555 " pdb=" OG SER F 228 " model vdw 2.178 3.040 nonbonded pdb=" OD2 ASP A 555 " pdb=" OG SER E 228 " model vdw 2.178 3.040 nonbonded pdb=" ND1 HIS E 188 " pdb=" O ASP E 190 " model vdw 2.216 3.120 ... (remaining 105148 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.190 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.980 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 12876 Z= 0.299 Angle : 0.813 12.064 17364 Z= 0.449 Chirality : 0.049 0.217 1918 Planarity : 0.005 0.050 2216 Dihedral : 14.539 126.909 4916 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.21), residues: 1538 helix: 0.59 (0.17), residues: 874 sheet: -2.57 (0.45), residues: 96 loop : -1.01 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 228 TYR 0.033 0.002 TYR D 185 PHE 0.032 0.002 PHE D 180 TRP 0.024 0.003 TRP D 234 HIS 0.009 0.002 HIS D 170 Details of bonding type rmsd covalent geometry : bond 0.00564 (12876) covalent geometry : angle 0.81298 (17364) hydrogen bonds : bond 0.12629 ( 710) hydrogen bonds : angle 5.77320 ( 2070) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 676 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 PHE cc_start: 0.7830 (t80) cc_final: 0.6731 (t80) REVERT: A 392 ASN cc_start: 0.8091 (m-40) cc_final: 0.7825 (m-40) REVERT: A 399 LYS cc_start: 0.8208 (mmtp) cc_final: 0.7757 (mmtp) REVERT: A 412 MET cc_start: 0.6490 (ppp) cc_final: 0.6146 (ppp) REVERT: A 421 THR cc_start: 0.7766 (p) cc_final: 0.7516 (t) REVERT: A 431 LYS cc_start: 0.8085 (mppt) cc_final: 0.7809 (mppt) REVERT: A 439 LYS cc_start: 0.8126 (mppt) cc_final: 0.7572 (mppt) REVERT: A 442 MET cc_start: 0.6933 (mpp) cc_final: 0.6485 (mpp) REVERT: A 450 ARG cc_start: 0.8054 (ttp-170) cc_final: 0.7691 (ptm-80) REVERT: A 451 GLN cc_start: 0.7937 (mt0) cc_final: 0.6627 (tt0) REVERT: A 454 GLN cc_start: 0.8375 (mt0) cc_final: 0.7492 (mt0) REVERT: A 456 MET cc_start: 0.6524 (mmm) cc_final: 0.6161 (mmm) REVERT: A 460 HIS cc_start: 0.7686 (m170) cc_final: 0.7281 (m90) REVERT: A 463 ASN cc_start: 0.6322 (m-40) cc_final: 0.6094 (m-40) REVERT: A 470 LYS cc_start: 0.8051 (mtpt) cc_final: 0.7552 (mtpt) REVERT: A 516 VAL cc_start: 0.8865 (t) cc_final: 0.8463 (t) REVERT: A 517 ILE cc_start: 0.8731 (mt) cc_final: 0.8515 (mt) REVERT: A 528 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7557 (mm110) REVERT: A 541 LEU cc_start: 0.8164 (mt) cc_final: 0.7530 (mt) REVERT: A 542 MET cc_start: 0.6231 (mtp) cc_final: 0.6003 (mtp) REVERT: A 554 ARG cc_start: 0.7415 (tmm-80) cc_final: 0.6978 (tmm-80) REVERT: A 590 LYS cc_start: 0.7746 (mmtm) cc_final: 0.7312 (mmtm) REVERT: A 592 VAL cc_start: 0.8335 (t) cc_final: 0.7884 (m) REVERT: A 601 GLN cc_start: 0.7965 (tt0) cc_final: 0.7672 (tm-30) REVERT: A 609 LEU cc_start: 0.8494 (tp) cc_final: 0.7764 (tt) REVERT: B 351 LEU cc_start: 0.8234 (mp) cc_final: 0.7943 (mt) REVERT: B 365 LYS cc_start: 0.7472 (tttt) cc_final: 0.6803 (tttt) REVERT: B 367 LYS cc_start: 0.7555 (mmtt) cc_final: 0.6679 (mmtt) REVERT: B 393 GLU cc_start: 0.6785 (tp30) cc_final: 0.6310 (tp30) REVERT: B 399 LYS cc_start: 0.8298 (mmtp) cc_final: 0.7783 (mmtp) REVERT: B 412 MET cc_start: 0.6493 (ppp) cc_final: 0.5953 (ppp) REVERT: B 419 ILE cc_start: 0.7133 (mm) cc_final: 0.6847 (mm) REVERT: B 421 THR cc_start: 0.7815 (p) cc_final: 0.7427 (t) REVERT: B 432 HIS cc_start: 0.7013 (m90) cc_final: 0.6308 (m90) REVERT: B 439 LYS cc_start: 0.8352 (mppt) cc_final: 0.7856 (mppt) REVERT: B 441 GLN cc_start: 0.7276 (mt0) cc_final: 0.6891 (mt0) REVERT: B 442 MET cc_start: 0.6918 (mpp) cc_final: 0.6632 (mpp) REVERT: B 450 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.7813 (ttp-170) REVERT: B 458 TYR cc_start: 0.7973 (t80) cc_final: 0.7687 (t80) REVERT: B 470 LYS cc_start: 0.8018 (mtpt) cc_final: 0.7457 (mtpt) REVERT: B 492 VAL cc_start: 0.7925 (t) cc_final: 0.7647 (t) REVERT: B 516 VAL cc_start: 0.8821 (t) cc_final: 0.8505 (t) REVERT: B 517 ILE cc_start: 0.8732 (mt) cc_final: 0.8408 (mt) REVERT: B 528 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7534 (mm110) REVERT: B 541 LEU cc_start: 0.8177 (mt) cc_final: 0.7883 (mt) REVERT: B 542 MET cc_start: 0.6488 (mtp) cc_final: 0.6246 (mtp) REVERT: B 545 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7248 (mt-10) REVERT: B 554 ARG cc_start: 0.7418 (tmm-80) cc_final: 0.6913 (tmm-80) REVERT: B 560 MET cc_start: 0.7617 (mmp) cc_final: 0.7058 (mmp) REVERT: B 581 MET cc_start: 0.6798 (tpt) cc_final: 0.6551 (tpt) REVERT: B 583 ARG cc_start: 0.8214 (ptp-170) cc_final: 0.7919 (ptp-110) REVERT: B 590 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7370 (mmtm) REVERT: B 592 VAL cc_start: 0.8199 (t) cc_final: 0.7709 (m) REVERT: B 613 LEU cc_start: 0.8573 (mt) cc_final: 0.8221 (mt) REVERT: B 615 LYS cc_start: 0.7633 (mttm) cc_final: 0.7338 (mttm) REVERT: B 622 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6970 (tm-30) REVERT: C 20 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6999 (tm-30) REVERT: C 29 MET cc_start: 0.8854 (tpp) cc_final: 0.8518 (mmm) REVERT: C 43 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8242 (mt-10) REVERT: C 49 VAL cc_start: 0.7897 (t) cc_final: 0.7402 (t) REVERT: C 51 TYR cc_start: 0.7798 (m-10) cc_final: 0.7597 (m-10) REVERT: C 52 LYS cc_start: 0.8177 (tptm) cc_final: 0.7977 (tptm) REVERT: C 53 ASN cc_start: 0.7965 (m-40) cc_final: 0.7611 (m-40) REVERT: C 87 GLU cc_start: 0.8098 (pt0) cc_final: 0.7862 (pt0) REVERT: C 91 LYS cc_start: 0.8529 (tppt) cc_final: 0.7705 (tppt) REVERT: C 95 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7472 (mt-10) REVERT: C 97 ARG cc_start: 0.8630 (mtm110) cc_final: 0.7846 (mtm110) REVERT: C 98 GLU cc_start: 0.6698 (tp30) cc_final: 0.5793 (tp30) REVERT: C 102 ASP cc_start: 0.7639 (m-30) cc_final: 0.6886 (m-30) REVERT: C 119 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8023 (mt-10) REVERT: C 125 LEU cc_start: 0.8160 (mt) cc_final: 0.7803 (mt) REVERT: C 126 LYS cc_start: 0.8561 (tttm) cc_final: 0.8350 (tttm) REVERT: C 127 MET cc_start: 0.8016 (mmm) cc_final: 0.7567 (mmp) REVERT: C 132 TYR cc_start: 0.7918 (m-80) cc_final: 0.7260 (m-80) REVERT: C 150 ASP cc_start: 0.8065 (m-30) cc_final: 0.7749 (m-30) REVERT: C 153 LYS cc_start: 0.8760 (tppt) cc_final: 0.7974 (tppt) REVERT: C 157 ASP cc_start: 0.7359 (t0) cc_final: 0.7063 (t0) REVERT: C 159 PHE cc_start: 0.8056 (t80) cc_final: 0.7812 (t80) REVERT: C 176 LEU cc_start: 0.8745 (tt) cc_final: 0.8136 (tt) REVERT: C 180 PHE cc_start: 0.8064 (m-80) cc_final: 0.7421 (m-80) REVERT: C 195 CYS cc_start: 0.8070 (m) cc_final: 0.7809 (m) REVERT: C 224 MET cc_start: 0.7304 (ptm) cc_final: 0.6601 (ptm) REVERT: C 225 GLN cc_start: 0.7477 (mm110) cc_final: 0.6814 (mm110) REVERT: D 14 LYS cc_start: 0.8789 (mttt) cc_final: 0.8546 (mttt) REVERT: D 20 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7227 (tm-30) REVERT: D 29 MET cc_start: 0.8646 (tpp) cc_final: 0.8280 (mmm) REVERT: D 32 VAL cc_start: 0.8272 (t) cc_final: 0.8038 (t) REVERT: D 34 GLU cc_start: 0.7845 (pp20) cc_final: 0.7465 (pp20) REVERT: D 43 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8511 (mp0) REVERT: D 53 ASN cc_start: 0.7847 (m-40) cc_final: 0.7397 (m-40) REVERT: D 59 ARG cc_start: 0.8158 (mtp-110) cc_final: 0.7601 (mtp180) REVERT: D 65 ILE cc_start: 0.8688 (pt) cc_final: 0.8241 (pt) REVERT: D 66 SER cc_start: 0.8004 (m) cc_final: 0.7337 (m) REVERT: D 91 LYS cc_start: 0.8545 (tppt) cc_final: 0.7601 (tppt) REVERT: D 93 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7950 (mt-10) REVERT: D 95 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7412 (mt-10) REVERT: D 119 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7804 (tp30) REVERT: D 128 LYS cc_start: 0.8076 (tttt) cc_final: 0.7636 (tttt) REVERT: D 133 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.7880 (ttp80) REVERT: D 153 LYS cc_start: 0.8501 (tppt) cc_final: 0.7671 (tppt) REVERT: D 167 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7735 (tp-100) REVERT: D 176 LEU cc_start: 0.8871 (tt) cc_final: 0.8287 (tt) REVERT: D 180 PHE cc_start: 0.8051 (m-80) cc_final: 0.7248 (m-80) REVERT: D 192 ASP cc_start: 0.8336 (p0) cc_final: 0.7518 (p0) REVERT: D 193 LYS cc_start: 0.8249 (mttt) cc_final: 0.7780 (mptt) REVERT: D 195 CYS cc_start: 0.7952 (m) cc_final: 0.7656 (m) REVERT: D 197 LEU cc_start: 0.8455 (mm) cc_final: 0.8222 (mm) REVERT: D 220 SER cc_start: 0.7058 (m) cc_final: 0.6813 (m) REVERT: D 224 MET cc_start: 0.7170 (ptm) cc_final: 0.6365 (ptm) REVERT: D 225 GLN cc_start: 0.7426 (mm110) cc_final: 0.6748 (mm110) REVERT: E 88 LYS cc_start: 0.8395 (mmmt) cc_final: 0.7976 (mmmt) REVERT: E 121 CYS cc_start: 0.7603 (m) cc_final: 0.7292 (m) REVERT: E 160 ARG cc_start: 0.7508 (mpp80) cc_final: 0.6223 (mtt90) REVERT: E 175 LYS cc_start: 0.8653 (ptmt) cc_final: 0.8128 (ptmt) REVERT: E 187 MET cc_start: 0.6403 (mtt) cc_final: 0.6142 (mtm) REVERT: E 206 LEU cc_start: 0.6979 (tp) cc_final: 0.6641 (tp) REVERT: E 219 MET cc_start: 0.7653 (mtp) cc_final: 0.7429 (mtp) REVERT: E 236 GLN cc_start: 0.7467 (tm-30) cc_final: 0.7170 (tm-30) REVERT: E 253 LEU cc_start: 0.8769 (mt) cc_final: 0.8563 (mt) REVERT: E 270 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7443 (mt-10) REVERT: E 274 MET cc_start: 0.5958 (ppp) cc_final: 0.5678 (ppp) REVERT: E 311 PHE cc_start: 0.6751 (t80) cc_final: 0.6096 (t80) REVERT: E 316 TYR cc_start: 0.7713 (t80) cc_final: 0.7252 (t80) REVERT: E 319 ASN cc_start: 0.7805 (t0) cc_final: 0.6722 (t0) REVERT: E 320 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7502 (mm-30) REVERT: E 333 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8319 (mt-10) REVERT: E 344 LYS cc_start: 0.8461 (tttt) cc_final: 0.8125 (mttt) REVERT: F 88 LYS cc_start: 0.8471 (mmmt) cc_final: 0.7958 (mmmt) REVERT: F 96 ARG cc_start: 0.7370 (ptm160) cc_final: 0.6737 (ptm160) REVERT: F 110 GLN cc_start: 0.8492 (mm110) cc_final: 0.8259 (mp10) REVERT: F 125 TYR cc_start: 0.8052 (m-80) cc_final: 0.7161 (m-80) REVERT: F 168 LYS cc_start: 0.8496 (ttmm) cc_final: 0.8060 (ttmm) REVERT: F 175 LYS cc_start: 0.8685 (ptmt) cc_final: 0.8171 (ptmt) REVERT: F 195 ASN cc_start: 0.7088 (t0) cc_final: 0.6873 (t0) REVERT: F 206 LEU cc_start: 0.6739 (tp) cc_final: 0.6418 (tp) REVERT: F 219 MET cc_start: 0.7549 (mtp) cc_final: 0.7326 (mtp) REVERT: F 270 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7602 (mt-10) REVERT: F 316 TYR cc_start: 0.7743 (t80) cc_final: 0.7209 (t80) REVERT: F 318 VAL cc_start: 0.8492 (p) cc_final: 0.8214 (m) REVERT: F 319 ASN cc_start: 0.7733 (t0) cc_final: 0.6505 (t0) REVERT: F 320 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7449 (mm-30) outliers start: 0 outliers final: 0 residues processed: 676 average time/residue: 0.1323 time to fit residues: 123.5858 Evaluate side-chains 658 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 658 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS A 432 HIS ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.136451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.111159 restraints weight = 28247.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.115592 restraints weight = 15602.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.118670 restraints weight = 10127.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.120876 restraints weight = 7240.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.122370 restraints weight = 5528.830| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12876 Z= 0.223 Angle : 0.715 12.669 17364 Z= 0.380 Chirality : 0.047 0.198 1918 Planarity : 0.005 0.089 2216 Dihedral : 6.493 112.426 1740 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.22 % Allowed : 5.69 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.20), residues: 1538 helix: 0.45 (0.16), residues: 890 sheet: -2.93 (0.47), residues: 88 loop : -1.09 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 181 TYR 0.039 0.003 TYR C 101 PHE 0.014 0.002 PHE F 360 TRP 0.021 0.002 TRP B 368 HIS 0.007 0.002 HIS E 188 Details of bonding type rmsd covalent geometry : bond 0.00427 (12876) covalent geometry : angle 0.71511 (17364) hydrogen bonds : bond 0.04591 ( 710) hydrogen bonds : angle 5.05883 ( 2070) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 682 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.7528 (mtm) cc_final: 0.7128 (mtm) REVERT: A 359 SER cc_start: 0.8249 (m) cc_final: 0.7787 (p) REVERT: A 367 LYS cc_start: 0.7563 (mmtt) cc_final: 0.6693 (mmtt) REVERT: A 386 GLN cc_start: 0.8707 (mt0) cc_final: 0.8425 (mt0) REVERT: A 387 PHE cc_start: 0.8194 (t80) cc_final: 0.7449 (t80) REVERT: A 391 ARG cc_start: 0.8388 (mmt90) cc_final: 0.7798 (mmm-85) REVERT: A 392 ASN cc_start: 0.8390 (m-40) cc_final: 0.8047 (m-40) REVERT: A 397 LEU cc_start: 0.8518 (mm) cc_final: 0.8266 (mt) REVERT: A 399 LYS cc_start: 0.8351 (mmtp) cc_final: 0.7884 (mmtp) REVERT: A 402 HIS cc_start: 0.7875 (t-90) cc_final: 0.7395 (t-90) REVERT: A 409 MET cc_start: 0.7488 (mtt) cc_final: 0.7277 (mtt) REVERT: A 412 MET cc_start: 0.6300 (ppp) cc_final: 0.5707 (ppp) REVERT: A 422 GLN cc_start: 0.8425 (tt0) cc_final: 0.8073 (tt0) REVERT: A 439 LYS cc_start: 0.8296 (mppt) cc_final: 0.7773 (mppt) REVERT: A 442 MET cc_start: 0.7453 (mpp) cc_final: 0.7165 (mpp) REVERT: A 445 LEU cc_start: 0.8682 (tp) cc_final: 0.8449 (tp) REVERT: A 451 GLN cc_start: 0.8213 (mt0) cc_final: 0.7009 (mt0) REVERT: A 456 MET cc_start: 0.8239 (mmm) cc_final: 0.7898 (mmm) REVERT: A 457 ASP cc_start: 0.8057 (t0) cc_final: 0.7640 (t0) REVERT: A 458 TYR cc_start: 0.8596 (t80) cc_final: 0.8234 (t80) REVERT: A 466 HIS cc_start: 0.8603 (t-90) cc_final: 0.8028 (t-90) REVERT: A 512 MET cc_start: 0.5862 (ttm) cc_final: 0.5521 (ttm) REVERT: A 528 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7562 (mm-40) REVERT: A 532 TYR cc_start: 0.8145 (t80) cc_final: 0.7856 (t80) REVERT: A 534 TYR cc_start: 0.8522 (t80) cc_final: 0.8244 (t80) REVERT: A 541 LEU cc_start: 0.8747 (mt) cc_final: 0.8457 (mt) REVERT: A 542 MET cc_start: 0.7201 (mtp) cc_final: 0.6787 (mtp) REVERT: A 560 MET cc_start: 0.8443 (mmp) cc_final: 0.8205 (mmt) REVERT: A 563 ARG cc_start: 0.8762 (mmm-85) cc_final: 0.8528 (mmm-85) REVERT: A 581 MET cc_start: 0.7777 (mmm) cc_final: 0.7128 (mmm) REVERT: A 590 LYS cc_start: 0.7731 (mmtm) cc_final: 0.7455 (mmtm) REVERT: A 592 VAL cc_start: 0.7867 (t) cc_final: 0.7469 (m) REVERT: A 601 GLN cc_start: 0.8451 (tt0) cc_final: 0.8171 (tm-30) REVERT: A 609 LEU cc_start: 0.8339 (tp) cc_final: 0.7819 (tt) REVERT: B 350 MET cc_start: 0.7528 (mtm) cc_final: 0.7084 (mtm) REVERT: B 367 LYS cc_start: 0.7683 (mmtt) cc_final: 0.6771 (mmtt) REVERT: B 383 THR cc_start: 0.8373 (p) cc_final: 0.8044 (p) REVERT: B 386 GLN cc_start: 0.8679 (mt0) cc_final: 0.8421 (mt0) REVERT: B 387 PHE cc_start: 0.8261 (t80) cc_final: 0.8002 (t80) REVERT: B 393 GLU cc_start: 0.7849 (tp30) cc_final: 0.7260 (tp30) REVERT: B 399 LYS cc_start: 0.8332 (mmtp) cc_final: 0.7845 (mmtp) REVERT: B 402 HIS cc_start: 0.7979 (t-90) cc_final: 0.7372 (t-90) REVERT: B 409 MET cc_start: 0.7455 (mtm) cc_final: 0.6789 (mtm) REVERT: B 412 MET cc_start: 0.6326 (ppp) cc_final: 0.5705 (ppp) REVERT: B 416 ASN cc_start: 0.7775 (p0) cc_final: 0.7345 (p0) REVERT: B 419 ILE cc_start: 0.7547 (mm) cc_final: 0.7228 (mm) REVERT: B 429 LEU cc_start: 0.8385 (tp) cc_final: 0.8090 (tp) REVERT: B 432 HIS cc_start: 0.7637 (m90) cc_final: 0.6615 (m90) REVERT: B 433 LEU cc_start: 0.8466 (mt) cc_final: 0.8263 (mt) REVERT: B 439 LYS cc_start: 0.8536 (mppt) cc_final: 0.8055 (mppt) REVERT: B 442 MET cc_start: 0.7640 (mpp) cc_final: 0.7086 (mpp) REVERT: B 450 ARG cc_start: 0.8539 (ttp-170) cc_final: 0.7840 (ttp-170) REVERT: B 458 TYR cc_start: 0.8491 (t80) cc_final: 0.7446 (t80) REVERT: B 460 HIS cc_start: 0.8341 (m170) cc_final: 0.8009 (m-70) REVERT: B 466 HIS cc_start: 0.8510 (t-90) cc_final: 0.8078 (t-90) REVERT: B 512 MET cc_start: 0.5751 (ttm) cc_final: 0.5270 (ttm) REVERT: B 516 VAL cc_start: 0.8747 (t) cc_final: 0.8429 (t) REVERT: B 518 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7026 (mtm-85) REVERT: B 528 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7264 (mm110) REVERT: B 532 TYR cc_start: 0.8200 (t80) cc_final: 0.7978 (t80) REVERT: B 534 TYR cc_start: 0.8505 (t80) cc_final: 0.8120 (t80) REVERT: B 541 LEU cc_start: 0.8746 (mt) cc_final: 0.8518 (mt) REVERT: B 545 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7245 (mt-10) REVERT: B 551 ILE cc_start: 0.8792 (mp) cc_final: 0.8525 (mp) REVERT: B 556 GLN cc_start: 0.8306 (tt0) cc_final: 0.7964 (tp40) REVERT: B 563 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.7573 (ttm-80) REVERT: B 574 TYR cc_start: 0.7952 (m-80) cc_final: 0.7691 (m-10) REVERT: B 576 ASN cc_start: 0.7839 (t0) cc_final: 0.7307 (t0) REVERT: B 583 ARG cc_start: 0.8569 (ptp-170) cc_final: 0.8042 (ptp-110) REVERT: B 592 VAL cc_start: 0.7780 (t) cc_final: 0.7341 (m) REVERT: B 601 GLN cc_start: 0.8604 (tt0) cc_final: 0.8281 (tt0) REVERT: B 615 LYS cc_start: 0.8046 (mttm) cc_final: 0.7719 (mttm) REVERT: B 622 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6884 (tm-30) REVERT: C 20 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7330 (tm-30) REVERT: C 25 MET cc_start: 0.7779 (pmm) cc_final: 0.7221 (pmm) REVERT: C 29 MET cc_start: 0.9112 (tpp) cc_final: 0.8712 (mmm) REVERT: C 43 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8451 (mt-10) REVERT: C 49 VAL cc_start: 0.8136 (t) cc_final: 0.7740 (m) REVERT: C 52 LYS cc_start: 0.8448 (tptm) cc_final: 0.8224 (tptm) REVERT: C 53 ASN cc_start: 0.8208 (m-40) cc_final: 0.7969 (m-40) REVERT: C 59 ARG cc_start: 0.8356 (mtp-110) cc_final: 0.7836 (mtp180) REVERT: C 69 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8273 (tm-30) REVERT: C 81 LYS cc_start: 0.8098 (ptpp) cc_final: 0.7850 (pptt) REVERT: C 87 GLU cc_start: 0.8295 (pt0) cc_final: 0.8060 (pt0) REVERT: C 91 LYS cc_start: 0.8670 (tppt) cc_final: 0.7800 (tppt) REVERT: C 94 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8421 (ttpt) REVERT: C 95 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7672 (mt-10) REVERT: C 97 ARG cc_start: 0.8611 (mtm110) cc_final: 0.8319 (mtm110) REVERT: C 98 GLU cc_start: 0.7225 (tp30) cc_final: 0.6110 (tp30) REVERT: C 102 ASP cc_start: 0.7879 (m-30) cc_final: 0.6995 (m-30) REVERT: C 119 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7951 (tp30) REVERT: C 125 LEU cc_start: 0.8317 (mt) cc_final: 0.8072 (mt) REVERT: C 126 LYS cc_start: 0.8825 (tttm) cc_final: 0.8621 (tttm) REVERT: C 127 MET cc_start: 0.8369 (mmm) cc_final: 0.7698 (mmp) REVERT: C 133 ARG cc_start: 0.8746 (ttp-110) cc_final: 0.8014 (ttp80) REVERT: C 149 GLU cc_start: 0.8406 (tp30) cc_final: 0.8082 (tp30) REVERT: C 155 TYR cc_start: 0.7920 (m-10) cc_final: 0.7234 (m-80) REVERT: C 170 HIS cc_start: 0.8132 (t-90) cc_final: 0.7553 (t-90) REVERT: C 180 PHE cc_start: 0.8542 (m-80) cc_final: 0.7775 (m-80) REVERT: C 196 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8005 (pp30) REVERT: C 200 GLN cc_start: 0.8785 (pt0) cc_final: 0.8509 (pt0) REVERT: C 224 MET cc_start: 0.7350 (ptm) cc_final: 0.6540 (ptm) REVERT: C 225 GLN cc_start: 0.7459 (mm110) cc_final: 0.6742 (mm110) REVERT: D 7 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8258 (mm-30) REVERT: D 14 LYS cc_start: 0.8724 (mttt) cc_final: 0.8427 (mttt) REVERT: D 20 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7501 (tm-30) REVERT: D 25 MET cc_start: 0.7853 (pmm) cc_final: 0.7436 (pmm) REVERT: D 29 MET cc_start: 0.9021 (tpp) cc_final: 0.8707 (mmm) REVERT: D 34 GLU cc_start: 0.8081 (pp20) cc_final: 0.7799 (pp20) REVERT: D 43 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8602 (mt-10) REVERT: D 65 ILE cc_start: 0.8769 (pt) cc_final: 0.8498 (pt) REVERT: D 66 SER cc_start: 0.8053 (m) cc_final: 0.7534 (m) REVERT: D 87 GLU cc_start: 0.8329 (pt0) cc_final: 0.8064 (pt0) REVERT: D 91 LYS cc_start: 0.8723 (tppt) cc_final: 0.8039 (tppt) REVERT: D 93 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8287 (mt-10) REVERT: D 97 ARG cc_start: 0.8847 (mtm110) cc_final: 0.8437 (mtm110) REVERT: D 119 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7939 (tp30) REVERT: D 125 LEU cc_start: 0.8289 (mt) cc_final: 0.8062 (mt) REVERT: D 127 MET cc_start: 0.8423 (mmm) cc_final: 0.7712 (mmp) REVERT: D 130 ASP cc_start: 0.7907 (m-30) cc_final: 0.7482 (m-30) REVERT: D 132 TYR cc_start: 0.8483 (m-80) cc_final: 0.7345 (m-80) REVERT: D 133 ARG cc_start: 0.8637 (ttp-110) cc_final: 0.8389 (ttp-110) REVERT: D 150 ASP cc_start: 0.8213 (m-30) cc_final: 0.7892 (p0) REVERT: D 155 TYR cc_start: 0.7825 (m-10) cc_final: 0.6951 (m-80) REVERT: D 170 HIS cc_start: 0.8305 (t-90) cc_final: 0.7971 (t-90) REVERT: D 180 PHE cc_start: 0.8604 (m-80) cc_final: 0.7827 (m-80) REVERT: D 192 ASP cc_start: 0.8399 (p0) cc_final: 0.7826 (p0) REVERT: D 196 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8094 (pm20) REVERT: D 197 LEU cc_start: 0.8429 (mm) cc_final: 0.8211 (mm) REVERT: D 206 ILE cc_start: 0.7743 (mt) cc_final: 0.7521 (mt) REVERT: D 220 SER cc_start: 0.7367 (m) cc_final: 0.6655 (p) REVERT: D 224 MET cc_start: 0.7427 (ptm) cc_final: 0.6674 (ptm) REVERT: D 225 GLN cc_start: 0.7480 (mm110) cc_final: 0.6797 (mm110) REVERT: E 88 LYS cc_start: 0.8438 (mmmt) cc_final: 0.7990 (mmmt) REVERT: E 121 CYS cc_start: 0.7763 (m) cc_final: 0.7482 (m) REVERT: E 125 TYR cc_start: 0.8099 (m-80) cc_final: 0.7199 (m-80) REVERT: E 175 LYS cc_start: 0.8666 (ptmt) cc_final: 0.8137 (ptmt) REVERT: E 187 MET cc_start: 0.6459 (mtt) cc_final: 0.5728 (mtm) REVERT: E 195 ASN cc_start: 0.7783 (t0) cc_final: 0.7507 (t0) REVERT: E 212 SER cc_start: 0.7645 (p) cc_final: 0.7354 (p) REVERT: E 215 LEU cc_start: 0.5241 (tp) cc_final: 0.5001 (tt) REVERT: E 219 MET cc_start: 0.7873 (mtp) cc_final: 0.7529 (mtp) REVERT: E 227 ARG cc_start: 0.7634 (mtm180) cc_final: 0.7194 (mtp180) REVERT: E 236 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7788 (tm-30) REVERT: E 249 MET cc_start: 0.8325 (ppp) cc_final: 0.8051 (ppp) REVERT: E 253 LEU cc_start: 0.8811 (mt) cc_final: 0.8587 (mt) REVERT: E 256 MET cc_start: 0.7703 (ptm) cc_final: 0.7316 (ptm) REVERT: E 310 ILE cc_start: 0.8696 (mp) cc_final: 0.8476 (mp) REVERT: E 312 GLU cc_start: 0.7775 (pp20) cc_final: 0.7336 (pp20) REVERT: E 313 LEU cc_start: 0.8254 (mt) cc_final: 0.7982 (mt) REVERT: E 316 TYR cc_start: 0.8111 (t80) cc_final: 0.7589 (t80) REVERT: E 319 ASN cc_start: 0.8112 (t0) cc_final: 0.6941 (t0) REVERT: E 320 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7676 (mm-30) REVERT: E 333 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8344 (mt-10) REVERT: E 344 LYS cc_start: 0.8422 (tttt) cc_final: 0.7976 (mttt) REVERT: E 353 LYS cc_start: 0.7944 (mmpt) cc_final: 0.7735 (mmpt) REVERT: F 88 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8020 (mmmt) REVERT: F 96 ARG cc_start: 0.7561 (ptm160) cc_final: 0.6888 (ptm160) REVERT: F 125 TYR cc_start: 0.8190 (m-80) cc_final: 0.7281 (m-80) REVERT: F 163 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7966 (mt-10) REVERT: F 175 LYS cc_start: 0.8611 (ptmt) cc_final: 0.8109 (ptmt) REVERT: F 187 MET cc_start: 0.6317 (mtm) cc_final: 0.5725 (mtm) REVERT: F 195 ASN cc_start: 0.7728 (t0) cc_final: 0.7334 (t0) REVERT: F 206 LEU cc_start: 0.6787 (tp) cc_final: 0.6256 (tp) REVERT: F 219 MET cc_start: 0.7801 (mtp) cc_final: 0.7499 (mtp) REVERT: F 227 ARG cc_start: 0.7613 (mtm180) cc_final: 0.7188 (mtm180) REVERT: F 230 MET cc_start: 0.7814 (tpt) cc_final: 0.7597 (tpp) REVERT: F 236 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7891 (tm-30) REVERT: F 249 MET cc_start: 0.8347 (ppp) cc_final: 0.8067 (ppp) REVERT: F 256 MET cc_start: 0.7708 (ptm) cc_final: 0.7406 (ptm) REVERT: F 267 ASP cc_start: 0.7388 (p0) cc_final: 0.6614 (p0) REVERT: F 270 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7641 (mt-10) REVERT: F 316 TYR cc_start: 0.8122 (t80) cc_final: 0.7514 (t80) REVERT: F 318 VAL cc_start: 0.8549 (p) cc_final: 0.8275 (m) REVERT: F 319 ASN cc_start: 0.7896 (t0) cc_final: 0.6649 (t0) REVERT: F 320 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7524 (mm-30) REVERT: F 333 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8268 (mt-10) REVERT: F 334 PHE cc_start: 0.8617 (t80) cc_final: 0.8380 (t80) REVERT: F 356 MET cc_start: 0.6812 (ppp) cc_final: 0.6494 (ppp) outliers start: 3 outliers final: 0 residues processed: 684 average time/residue: 0.1268 time to fit residues: 119.6032 Evaluate side-chains 678 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 676 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN C 200 GLN D 11 GLN D 200 GLN E 109 ASN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.125617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.102391 restraints weight = 29140.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.106850 restraints weight = 15826.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.109975 restraints weight = 10005.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.112155 restraints weight = 6934.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.113729 restraints weight = 5152.517| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12876 Z= 0.157 Angle : 0.645 9.764 17364 Z= 0.341 Chirality : 0.045 0.250 1918 Planarity : 0.004 0.054 2216 Dihedral : 6.046 90.992 1740 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.14 % Allowed : 4.03 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.21), residues: 1538 helix: 0.54 (0.16), residues: 894 sheet: -2.98 (0.46), residues: 88 loop : -1.08 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 160 TYR 0.027 0.002 TYR C 101 PHE 0.011 0.002 PHE E 360 TRP 0.033 0.002 TRP B 368 HIS 0.010 0.001 HIS E 358 Details of bonding type rmsd covalent geometry : bond 0.00322 (12876) covalent geometry : angle 0.64504 (17364) hydrogen bonds : bond 0.04202 ( 710) hydrogen bonds : angle 4.84587 ( 2070) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 674 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.7534 (mtm) cc_final: 0.7088 (mtm) REVERT: A 359 SER cc_start: 0.8254 (m) cc_final: 0.7804 (p) REVERT: A 367 LYS cc_start: 0.7569 (mmtt) cc_final: 0.6677 (mmtt) REVERT: A 368 TRP cc_start: 0.8494 (t60) cc_final: 0.8224 (t60) REVERT: A 387 PHE cc_start: 0.8146 (t80) cc_final: 0.7297 (t80) REVERT: A 391 ARG cc_start: 0.8342 (mmt90) cc_final: 0.7760 (mmm-85) REVERT: A 392 ASN cc_start: 0.8338 (m-40) cc_final: 0.7964 (m-40) REVERT: A 397 LEU cc_start: 0.8506 (mm) cc_final: 0.8217 (mt) REVERT: A 399 LYS cc_start: 0.8365 (mmtp) cc_final: 0.7943 (mmtp) REVERT: A 402 HIS cc_start: 0.7809 (t-90) cc_final: 0.7440 (t-90) REVERT: A 409 MET cc_start: 0.7442 (mtt) cc_final: 0.7238 (mtt) REVERT: A 411 TYR cc_start: 0.7154 (p90) cc_final: 0.6925 (p90) REVERT: A 412 MET cc_start: 0.6051 (ppp) cc_final: 0.5531 (ppp) REVERT: A 414 LYS cc_start: 0.8209 (tppt) cc_final: 0.7811 (tppt) REVERT: A 416 ASN cc_start: 0.7467 (p0) cc_final: 0.7092 (p0) REVERT: A 422 GLN cc_start: 0.8317 (tt0) cc_final: 0.7307 (pt0) REVERT: A 425 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6944 (mm-30) REVERT: A 439 LYS cc_start: 0.8257 (mppt) cc_final: 0.7626 (mppt) REVERT: A 444 GLN cc_start: 0.7959 (mt0) cc_final: 0.7638 (mp10) REVERT: A 456 MET cc_start: 0.8327 (mmm) cc_final: 0.7436 (mmm) REVERT: A 458 TYR cc_start: 0.8582 (t80) cc_final: 0.8240 (t80) REVERT: A 460 HIS cc_start: 0.8264 (m170) cc_final: 0.7683 (m-70) REVERT: A 463 ASN cc_start: 0.7234 (m-40) cc_final: 0.6999 (m-40) REVERT: A 466 HIS cc_start: 0.8662 (t-90) cc_final: 0.8036 (t-90) REVERT: A 477 HIS cc_start: 0.6491 (t70) cc_final: 0.6279 (t-90) REVERT: A 511 TRP cc_start: 0.7389 (m-90) cc_final: 0.7175 (m-90) REVERT: A 512 MET cc_start: 0.5897 (ttm) cc_final: 0.5578 (ttm) REVERT: A 518 ARG cc_start: 0.8187 (ptp-110) cc_final: 0.7456 (ptp-110) REVERT: A 528 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7480 (mm-40) REVERT: A 532 TYR cc_start: 0.8093 (t80) cc_final: 0.7843 (t80) REVERT: A 534 TYR cc_start: 0.8518 (t80) cc_final: 0.8093 (t80) REVERT: A 541 LEU cc_start: 0.8703 (mt) cc_final: 0.8333 (mt) REVERT: A 560 MET cc_start: 0.8371 (mmp) cc_final: 0.8097 (mmt) REVERT: A 574 TYR cc_start: 0.7687 (m-80) cc_final: 0.7401 (m-10) REVERT: A 581 MET cc_start: 0.7785 (mmm) cc_final: 0.7067 (mmm) REVERT: A 590 LYS cc_start: 0.7731 (mmtm) cc_final: 0.7427 (mmtm) REVERT: A 592 VAL cc_start: 0.7822 (t) cc_final: 0.7369 (m) REVERT: A 601 GLN cc_start: 0.8385 (tt0) cc_final: 0.8112 (tm-30) REVERT: A 606 ILE cc_start: 0.9041 (mm) cc_final: 0.8746 (tp) REVERT: A 609 LEU cc_start: 0.8425 (tp) cc_final: 0.7904 (tt) REVERT: A 622 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7129 (tm-30) REVERT: B 342 TRP cc_start: 0.8730 (m100) cc_final: 0.8011 (m100) REVERT: B 350 MET cc_start: 0.7468 (mtm) cc_final: 0.6999 (mtm) REVERT: B 367 LYS cc_start: 0.7634 (mmtt) cc_final: 0.6735 (mmtt) REVERT: B 387 PHE cc_start: 0.8238 (t80) cc_final: 0.7974 (t80) REVERT: B 393 GLU cc_start: 0.7894 (tp30) cc_final: 0.7264 (tp30) REVERT: B 399 LYS cc_start: 0.8388 (mmtp) cc_final: 0.7903 (mmtp) REVERT: B 402 HIS cc_start: 0.7901 (t-90) cc_final: 0.7487 (t-90) REVERT: B 409 MET cc_start: 0.7485 (mtm) cc_final: 0.6531 (mtm) REVERT: B 411 TYR cc_start: 0.7255 (p90) cc_final: 0.7028 (p90) REVERT: B 412 MET cc_start: 0.5955 (ppp) cc_final: 0.5478 (ppp) REVERT: B 414 LYS cc_start: 0.8298 (tppt) cc_final: 0.8049 (mmmt) REVERT: B 416 ASN cc_start: 0.7743 (p0) cc_final: 0.7349 (p0) REVERT: B 419 ILE cc_start: 0.7412 (mm) cc_final: 0.7011 (mm) REVERT: B 422 GLN cc_start: 0.8292 (tt0) cc_final: 0.7341 (pt0) REVERT: B 425 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7026 (mm-30) REVERT: B 432 HIS cc_start: 0.7606 (m90) cc_final: 0.6610 (m90) REVERT: B 433 LEU cc_start: 0.8452 (mt) cc_final: 0.8205 (mt) REVERT: B 439 LYS cc_start: 0.8476 (mppt) cc_final: 0.7974 (mppt) REVERT: B 442 MET cc_start: 0.7599 (mpp) cc_final: 0.7237 (mpp) REVERT: B 450 ARG cc_start: 0.8392 (ttp-170) cc_final: 0.7770 (ttp-170) REVERT: B 456 MET cc_start: 0.8098 (mmm) cc_final: 0.7842 (mmm) REVERT: B 457 ASP cc_start: 0.7953 (t70) cc_final: 0.7716 (t70) REVERT: B 466 HIS cc_start: 0.8542 (t-90) cc_final: 0.8202 (t-90) REVERT: B 470 LYS cc_start: 0.8414 (mtpt) cc_final: 0.8006 (mtpt) REVERT: B 483 LYS cc_start: 0.8279 (mttm) cc_final: 0.7440 (mttm) REVERT: B 484 ILE cc_start: 0.8008 (mt) cc_final: 0.7655 (mt) REVERT: B 511 TRP cc_start: 0.7401 (m-90) cc_final: 0.7083 (m-90) REVERT: B 512 MET cc_start: 0.5951 (ttm) cc_final: 0.5562 (ttm) REVERT: B 516 VAL cc_start: 0.8774 (t) cc_final: 0.8452 (t) REVERT: B 528 GLN cc_start: 0.7658 (mm-40) cc_final: 0.6943 (mm110) REVERT: B 534 TYR cc_start: 0.8463 (t80) cc_final: 0.8080 (t80) REVERT: B 541 LEU cc_start: 0.8770 (mt) cc_final: 0.8562 (mt) REVERT: B 545 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7337 (mt-10) REVERT: B 551 ILE cc_start: 0.8755 (mp) cc_final: 0.8508 (mp) REVERT: B 554 ARG cc_start: 0.7417 (tmm-80) cc_final: 0.7139 (tmm-80) REVERT: B 556 GLN cc_start: 0.8347 (tt0) cc_final: 0.7944 (tp40) REVERT: B 560 MET cc_start: 0.8080 (tpp) cc_final: 0.7835 (tpp) REVERT: B 563 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.7629 (ttm-80) REVERT: B 583 ARG cc_start: 0.8562 (ptp-170) cc_final: 0.8070 (ptp-110) REVERT: B 592 VAL cc_start: 0.7671 (t) cc_final: 0.7230 (m) REVERT: B 601 GLN cc_start: 0.8572 (tt0) cc_final: 0.8232 (tt0) REVERT: B 622 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7035 (tm-30) REVERT: C 25 MET cc_start: 0.7720 (pmm) cc_final: 0.7187 (pmm) REVERT: C 29 MET cc_start: 0.9093 (tpp) cc_final: 0.8603 (mmm) REVERT: C 43 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8407 (mp0) REVERT: C 49 VAL cc_start: 0.8117 (t) cc_final: 0.7678 (m) REVERT: C 53 ASN cc_start: 0.8312 (m-40) cc_final: 0.7999 (m-40) REVERT: C 59 ARG cc_start: 0.8367 (mtp-110) cc_final: 0.7164 (mtp-110) REVERT: C 81 LYS cc_start: 0.8108 (ptpp) cc_final: 0.7887 (pptt) REVERT: C 87 GLU cc_start: 0.8334 (pt0) cc_final: 0.8094 (pt0) REVERT: C 91 LYS cc_start: 0.8688 (tppt) cc_final: 0.7710 (tppt) REVERT: C 94 LYS cc_start: 0.8742 (ttpt) cc_final: 0.8404 (ttpt) REVERT: C 95 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7599 (mt-10) REVERT: C 97 ARG cc_start: 0.8624 (mtm110) cc_final: 0.8313 (mtm110) REVERT: C 98 GLU cc_start: 0.7183 (tp30) cc_final: 0.6043 (tp30) REVERT: C 102 ASP cc_start: 0.7848 (m-30) cc_final: 0.6956 (m-30) REVERT: C 119 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7858 (tp30) REVERT: C 126 LYS cc_start: 0.8745 (tttm) cc_final: 0.8476 (tttm) REVERT: C 127 MET cc_start: 0.8369 (mmm) cc_final: 0.7705 (mmp) REVERT: C 130 ASP cc_start: 0.7739 (m-30) cc_final: 0.7511 (m-30) REVERT: C 133 ARG cc_start: 0.8695 (ttp-110) cc_final: 0.8353 (ttp80) REVERT: C 134 TYR cc_start: 0.8395 (m-10) cc_final: 0.7650 (m-10) REVERT: C 149 GLU cc_start: 0.8362 (tp30) cc_final: 0.8049 (tp30) REVERT: C 153 LYS cc_start: 0.8822 (tppt) cc_final: 0.8148 (tppt) REVERT: C 155 TYR cc_start: 0.7909 (m-10) cc_final: 0.7512 (m-80) REVERT: C 170 HIS cc_start: 0.8222 (t-90) cc_final: 0.7867 (t-90) REVERT: C 174 LEU cc_start: 0.8107 (mt) cc_final: 0.7749 (mt) REVERT: C 224 MET cc_start: 0.7368 (ptm) cc_final: 0.6462 (ptm) REVERT: C 225 GLN cc_start: 0.7470 (mm110) cc_final: 0.6668 (mm110) REVERT: D 7 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8206 (mm-30) REVERT: D 14 LYS cc_start: 0.8713 (mttt) cc_final: 0.8388 (mttt) REVERT: D 20 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7333 (tm-30) REVERT: D 25 MET cc_start: 0.7646 (pmm) cc_final: 0.7191 (pmm) REVERT: D 29 MET cc_start: 0.8937 (tpp) cc_final: 0.8595 (mmm) REVERT: D 34 GLU cc_start: 0.7971 (pp20) cc_final: 0.7674 (pp20) REVERT: D 43 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8514 (mt-10) REVERT: D 52 LYS cc_start: 0.8678 (tptm) cc_final: 0.8291 (tptm) REVERT: D 59 ARG cc_start: 0.8415 (mtp-110) cc_final: 0.7958 (mtp180) REVERT: D 65 ILE cc_start: 0.8769 (pt) cc_final: 0.8487 (pt) REVERT: D 66 SER cc_start: 0.8032 (m) cc_final: 0.7531 (m) REVERT: D 87 GLU cc_start: 0.8347 (pt0) cc_final: 0.8046 (pt0) REVERT: D 91 LYS cc_start: 0.8725 (tppt) cc_final: 0.7997 (tppt) REVERT: D 93 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8310 (mt-10) REVERT: D 94 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8721 (ttpt) REVERT: D 97 ARG cc_start: 0.8863 (mtm110) cc_final: 0.8489 (mtm110) REVERT: D 102 ASP cc_start: 0.7596 (m-30) cc_final: 0.7206 (m-30) REVERT: D 119 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7784 (tp30) REVERT: D 127 MET cc_start: 0.8402 (mmm) cc_final: 0.7777 (mmp) REVERT: D 130 ASP cc_start: 0.7663 (m-30) cc_final: 0.7406 (m-30) REVERT: D 132 TYR cc_start: 0.8444 (m-80) cc_final: 0.7323 (m-80) REVERT: D 150 ASP cc_start: 0.8201 (m-30) cc_final: 0.7946 (p0) REVERT: D 153 LYS cc_start: 0.8596 (tppt) cc_final: 0.7853 (tppt) REVERT: D 155 TYR cc_start: 0.7860 (m-10) cc_final: 0.7363 (m-80) REVERT: D 167 GLN cc_start: 0.8190 (tp-100) cc_final: 0.7990 (tp-100) REVERT: D 170 HIS cc_start: 0.8362 (t-90) cc_final: 0.7951 (t-90) REVERT: D 174 LEU cc_start: 0.8127 (mt) cc_final: 0.7843 (mt) REVERT: D 192 ASP cc_start: 0.8321 (p0) cc_final: 0.7873 (p0) REVERT: D 193 LYS cc_start: 0.8132 (mppt) cc_final: 0.7799 (mptt) REVERT: D 220 SER cc_start: 0.7367 (m) cc_final: 0.7108 (m) REVERT: D 224 MET cc_start: 0.7452 (ptm) cc_final: 0.6676 (ptm) REVERT: D 225 GLN cc_start: 0.7492 (mm110) cc_final: 0.6676 (mm110) REVERT: E 121 CYS cc_start: 0.7559 (m) cc_final: 0.7234 (m) REVERT: E 125 TYR cc_start: 0.7948 (m-80) cc_final: 0.6984 (m-80) REVERT: E 146 MET cc_start: 0.6853 (tpp) cc_final: 0.6509 (tpp) REVERT: E 168 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7704 (ttmm) REVERT: E 175 LYS cc_start: 0.8642 (ptmt) cc_final: 0.8121 (ptmt) REVERT: E 181 ARG cc_start: 0.8403 (tpm170) cc_final: 0.8052 (tpm170) REVERT: E 187 MET cc_start: 0.6250 (mtt) cc_final: 0.5516 (mtm) REVERT: E 189 ARG cc_start: 0.7970 (tpp-160) cc_final: 0.7502 (tpp80) REVERT: E 195 ASN cc_start: 0.7663 (t0) cc_final: 0.7449 (t0) REVERT: E 206 LEU cc_start: 0.6841 (tp) cc_final: 0.6407 (tp) REVERT: E 219 MET cc_start: 0.7850 (mtp) cc_final: 0.7517 (mtp) REVERT: E 227 ARG cc_start: 0.7569 (mtm180) cc_final: 0.7129 (mtp180) REVERT: E 236 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7755 (tm-30) REVERT: E 249 MET cc_start: 0.8307 (ppp) cc_final: 0.8043 (ppp) REVERT: E 253 LEU cc_start: 0.8777 (mt) cc_final: 0.8530 (mt) REVERT: E 256 MET cc_start: 0.7657 (ptm) cc_final: 0.7253 (ptm) REVERT: E 316 TYR cc_start: 0.8090 (t80) cc_final: 0.7604 (t80) REVERT: E 319 ASN cc_start: 0.8084 (t0) cc_final: 0.6903 (t0) REVERT: E 320 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7716 (mm-30) REVERT: E 333 GLU cc_start: 0.8663 (mt-10) cc_final: 0.7980 (mt-10) REVERT: E 334 PHE cc_start: 0.8519 (t80) cc_final: 0.8249 (t80) REVERT: E 344 LYS cc_start: 0.8491 (tttt) cc_final: 0.8086 (mttt) REVERT: E 356 MET cc_start: 0.6880 (ppp) cc_final: 0.6549 (ppp) REVERT: F 88 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8000 (mmmt) REVERT: F 96 ARG cc_start: 0.7591 (ptm160) cc_final: 0.7016 (ptm160) REVERT: F 125 TYR cc_start: 0.8077 (m-80) cc_final: 0.7212 (m-80) REVERT: F 146 MET cc_start: 0.6825 (tpp) cc_final: 0.6335 (tpp) REVERT: F 175 LYS cc_start: 0.8585 (ptmt) cc_final: 0.8078 (ptmt) REVERT: F 195 ASN cc_start: 0.7596 (t0) cc_final: 0.7172 (t0) REVERT: F 206 LEU cc_start: 0.6747 (tp) cc_final: 0.6372 (tp) REVERT: F 219 MET cc_start: 0.7748 (mtp) cc_final: 0.7454 (mtp) REVERT: F 227 ARG cc_start: 0.7582 (mtm180) cc_final: 0.7136 (mtm180) REVERT: F 236 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7886 (tm-30) REVERT: F 249 MET cc_start: 0.8316 (ppp) cc_final: 0.8063 (ppp) REVERT: F 256 MET cc_start: 0.7746 (ptm) cc_final: 0.7365 (ptm) REVERT: F 316 TYR cc_start: 0.8070 (t80) cc_final: 0.7489 (t80) REVERT: F 318 VAL cc_start: 0.8517 (p) cc_final: 0.8227 (m) REVERT: F 319 ASN cc_start: 0.7895 (t0) cc_final: 0.6643 (t0) REVERT: F 320 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7506 (mm-30) REVERT: F 330 PHE cc_start: 0.8224 (m-80) cc_final: 0.7981 (m-80) outliers start: 2 outliers final: 0 residues processed: 676 average time/residue: 0.1342 time to fit residues: 124.1911 Evaluate side-chains 670 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 670 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 64 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN D 200 GLN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.130304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.106599 restraints weight = 28769.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.110906 restraints weight = 15846.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.113956 restraints weight = 10198.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.116067 restraints weight = 7173.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.117613 restraints weight = 5407.802| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12876 Z= 0.179 Angle : 0.652 9.320 17364 Z= 0.348 Chirality : 0.045 0.206 1918 Planarity : 0.005 0.069 2216 Dihedral : 5.805 74.400 1740 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.07 % Allowed : 3.75 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.21), residues: 1538 helix: 0.49 (0.16), residues: 894 sheet: -2.97 (0.46), residues: 88 loop : -1.11 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 181 TYR 0.025 0.002 TYR B 532 PHE 0.019 0.002 PHE B 527 TRP 0.043 0.002 TRP B 368 HIS 0.013 0.001 HIS E 358 Details of bonding type rmsd covalent geometry : bond 0.00351 (12876) covalent geometry : angle 0.65222 (17364) hydrogen bonds : bond 0.04049 ( 710) hydrogen bonds : angle 4.87113 ( 2070) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 665 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.7539 (mtm) cc_final: 0.7110 (mtm) REVERT: A 367 LYS cc_start: 0.7543 (mmtt) cc_final: 0.6632 (mmtt) REVERT: A 368 TRP cc_start: 0.8495 (t60) cc_final: 0.8088 (t60) REVERT: A 387 PHE cc_start: 0.8122 (t80) cc_final: 0.7291 (t80) REVERT: A 391 ARG cc_start: 0.8331 (mmt90) cc_final: 0.7722 (mmm-85) REVERT: A 399 LYS cc_start: 0.8435 (mmtp) cc_final: 0.8044 (mmtp) REVERT: A 402 HIS cc_start: 0.7703 (t-90) cc_final: 0.7444 (t-90) REVERT: A 411 TYR cc_start: 0.7268 (p90) cc_final: 0.7031 (p90) REVERT: A 412 MET cc_start: 0.6209 (ppp) cc_final: 0.5621 (ppp) REVERT: A 414 LYS cc_start: 0.8260 (tppt) cc_final: 0.7910 (tppt) REVERT: A 416 ASN cc_start: 0.7514 (p0) cc_final: 0.7275 (p0) REVERT: A 417 LEU cc_start: 0.8127 (pt) cc_final: 0.7921 (pt) REVERT: A 425 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7040 (mm-30) REVERT: A 429 LEU cc_start: 0.8173 (tp) cc_final: 0.7901 (tp) REVERT: A 439 LYS cc_start: 0.8288 (mppt) cc_final: 0.7649 (mppt) REVERT: A 442 MET cc_start: 0.7457 (mpp) cc_final: 0.7077 (mpp) REVERT: A 445 LEU cc_start: 0.8723 (tp) cc_final: 0.8521 (tp) REVERT: A 446 ILE cc_start: 0.8671 (mt) cc_final: 0.8468 (mt) REVERT: A 450 ARG cc_start: 0.8379 (ttp-170) cc_final: 0.7869 (ptm-80) REVERT: A 456 MET cc_start: 0.8265 (mmm) cc_final: 0.7098 (mmm) REVERT: A 458 TYR cc_start: 0.8571 (t80) cc_final: 0.8086 (t80) REVERT: A 460 HIS cc_start: 0.8259 (m170) cc_final: 0.7836 (m170) REVERT: A 463 ASN cc_start: 0.7316 (m-40) cc_final: 0.7075 (m-40) REVERT: A 466 HIS cc_start: 0.8524 (t-90) cc_final: 0.8016 (t-90) REVERT: A 477 HIS cc_start: 0.6473 (t70) cc_final: 0.6199 (t-90) REVERT: A 512 MET cc_start: 0.6035 (ttm) cc_final: 0.5606 (ttm) REVERT: A 518 ARG cc_start: 0.8192 (ptp-110) cc_final: 0.7500 (ptp-110) REVERT: A 528 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7305 (mm-40) REVERT: A 532 TYR cc_start: 0.8011 (t80) cc_final: 0.7798 (t80) REVERT: A 534 TYR cc_start: 0.8501 (t80) cc_final: 0.8062 (t80) REVERT: A 541 LEU cc_start: 0.8762 (mt) cc_final: 0.8490 (mt) REVERT: A 542 MET cc_start: 0.7223 (mtp) cc_final: 0.6975 (mtp) REVERT: A 560 MET cc_start: 0.8372 (mmp) cc_final: 0.8071 (mmp) REVERT: A 563 ARG cc_start: 0.8727 (mmm-85) cc_final: 0.8122 (ttm-80) REVERT: A 572 LYS cc_start: 0.8128 (mmmm) cc_final: 0.7630 (mmmm) REVERT: A 581 MET cc_start: 0.7722 (mmm) cc_final: 0.7200 (mmm) REVERT: A 592 VAL cc_start: 0.7811 (t) cc_final: 0.7377 (m) REVERT: A 601 GLN cc_start: 0.8410 (tt0) cc_final: 0.8113 (tm-30) REVERT: A 622 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7354 (tm-30) REVERT: B 342 TRP cc_start: 0.8639 (m100) cc_final: 0.8117 (m100) REVERT: B 350 MET cc_start: 0.7470 (mtm) cc_final: 0.7017 (mtm) REVERT: B 367 LYS cc_start: 0.7659 (mmtt) cc_final: 0.6750 (mmtt) REVERT: B 383 THR cc_start: 0.8363 (p) cc_final: 0.7951 (p) REVERT: B 386 GLN cc_start: 0.8672 (mt0) cc_final: 0.8405 (mt0) REVERT: B 399 LYS cc_start: 0.8410 (mmtp) cc_final: 0.7882 (mmtp) REVERT: B 402 HIS cc_start: 0.7785 (t-90) cc_final: 0.7365 (t-90) REVERT: B 409 MET cc_start: 0.7462 (mtm) cc_final: 0.6724 (mtm) REVERT: B 412 MET cc_start: 0.6034 (ppp) cc_final: 0.5563 (ppp) REVERT: B 416 ASN cc_start: 0.7718 (p0) cc_final: 0.7472 (p0) REVERT: B 419 ILE cc_start: 0.7404 (mm) cc_final: 0.6993 (mm) REVERT: B 432 HIS cc_start: 0.7682 (m90) cc_final: 0.6793 (m90) REVERT: B 439 LYS cc_start: 0.8531 (mppt) cc_final: 0.8044 (mppt) REVERT: B 442 MET cc_start: 0.7417 (mpp) cc_final: 0.7152 (mpp) REVERT: B 450 ARG cc_start: 0.8504 (ttp-170) cc_final: 0.8000 (ttp-170) REVERT: B 456 MET cc_start: 0.8145 (mmm) cc_final: 0.7649 (mmm) REVERT: B 457 ASP cc_start: 0.7925 (t70) cc_final: 0.7692 (t70) REVERT: B 458 TYR cc_start: 0.8558 (t80) cc_final: 0.7637 (t80) REVERT: B 463 ASN cc_start: 0.7366 (m-40) cc_final: 0.7164 (m-40) REVERT: B 466 HIS cc_start: 0.8444 (t-90) cc_final: 0.7976 (t70) REVERT: B 470 LYS cc_start: 0.8481 (mtpt) cc_final: 0.8236 (mtpt) REVERT: B 484 ILE cc_start: 0.8023 (mt) cc_final: 0.7764 (mt) REVERT: B 511 TRP cc_start: 0.7447 (m-90) cc_final: 0.7138 (m-90) REVERT: B 512 MET cc_start: 0.5932 (ttm) cc_final: 0.5441 (ttm) REVERT: B 516 VAL cc_start: 0.8796 (t) cc_final: 0.8360 (t) REVERT: B 528 GLN cc_start: 0.7592 (mm-40) cc_final: 0.6890 (mm-40) REVERT: B 534 TYR cc_start: 0.8474 (t80) cc_final: 0.8117 (t80) REVERT: B 545 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7323 (mt-10) REVERT: B 551 ILE cc_start: 0.8742 (mp) cc_final: 0.8432 (mp) REVERT: B 554 ARG cc_start: 0.7453 (tmm-80) cc_final: 0.7099 (tmm-80) REVERT: B 560 MET cc_start: 0.8202 (tpp) cc_final: 0.7796 (tpp) REVERT: B 563 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.7914 (ttm-80) REVERT: B 567 SER cc_start: 0.7949 (t) cc_final: 0.7618 (t) REVERT: B 581 MET cc_start: 0.7933 (tpt) cc_final: 0.7660 (tpt) REVERT: B 601 GLN cc_start: 0.8591 (tt0) cc_final: 0.8268 (tt0) REVERT: B 610 GLN cc_start: 0.8502 (mm110) cc_final: 0.8159 (mm110) REVERT: C 9 LEU cc_start: 0.8213 (mt) cc_final: 0.8005 (mt) REVERT: C 25 MET cc_start: 0.7671 (pmm) cc_final: 0.7154 (pmm) REVERT: C 29 MET cc_start: 0.9096 (tpp) cc_final: 0.8605 (mmm) REVERT: C 49 VAL cc_start: 0.8175 (t) cc_final: 0.7736 (m) REVERT: C 53 ASN cc_start: 0.8348 (m-40) cc_final: 0.8029 (m-40) REVERT: C 69 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8287 (tm-30) REVERT: C 81 LYS cc_start: 0.8229 (ptpp) cc_final: 0.7983 (pptt) REVERT: C 84 MET cc_start: 0.7763 (ptp) cc_final: 0.7466 (ptp) REVERT: C 87 GLU cc_start: 0.8318 (pt0) cc_final: 0.8040 (pt0) REVERT: C 91 LYS cc_start: 0.8689 (tppt) cc_final: 0.7745 (tppt) REVERT: C 94 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8413 (ttpt) REVERT: C 95 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 97 ARG cc_start: 0.8618 (mtm110) cc_final: 0.8260 (mtm110) REVERT: C 98 GLU cc_start: 0.7184 (tp30) cc_final: 0.6016 (tp30) REVERT: C 102 ASP cc_start: 0.7883 (m-30) cc_final: 0.6973 (m-30) REVERT: C 119 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7849 (tp30) REVERT: C 126 LYS cc_start: 0.8713 (tttm) cc_final: 0.8369 (tttm) REVERT: C 127 MET cc_start: 0.8312 (mmm) cc_final: 0.7716 (mmp) REVERT: C 130 ASP cc_start: 0.7656 (m-30) cc_final: 0.7267 (m-30) REVERT: C 132 TYR cc_start: 0.8499 (m-80) cc_final: 0.7882 (m-80) REVERT: C 133 ARG cc_start: 0.8704 (ttp-110) cc_final: 0.8339 (ttp-110) REVERT: C 149 GLU cc_start: 0.8319 (tp30) cc_final: 0.8078 (tp30) REVERT: C 153 LYS cc_start: 0.8761 (tppt) cc_final: 0.8097 (tppt) REVERT: C 155 TYR cc_start: 0.7948 (m-10) cc_final: 0.7107 (m-80) REVERT: C 170 HIS cc_start: 0.8188 (t-90) cc_final: 0.7796 (t-90) REVERT: C 174 LEU cc_start: 0.8136 (mt) cc_final: 0.7780 (mt) REVERT: C 180 PHE cc_start: 0.8555 (m-80) cc_final: 0.7736 (m-80) REVERT: C 202 PHE cc_start: 0.9049 (t80) cc_final: 0.8806 (t80) REVERT: C 204 ASP cc_start: 0.8184 (t0) cc_final: 0.7911 (t0) REVERT: C 206 ILE cc_start: 0.8019 (mt) cc_final: 0.7772 (mt) REVERT: C 218 LYS cc_start: 0.7579 (mmpt) cc_final: 0.7344 (mmpt) REVERT: C 224 MET cc_start: 0.7404 (ptm) cc_final: 0.6555 (ptm) REVERT: C 225 GLN cc_start: 0.7478 (mm110) cc_final: 0.6678 (mm110) REVERT: D 7 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8181 (mm-30) REVERT: D 14 LYS cc_start: 0.8726 (mttt) cc_final: 0.8370 (mttm) REVERT: D 20 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7311 (tm-30) REVERT: D 25 MET cc_start: 0.7734 (pmm) cc_final: 0.7307 (pmm) REVERT: D 29 MET cc_start: 0.8960 (tpp) cc_final: 0.8577 (mmm) REVERT: D 30 LYS cc_start: 0.8027 (mtmt) cc_final: 0.7825 (mttt) REVERT: D 34 GLU cc_start: 0.8028 (pp20) cc_final: 0.7727 (pp20) REVERT: D 43 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8453 (mt-10) REVERT: D 52 LYS cc_start: 0.8632 (tptm) cc_final: 0.8278 (tptm) REVERT: D 59 ARG cc_start: 0.8396 (mtp-110) cc_final: 0.8003 (mtp180) REVERT: D 65 ILE cc_start: 0.8768 (pt) cc_final: 0.8500 (pt) REVERT: D 66 SER cc_start: 0.8046 (m) cc_final: 0.7577 (m) REVERT: D 84 MET cc_start: 0.7839 (ptp) cc_final: 0.7369 (ptp) REVERT: D 87 GLU cc_start: 0.8368 (pt0) cc_final: 0.8035 (pt0) REVERT: D 91 LYS cc_start: 0.8744 (tppt) cc_final: 0.7967 (tppt) REVERT: D 94 LYS cc_start: 0.8947 (ttpt) cc_final: 0.8745 (ttpt) REVERT: D 97 ARG cc_start: 0.8849 (mtm110) cc_final: 0.8506 (mtm110) REVERT: D 102 ASP cc_start: 0.7628 (m-30) cc_final: 0.7264 (m-30) REVERT: D 119 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7747 (tp30) REVERT: D 125 LEU cc_start: 0.8226 (mt) cc_final: 0.8006 (mt) REVERT: D 127 MET cc_start: 0.8356 (mmm) cc_final: 0.7710 (mmp) REVERT: D 130 ASP cc_start: 0.7756 (m-30) cc_final: 0.7231 (m-30) REVERT: D 133 ARG cc_start: 0.8835 (ttp-110) cc_final: 0.8335 (ttp-110) REVERT: D 153 LYS cc_start: 0.8560 (tppt) cc_final: 0.7823 (tppt) REVERT: D 155 TYR cc_start: 0.7936 (m-10) cc_final: 0.7064 (m-80) REVERT: D 167 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7952 (tp-100) REVERT: D 170 HIS cc_start: 0.8374 (t-90) cc_final: 0.7917 (t-90) REVERT: D 174 LEU cc_start: 0.8173 (mt) cc_final: 0.7918 (mt) REVERT: D 176 LEU cc_start: 0.8842 (tt) cc_final: 0.8007 (tt) REVERT: D 180 PHE cc_start: 0.8594 (m-80) cc_final: 0.7902 (m-80) REVERT: D 192 ASP cc_start: 0.8345 (p0) cc_final: 0.7674 (p0) REVERT: D 193 LYS cc_start: 0.8109 (mppt) cc_final: 0.7653 (mppt) REVERT: D 220 SER cc_start: 0.7317 (m) cc_final: 0.7051 (m) REVERT: D 224 MET cc_start: 0.7484 (ptm) cc_final: 0.6603 (ptm) REVERT: D 225 GLN cc_start: 0.7560 (mm110) cc_final: 0.6767 (mm110) REVERT: E 94 MET cc_start: 0.0177 (mmm) cc_final: -0.0125 (mmm) REVERT: E 96 ARG cc_start: 0.7464 (ptm160) cc_final: 0.7252 (ptm160) REVERT: E 121 CYS cc_start: 0.7654 (m) cc_final: 0.7300 (m) REVERT: E 125 TYR cc_start: 0.7990 (m-80) cc_final: 0.7045 (m-80) REVERT: E 142 CYS cc_start: 0.7009 (t) cc_final: 0.6783 (m) REVERT: E 146 MET cc_start: 0.6864 (tpp) cc_final: 0.6599 (tpp) REVERT: E 160 ARG cc_start: 0.7450 (mpp80) cc_final: 0.6635 (mpt-90) REVERT: E 168 LYS cc_start: 0.8260 (ttmm) cc_final: 0.7699 (ttmm) REVERT: E 175 LYS cc_start: 0.8688 (ptmt) cc_final: 0.8148 (ptmt) REVERT: E 187 MET cc_start: 0.6260 (mtt) cc_final: 0.5929 (mtm) REVERT: E 195 ASN cc_start: 0.7919 (t0) cc_final: 0.7692 (t0) REVERT: E 206 LEU cc_start: 0.6801 (tp) cc_final: 0.6263 (tp) REVERT: E 219 MET cc_start: 0.7886 (mtp) cc_final: 0.7530 (mtp) REVERT: E 227 ARG cc_start: 0.7594 (mtm180) cc_final: 0.7086 (mtm180) REVERT: E 233 GLU cc_start: 0.8489 (pt0) cc_final: 0.8281 (pt0) REVERT: E 249 MET cc_start: 0.8310 (ppp) cc_final: 0.8037 (ppp) REVERT: E 253 LEU cc_start: 0.8765 (mt) cc_final: 0.8540 (mt) REVERT: E 256 MET cc_start: 0.7687 (ptm) cc_final: 0.7292 (ptm) REVERT: E 316 TYR cc_start: 0.8044 (t80) cc_final: 0.7594 (t80) REVERT: E 319 ASN cc_start: 0.8106 (t0) cc_final: 0.6885 (t0) REVERT: E 320 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7734 (mm-30) REVERT: E 334 PHE cc_start: 0.8504 (t80) cc_final: 0.8228 (t80) REVERT: E 356 MET cc_start: 0.6863 (ppp) cc_final: 0.6372 (ppp) REVERT: E 360 PHE cc_start: 0.8344 (p90) cc_final: 0.8009 (p90) REVERT: E 362 LYS cc_start: 0.8849 (mptt) cc_final: 0.8553 (mptt) REVERT: F 88 LYS cc_start: 0.8488 (mmmt) cc_final: 0.7981 (mmmt) REVERT: F 96 ARG cc_start: 0.7551 (ptm160) cc_final: 0.6987 (ptm160) REVERT: F 110 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8238 (mp10) REVERT: F 125 TYR cc_start: 0.8052 (m-80) cc_final: 0.7249 (m-80) REVERT: F 175 LYS cc_start: 0.8653 (ptmt) cc_final: 0.8166 (ptmt) REVERT: F 219 MET cc_start: 0.7743 (mtp) cc_final: 0.7428 (mtp) REVERT: F 227 ARG cc_start: 0.7655 (mtm180) cc_final: 0.7178 (mtm180) REVERT: F 230 MET cc_start: 0.7617 (tpp) cc_final: 0.7325 (tpt) REVERT: F 249 MET cc_start: 0.8299 (ppp) cc_final: 0.8039 (ppp) REVERT: F 253 LEU cc_start: 0.8749 (mt) cc_final: 0.8543 (mt) REVERT: F 256 MET cc_start: 0.7767 (ptm) cc_final: 0.7390 (ptm) REVERT: F 316 TYR cc_start: 0.8042 (t80) cc_final: 0.7505 (t80) REVERT: F 318 VAL cc_start: 0.8473 (p) cc_final: 0.8163 (m) REVERT: F 319 ASN cc_start: 0.7947 (t0) cc_final: 0.6646 (t0) REVERT: F 320 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7574 (mm-30) REVERT: F 324 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7540 (mmtt) REVERT: F 333 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8292 (mt-10) REVERT: F 344 LYS cc_start: 0.8305 (tmmt) cc_final: 0.8093 (tmmt) outliers start: 1 outliers final: 0 residues processed: 665 average time/residue: 0.1405 time to fit residues: 128.3495 Evaluate side-chains 655 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.121869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.098947 restraints weight = 29306.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103200 restraints weight = 15860.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.106145 restraints weight = 9999.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.108305 restraints weight = 6953.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.109774 restraints weight = 5155.440| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 12876 Z= 0.279 Angle : 0.739 15.664 17364 Z= 0.396 Chirality : 0.047 0.174 1918 Planarity : 0.005 0.085 2216 Dihedral : 5.880 55.536 1740 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.20), residues: 1538 helix: 0.16 (0.16), residues: 896 sheet: -2.59 (0.53), residues: 68 loop : -1.17 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 181 TYR 0.024 0.002 TYR D 131 PHE 0.034 0.002 PHE C 180 TRP 0.047 0.003 TRP B 368 HIS 0.011 0.001 HIS E 358 Details of bonding type rmsd covalent geometry : bond 0.00505 (12876) covalent geometry : angle 0.73861 (17364) hydrogen bonds : bond 0.04416 ( 710) hydrogen bonds : angle 5.17518 ( 2070) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 672 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.7552 (mtm) cc_final: 0.7146 (mtm) REVERT: A 367 LYS cc_start: 0.7514 (mmtt) cc_final: 0.6758 (mmtt) REVERT: A 386 GLN cc_start: 0.8621 (mt0) cc_final: 0.8318 (mt0) REVERT: A 387 PHE cc_start: 0.8167 (t80) cc_final: 0.7264 (t80) REVERT: A 390 PHE cc_start: 0.8097 (t80) cc_final: 0.7561 (t80) REVERT: A 391 ARG cc_start: 0.8386 (mmt90) cc_final: 0.7728 (mmm-85) REVERT: A 399 LYS cc_start: 0.8410 (mmtp) cc_final: 0.8049 (mmtp) REVERT: A 402 HIS cc_start: 0.7609 (t-90) cc_final: 0.7381 (t-90) REVERT: A 412 MET cc_start: 0.6299 (ppp) cc_final: 0.5650 (ppp) REVERT: A 414 LYS cc_start: 0.8266 (tppt) cc_final: 0.7954 (tppt) REVERT: A 417 LEU cc_start: 0.8066 (pt) cc_final: 0.7568 (pt) REVERT: A 419 ILE cc_start: 0.7398 (mm) cc_final: 0.7068 (mm) REVERT: A 422 GLN cc_start: 0.8256 (tt0) cc_final: 0.7091 (pt0) REVERT: A 429 LEU cc_start: 0.8193 (tp) cc_final: 0.7941 (tp) REVERT: A 439 LYS cc_start: 0.8437 (mppt) cc_final: 0.7802 (mppt) REVERT: A 444 GLN cc_start: 0.7737 (mt0) cc_final: 0.7484 (mp10) REVERT: A 445 LEU cc_start: 0.8749 (tp) cc_final: 0.8530 (tp) REVERT: A 456 MET cc_start: 0.8239 (mmm) cc_final: 0.7094 (mmm) REVERT: A 457 ASP cc_start: 0.7953 (t0) cc_final: 0.7630 (t0) REVERT: A 458 TYR cc_start: 0.8574 (t80) cc_final: 0.8108 (t80) REVERT: A 460 HIS cc_start: 0.8478 (m170) cc_final: 0.7575 (m-70) REVERT: A 463 ASN cc_start: 0.7264 (m-40) cc_final: 0.7023 (m-40) REVERT: A 466 HIS cc_start: 0.8498 (t-90) cc_final: 0.8042 (t-90) REVERT: A 470 LYS cc_start: 0.8462 (mtpt) cc_final: 0.7986 (mtpt) REVERT: A 477 HIS cc_start: 0.6490 (t70) cc_final: 0.6185 (t-90) REVERT: A 484 ILE cc_start: 0.7916 (mt) cc_final: 0.7505 (mt) REVERT: A 512 MET cc_start: 0.6267 (ttm) cc_final: 0.5524 (ttm) REVERT: A 517 ILE cc_start: 0.8645 (mt) cc_final: 0.8210 (mt) REVERT: A 518 ARG cc_start: 0.8315 (ptp-110) cc_final: 0.7660 (ptp-110) REVERT: A 528 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7184 (mm-40) REVERT: A 532 TYR cc_start: 0.8150 (t80) cc_final: 0.7874 (t80) REVERT: A 534 TYR cc_start: 0.8536 (t80) cc_final: 0.8096 (t80) REVERT: A 541 LEU cc_start: 0.8701 (mt) cc_final: 0.8344 (mt) REVERT: A 545 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7366 (mt-10) REVERT: A 556 GLN cc_start: 0.8447 (tt0) cc_final: 0.7603 (tt0) REVERT: A 560 MET cc_start: 0.8455 (mmp) cc_final: 0.7693 (mmp) REVERT: A 563 ARG cc_start: 0.8760 (mmm-85) cc_final: 0.8118 (ttm-80) REVERT: A 572 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7757 (mmmm) REVERT: A 574 TYR cc_start: 0.7737 (m-10) cc_final: 0.7350 (m-10) REVERT: A 576 ASN cc_start: 0.7876 (t0) cc_final: 0.7344 (t0) REVERT: A 581 MET cc_start: 0.7815 (mmm) cc_final: 0.7235 (mmm) REVERT: A 591 LYS cc_start: 0.8681 (ptpp) cc_final: 0.8474 (ptpp) REVERT: A 592 VAL cc_start: 0.7827 (t) cc_final: 0.7346 (m) REVERT: A 601 GLN cc_start: 0.8399 (tt0) cc_final: 0.8118 (tm-30) REVERT: A 622 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7118 (tm-30) REVERT: B 342 TRP cc_start: 0.8573 (m100) cc_final: 0.8188 (m100) REVERT: B 345 GLU cc_start: 0.7032 (mp0) cc_final: 0.6517 (mp0) REVERT: B 350 MET cc_start: 0.7477 (mtm) cc_final: 0.7037 (mtm) REVERT: B 362 THR cc_start: 0.7811 (m) cc_final: 0.7595 (m) REVERT: B 367 LYS cc_start: 0.7663 (mmtt) cc_final: 0.6846 (mmtt) REVERT: B 383 THR cc_start: 0.8337 (p) cc_final: 0.7916 (p) REVERT: B 385 GLU cc_start: 0.9068 (pm20) cc_final: 0.8843 (pm20) REVERT: B 386 GLN cc_start: 0.8642 (mt0) cc_final: 0.8344 (mt0) REVERT: B 387 PHE cc_start: 0.8260 (t80) cc_final: 0.7988 (t80) REVERT: B 393 GLU cc_start: 0.8100 (tp30) cc_final: 0.7486 (tp30) REVERT: B 399 LYS cc_start: 0.8466 (mmtp) cc_final: 0.7970 (mmtp) REVERT: B 402 HIS cc_start: 0.7706 (t-90) cc_final: 0.7132 (t-90) REVERT: B 409 MET cc_start: 0.7470 (mtm) cc_final: 0.6779 (mtm) REVERT: B 412 MET cc_start: 0.6125 (ppp) cc_final: 0.5594 (ppp) REVERT: B 414 LYS cc_start: 0.8344 (tppt) cc_final: 0.8079 (tptp) REVERT: B 416 ASN cc_start: 0.7783 (p0) cc_final: 0.7532 (p0) REVERT: B 419 ILE cc_start: 0.7423 (mm) cc_final: 0.7066 (mm) REVERT: B 422 GLN cc_start: 0.8237 (tt0) cc_final: 0.7390 (pt0) REVERT: B 425 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6977 (mm-30) REVERT: B 429 LEU cc_start: 0.8366 (tp) cc_final: 0.8160 (tp) REVERT: B 431 LYS cc_start: 0.8329 (mptt) cc_final: 0.8040 (mptt) REVERT: B 439 LYS cc_start: 0.8669 (mppt) cc_final: 0.8223 (mppt) REVERT: B 442 MET cc_start: 0.7591 (mpp) cc_final: 0.7153 (mpp) REVERT: B 456 MET cc_start: 0.8071 (mmm) cc_final: 0.6994 (mmm) REVERT: B 457 ASP cc_start: 0.7918 (t70) cc_final: 0.7635 (t70) REVERT: B 458 TYR cc_start: 0.8563 (t80) cc_final: 0.7573 (t80) REVERT: B 460 HIS cc_start: 0.8144 (m170) cc_final: 0.7269 (m-70) REVERT: B 463 ASN cc_start: 0.7377 (m-40) cc_final: 0.7080 (m-40) REVERT: B 466 HIS cc_start: 0.8457 (t-90) cc_final: 0.8032 (t-90) REVERT: B 470 LYS cc_start: 0.8415 (mtpt) cc_final: 0.7642 (mtpt) REVERT: B 483 LYS cc_start: 0.8272 (mttp) cc_final: 0.7424 (mttp) REVERT: B 484 ILE cc_start: 0.7928 (mt) cc_final: 0.7719 (mt) REVERT: B 511 TRP cc_start: 0.7527 (m-90) cc_final: 0.7112 (m-90) REVERT: B 512 MET cc_start: 0.6148 (ttm) cc_final: 0.5608 (ttm) REVERT: B 517 ILE cc_start: 0.8626 (mt) cc_final: 0.8168 (mt) REVERT: B 518 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7416 (mtm-85) REVERT: B 528 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7120 (mm-40) REVERT: B 534 TYR cc_start: 0.8478 (t80) cc_final: 0.8126 (t80) REVERT: B 541 LEU cc_start: 0.8795 (mt) cc_final: 0.8416 (mt) REVERT: B 545 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7293 (mt-10) REVERT: B 551 ILE cc_start: 0.8716 (mp) cc_final: 0.8410 (mp) REVERT: B 554 ARG cc_start: 0.7507 (tmm-80) cc_final: 0.7141 (tmm-80) REVERT: B 560 MET cc_start: 0.8357 (tpp) cc_final: 0.7658 (tpp) REVERT: B 563 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.7731 (ttm-80) REVERT: B 572 LYS cc_start: 0.8409 (mmmm) cc_final: 0.8028 (mmmm) REVERT: B 574 TYR cc_start: 0.8219 (m-10) cc_final: 0.7532 (m-10) REVERT: B 583 ARG cc_start: 0.8535 (ptp-170) cc_final: 0.8067 (ptp-110) REVERT: B 594 GLU cc_start: 0.8042 (pm20) cc_final: 0.7644 (pm20) REVERT: B 601 GLN cc_start: 0.8599 (tt0) cc_final: 0.8327 (tt0) REVERT: B 622 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7017 (tm-30) REVERT: C 9 LEU cc_start: 0.8214 (mt) cc_final: 0.8013 (mt) REVERT: C 12 ARG cc_start: 0.8899 (ttt180) cc_final: 0.8677 (ttt180) REVERT: C 25 MET cc_start: 0.7662 (pmm) cc_final: 0.7143 (pmm) REVERT: C 29 MET cc_start: 0.9096 (tpp) cc_final: 0.8605 (mmm) REVERT: C 42 GLU cc_start: 0.8035 (pm20) cc_final: 0.7809 (pm20) REVERT: C 43 GLU cc_start: 0.8723 (mt-10) cc_final: 0.7806 (mt-10) REVERT: C 52 LYS cc_start: 0.8650 (tttm) cc_final: 0.8321 (tttm) REVERT: C 53 ASN cc_start: 0.8331 (m-40) cc_final: 0.7986 (m-40) REVERT: C 59 ARG cc_start: 0.8203 (mtp-110) cc_final: 0.7466 (mtp-110) REVERT: C 69 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8305 (tm-30) REVERT: C 84 MET cc_start: 0.7809 (ptp) cc_final: 0.7511 (ptp) REVERT: C 87 GLU cc_start: 0.8305 (pt0) cc_final: 0.8009 (pt0) REVERT: C 91 LYS cc_start: 0.8739 (tppt) cc_final: 0.7876 (tppt) REVERT: C 95 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7727 (mt-10) REVERT: C 97 ARG cc_start: 0.8570 (mtm110) cc_final: 0.8316 (mtm110) REVERT: C 98 GLU cc_start: 0.7406 (tp30) cc_final: 0.6213 (tp30) REVERT: C 102 ASP cc_start: 0.8050 (m-30) cc_final: 0.7103 (m-30) REVERT: C 119 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7893 (tp30) REVERT: C 125 LEU cc_start: 0.8393 (mt) cc_final: 0.8172 (mt) REVERT: C 126 LYS cc_start: 0.8757 (tttm) cc_final: 0.8381 (tttm) REVERT: C 127 MET cc_start: 0.8344 (mmm) cc_final: 0.7717 (mmp) REVERT: C 130 ASP cc_start: 0.7639 (m-30) cc_final: 0.6873 (m-30) REVERT: C 132 TYR cc_start: 0.8662 (m-80) cc_final: 0.8043 (m-80) REVERT: C 133 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.7956 (ttp80) REVERT: C 134 TYR cc_start: 0.8392 (m-10) cc_final: 0.7637 (m-80) REVERT: C 149 GLU cc_start: 0.8393 (tp30) cc_final: 0.8162 (tp30) REVERT: C 153 LYS cc_start: 0.8791 (tppt) cc_final: 0.8136 (tppt) REVERT: C 155 TYR cc_start: 0.8040 (m-10) cc_final: 0.7366 (m-80) REVERT: C 170 HIS cc_start: 0.8251 (t-90) cc_final: 0.7814 (t-90) REVERT: C 174 LEU cc_start: 0.8170 (mt) cc_final: 0.7843 (mt) REVERT: C 176 LEU cc_start: 0.8703 (tt) cc_final: 0.8325 (tt) REVERT: C 180 PHE cc_start: 0.8715 (m-80) cc_final: 0.7851 (m-80) REVERT: C 197 LEU cc_start: 0.8506 (mm) cc_final: 0.8254 (mm) REVERT: C 202 PHE cc_start: 0.9086 (t80) cc_final: 0.8833 (t80) REVERT: C 206 ILE cc_start: 0.8025 (mt) cc_final: 0.7797 (mt) REVERT: C 218 LYS cc_start: 0.7596 (mmpt) cc_final: 0.7334 (mmpt) REVERT: C 224 MET cc_start: 0.7493 (ptm) cc_final: 0.6543 (ptm) REVERT: C 225 GLN cc_start: 0.7443 (mm110) cc_final: 0.6635 (mm110) REVERT: D 7 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8186 (mm-30) REVERT: D 9 LEU cc_start: 0.7985 (mt) cc_final: 0.7768 (mt) REVERT: D 14 LYS cc_start: 0.8801 (mttt) cc_final: 0.8409 (mttm) REVERT: D 20 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7457 (tm-30) REVERT: D 25 MET cc_start: 0.7723 (pmm) cc_final: 0.7334 (pmm) REVERT: D 29 MET cc_start: 0.8942 (tpp) cc_final: 0.8501 (mmm) REVERT: D 30 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7945 (mttt) REVERT: D 34 GLU cc_start: 0.8111 (pp20) cc_final: 0.7809 (pp20) REVERT: D 43 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8489 (mt-10) REVERT: D 52 LYS cc_start: 0.8673 (tptm) cc_final: 0.8292 (tptm) REVERT: D 59 ARG cc_start: 0.8398 (mtp-110) cc_final: 0.8046 (mtp180) REVERT: D 63 ARG cc_start: 0.8224 (tpp-160) cc_final: 0.7798 (tpp-160) REVERT: D 65 ILE cc_start: 0.8774 (pt) cc_final: 0.8526 (pt) REVERT: D 66 SER cc_start: 0.8047 (m) cc_final: 0.7522 (m) REVERT: D 84 MET cc_start: 0.7808 (ptp) cc_final: 0.7327 (ptp) REVERT: D 87 GLU cc_start: 0.8366 (pt0) cc_final: 0.8037 (pt0) REVERT: D 91 LYS cc_start: 0.8788 (tppt) cc_final: 0.8075 (tppt) REVERT: D 93 GLU cc_start: 0.8526 (tt0) cc_final: 0.8230 (tt0) REVERT: D 97 ARG cc_start: 0.8704 (mtm110) cc_final: 0.8466 (mtm110) REVERT: D 102 ASP cc_start: 0.7832 (m-30) cc_final: 0.7480 (m-30) REVERT: D 119 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7823 (tp30) REVERT: D 127 MET cc_start: 0.8349 (mmm) cc_final: 0.7705 (mmp) REVERT: D 128 LYS cc_start: 0.8118 (tttt) cc_final: 0.7740 (tttt) REVERT: D 130 ASP cc_start: 0.7582 (m-30) cc_final: 0.7286 (m-30) REVERT: D 133 ARG cc_start: 0.8655 (ttp-110) cc_final: 0.8272 (ttp-110) REVERT: D 153 LYS cc_start: 0.8565 (tppt) cc_final: 0.7785 (tppt) REVERT: D 155 TYR cc_start: 0.8129 (m-10) cc_final: 0.7194 (m-80) REVERT: D 170 HIS cc_start: 0.8353 (t-90) cc_final: 0.7901 (t-90) REVERT: D 174 LEU cc_start: 0.8297 (mt) cc_final: 0.8040 (mt) REVERT: D 176 LEU cc_start: 0.8862 (tt) cc_final: 0.7889 (tt) REVERT: D 180 PHE cc_start: 0.8669 (m-80) cc_final: 0.7892 (m-80) REVERT: D 192 ASP cc_start: 0.8403 (p0) cc_final: 0.7612 (p0) REVERT: D 193 LYS cc_start: 0.8199 (mppt) cc_final: 0.7746 (mppt) REVERT: D 220 SER cc_start: 0.7397 (m) cc_final: 0.7144 (m) REVERT: D 224 MET cc_start: 0.7764 (ptm) cc_final: 0.6729 (ptm) REVERT: D 225 GLN cc_start: 0.7619 (mm110) cc_final: 0.6860 (mm110) REVERT: E 96 ARG cc_start: 0.7576 (ptm160) cc_final: 0.7128 (ptm160) REVERT: E 121 CYS cc_start: 0.7405 (m) cc_final: 0.6990 (m) REVERT: E 125 TYR cc_start: 0.8037 (m-80) cc_final: 0.7261 (m-80) REVERT: E 160 ARG cc_start: 0.7343 (mpp80) cc_final: 0.6683 (mpt-90) REVERT: E 175 LYS cc_start: 0.8775 (ptmt) cc_final: 0.8257 (ptmt) REVERT: E 187 MET cc_start: 0.6008 (mtt) cc_final: 0.5798 (mtm) REVERT: E 195 ASN cc_start: 0.8085 (t0) cc_final: 0.7780 (t0) REVERT: E 206 LEU cc_start: 0.6787 (tp) cc_final: 0.6221 (tp) REVERT: E 219 MET cc_start: 0.7894 (mtp) cc_final: 0.7553 (mtp) REVERT: E 227 ARG cc_start: 0.7702 (mtm180) cc_final: 0.7115 (mtm180) REVERT: E 230 MET cc_start: 0.7779 (tpt) cc_final: 0.7406 (tpt) REVERT: E 233 GLU cc_start: 0.8489 (pt0) cc_final: 0.8248 (pt0) REVERT: E 234 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7323 (ttm-80) REVERT: E 235 LEU cc_start: 0.8768 (mt) cc_final: 0.8513 (mt) REVERT: E 249 MET cc_start: 0.8374 (ppp) cc_final: 0.8104 (ppp) REVERT: E 253 LEU cc_start: 0.8784 (mt) cc_final: 0.8528 (mt) REVERT: E 256 MET cc_start: 0.7745 (ptm) cc_final: 0.7387 (ptm) REVERT: E 316 TYR cc_start: 0.8040 (t80) cc_final: 0.7590 (t80) REVERT: E 319 ASN cc_start: 0.8144 (t0) cc_final: 0.6887 (t0) REVERT: E 320 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7750 (mm-30) REVERT: E 324 LYS cc_start: 0.8078 (mmtt) cc_final: 0.7658 (mmtt) REVERT: E 334 PHE cc_start: 0.8503 (t80) cc_final: 0.8241 (t80) REVERT: E 344 LYS cc_start: 0.8566 (tmmt) cc_final: 0.8227 (mttt) REVERT: E 356 MET cc_start: 0.6964 (ppp) cc_final: 0.6618 (ppp) REVERT: E 360 PHE cc_start: 0.8400 (p90) cc_final: 0.8048 (p90) REVERT: F 88 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8014 (mmmt) REVERT: F 125 TYR cc_start: 0.8117 (m-80) cc_final: 0.7434 (m-80) REVERT: F 175 LYS cc_start: 0.8757 (ptmt) cc_final: 0.8268 (ptmt) REVERT: F 195 ASN cc_start: 0.8225 (m110) cc_final: 0.7440 (t0) REVERT: F 219 MET cc_start: 0.7732 (mtp) cc_final: 0.7515 (mtp) REVERT: F 227 ARG cc_start: 0.7778 (mtm180) cc_final: 0.7240 (mtm180) REVERT: F 230 MET cc_start: 0.7649 (tpp) cc_final: 0.7416 (tpt) REVERT: F 249 MET cc_start: 0.8404 (ppp) cc_final: 0.8105 (ppp) REVERT: F 253 LEU cc_start: 0.8732 (mt) cc_final: 0.8518 (mt) REVERT: F 256 MET cc_start: 0.7856 (ptm) cc_final: 0.7523 (ptm) REVERT: F 316 TYR cc_start: 0.8015 (t80) cc_final: 0.7488 (t80) REVERT: F 319 ASN cc_start: 0.7969 (t0) cc_final: 0.6614 (t0) REVERT: F 320 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7627 (mm-30) REVERT: F 324 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7534 (mmtt) REVERT: F 333 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8343 (mt-10) REVERT: F 344 LYS cc_start: 0.8368 (tmmt) cc_final: 0.8129 (tmmt) outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 0.1440 time to fit residues: 132.0323 Evaluate side-chains 669 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 669 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 47 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 146 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 34 optimal weight: 0.4980 chunk 116 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS C 200 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.133948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.108402 restraints weight = 27756.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.112682 restraints weight = 15108.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.115794 restraints weight = 9812.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.117993 restraints weight = 7021.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.119582 restraints weight = 5402.769| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12876 Z= 0.146 Angle : 0.679 15.549 17364 Z= 0.348 Chirality : 0.046 0.247 1918 Planarity : 0.005 0.060 2216 Dihedral : 5.620 44.866 1740 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.21), residues: 1538 helix: 0.39 (0.16), residues: 894 sheet: -2.17 (0.53), residues: 80 loop : -1.10 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 181 TYR 0.023 0.002 TYR B 532 PHE 0.027 0.002 PHE E 371 TRP 0.047 0.003 TRP B 368 HIS 0.011 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00314 (12876) covalent geometry : angle 0.67893 (17364) hydrogen bonds : bond 0.03912 ( 710) hydrogen bonds : angle 4.83267 ( 2070) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 674 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.7498 (mtm) cc_final: 0.7069 (mtm) REVERT: A 359 SER cc_start: 0.8246 (m) cc_final: 0.7825 (p) REVERT: A 367 LYS cc_start: 0.7575 (mmtt) cc_final: 0.6732 (mmtt) REVERT: A 387 PHE cc_start: 0.8137 (t80) cc_final: 0.7204 (t80) REVERT: A 390 PHE cc_start: 0.8070 (t80) cc_final: 0.7456 (t80) REVERT: A 391 ARG cc_start: 0.8357 (mmt90) cc_final: 0.7709 (mmm-85) REVERT: A 393 GLU cc_start: 0.8041 (tp30) cc_final: 0.7647 (tp30) REVERT: A 399 LYS cc_start: 0.8364 (mmtp) cc_final: 0.7954 (mmtp) REVERT: A 412 MET cc_start: 0.6310 (ppp) cc_final: 0.5615 (ppp) REVERT: A 417 LEU cc_start: 0.8067 (pt) cc_final: 0.7605 (pt) REVERT: A 419 ILE cc_start: 0.7282 (mm) cc_final: 0.6884 (mm) REVERT: A 422 GLN cc_start: 0.8164 (tt0) cc_final: 0.7011 (pm20) REVERT: A 425 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6990 (mm-30) REVERT: A 439 LYS cc_start: 0.8312 (mppt) cc_final: 0.7724 (mppt) REVERT: A 444 GLN cc_start: 0.7766 (mt0) cc_final: 0.7501 (mp10) REVERT: A 445 LEU cc_start: 0.8753 (tp) cc_final: 0.8551 (tp) REVERT: A 446 ILE cc_start: 0.8665 (mt) cc_final: 0.8458 (mt) REVERT: A 450 ARG cc_start: 0.8322 (ttp-170) cc_final: 0.7836 (ptm-80) REVERT: A 456 MET cc_start: 0.8301 (mmm) cc_final: 0.7038 (mmm) REVERT: A 457 ASP cc_start: 0.8012 (t0) cc_final: 0.7532 (t0) REVERT: A 458 TYR cc_start: 0.8543 (t80) cc_final: 0.7988 (t80) REVERT: A 460 HIS cc_start: 0.8234 (m170) cc_final: 0.7647 (m170) REVERT: A 463 ASN cc_start: 0.7252 (m-40) cc_final: 0.7038 (m-40) REVERT: A 466 HIS cc_start: 0.8539 (t-90) cc_final: 0.8102 (t-90) REVERT: A 470 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8048 (mtpt) REVERT: A 477 HIS cc_start: 0.6468 (t70) cc_final: 0.6221 (t-90) REVERT: A 483 LYS cc_start: 0.8185 (mttt) cc_final: 0.7968 (mttt) REVERT: A 484 ILE cc_start: 0.7973 (mt) cc_final: 0.7718 (mt) REVERT: A 512 MET cc_start: 0.6098 (ttm) cc_final: 0.5564 (ttm) REVERT: A 518 ARG cc_start: 0.8207 (ptp-110) cc_final: 0.7536 (ptp-110) REVERT: A 528 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7128 (mm-40) REVERT: A 534 TYR cc_start: 0.8434 (t80) cc_final: 0.7917 (t80) REVERT: A 541 LEU cc_start: 0.8686 (mt) cc_final: 0.8286 (mt) REVERT: A 545 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7396 (mt-10) REVERT: A 551 ILE cc_start: 0.8852 (mp) cc_final: 0.8652 (mp) REVERT: A 556 GLN cc_start: 0.8347 (tt0) cc_final: 0.7409 (tt0) REVERT: A 559 PHE cc_start: 0.8613 (t80) cc_final: 0.7612 (t80) REVERT: A 560 MET cc_start: 0.8388 (mmp) cc_final: 0.7531 (mmp) REVERT: A 563 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.8251 (ttm-80) REVERT: A 572 LYS cc_start: 0.8233 (mmmm) cc_final: 0.7740 (mmmm) REVERT: A 574 TYR cc_start: 0.7797 (m-10) cc_final: 0.7374 (m-10) REVERT: A 581 MET cc_start: 0.7778 (mmm) cc_final: 0.7204 (mmm) REVERT: A 591 LYS cc_start: 0.8682 (ptpp) cc_final: 0.8475 (ptpp) REVERT: A 592 VAL cc_start: 0.7776 (t) cc_final: 0.7305 (m) REVERT: A 601 GLN cc_start: 0.8375 (tt0) cc_final: 0.8076 (tm-30) REVERT: A 622 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7201 (tm-30) REVERT: B 342 TRP cc_start: 0.8598 (m100) cc_final: 0.8090 (m100) REVERT: B 345 GLU cc_start: 0.7044 (mp0) cc_final: 0.6518 (mp0) REVERT: B 350 MET cc_start: 0.7468 (mtm) cc_final: 0.6975 (mtm) REVERT: B 362 THR cc_start: 0.7862 (m) cc_final: 0.7610 (m) REVERT: B 367 LYS cc_start: 0.7724 (mmtt) cc_final: 0.6841 (mmtt) REVERT: B 376 ILE cc_start: 0.7351 (tp) cc_final: 0.7067 (tp) REVERT: B 383 THR cc_start: 0.8336 (p) cc_final: 0.8001 (p) REVERT: B 386 GLN cc_start: 0.8654 (mt0) cc_final: 0.8358 (mt0) REVERT: B 387 PHE cc_start: 0.8249 (t80) cc_final: 0.7971 (t80) REVERT: B 393 GLU cc_start: 0.8102 (tp30) cc_final: 0.7491 (tp30) REVERT: B 399 LYS cc_start: 0.8388 (mmtp) cc_final: 0.7847 (mmtp) REVERT: B 402 HIS cc_start: 0.7792 (t-90) cc_final: 0.7317 (t-90) REVERT: B 409 MET cc_start: 0.7320 (mtm) cc_final: 0.6859 (mtm) REVERT: B 412 MET cc_start: 0.6242 (ppp) cc_final: 0.5672 (ppp) REVERT: B 416 ASN cc_start: 0.7727 (p0) cc_final: 0.7502 (p0) REVERT: B 417 LEU cc_start: 0.8266 (pt) cc_final: 0.8047 (pt) REVERT: B 422 GLN cc_start: 0.8178 (tt0) cc_final: 0.7362 (pt0) REVERT: B 425 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6899 (mm-30) REVERT: B 431 LYS cc_start: 0.8313 (mptt) cc_final: 0.8022 (mptt) REVERT: B 439 LYS cc_start: 0.8555 (mppt) cc_final: 0.8062 (mppt) REVERT: B 457 ASP cc_start: 0.7870 (t70) cc_final: 0.7567 (t70) REVERT: B 458 TYR cc_start: 0.8552 (t80) cc_final: 0.7645 (t80) REVERT: B 466 HIS cc_start: 0.8565 (t-90) cc_final: 0.8153 (t-90) REVERT: B 483 LYS cc_start: 0.8261 (mttp) cc_final: 0.7456 (mttp) REVERT: B 484 ILE cc_start: 0.7920 (mt) cc_final: 0.7608 (mt) REVERT: B 492 VAL cc_start: 0.7846 (t) cc_final: 0.7513 (m) REVERT: B 511 TRP cc_start: 0.7346 (m-90) cc_final: 0.7091 (m-90) REVERT: B 512 MET cc_start: 0.6106 (ttm) cc_final: 0.5673 (ttm) REVERT: B 518 ARG cc_start: 0.7701 (mtm-85) cc_final: 0.7270 (mtm-85) REVERT: B 528 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7081 (mm-40) REVERT: B 534 TYR cc_start: 0.8474 (t80) cc_final: 0.8085 (t80) REVERT: B 536 ILE cc_start: 0.8552 (mm) cc_final: 0.8246 (mm) REVERT: B 541 LEU cc_start: 0.8692 (mt) cc_final: 0.8280 (mt) REVERT: B 542 MET cc_start: 0.7468 (mtp) cc_final: 0.7009 (mtp) REVERT: B 545 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7288 (mt-10) REVERT: B 551 ILE cc_start: 0.8765 (mp) cc_final: 0.8411 (mp) REVERT: B 554 ARG cc_start: 0.7486 (tmm-80) cc_final: 0.7159 (tmm-80) REVERT: B 560 MET cc_start: 0.8250 (tpp) cc_final: 0.7549 (tpp) REVERT: B 563 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.7711 (ttm-80) REVERT: B 572 LYS cc_start: 0.8391 (mmmm) cc_final: 0.7986 (mmmm) REVERT: B 574 TYR cc_start: 0.7994 (m-10) cc_final: 0.7534 (m-10) REVERT: B 583 ARG cc_start: 0.8558 (ptp-170) cc_final: 0.8081 (ptp-110) REVERT: B 591 LYS cc_start: 0.8681 (ptpp) cc_final: 0.8479 (ptpp) REVERT: B 594 GLU cc_start: 0.8022 (pm20) cc_final: 0.7685 (pm20) REVERT: B 601 GLN cc_start: 0.8551 (tt0) cc_final: 0.8251 (tt0) REVERT: B 618 ARG cc_start: 0.7778 (ptm160) cc_final: 0.7489 (ptm160) REVERT: B 622 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7024 (tm-30) REVERT: C 10 VAL cc_start: 0.8857 (t) cc_final: 0.8484 (t) REVERT: C 14 LYS cc_start: 0.8665 (mttt) cc_final: 0.8291 (mtmm) REVERT: C 25 MET cc_start: 0.7652 (pmm) cc_final: 0.7134 (pmm) REVERT: C 29 MET cc_start: 0.9098 (tpp) cc_final: 0.8617 (mmm) REVERT: C 43 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8214 (mt-10) REVERT: C 52 LYS cc_start: 0.8631 (tttm) cc_final: 0.8307 (tttm) REVERT: C 59 ARG cc_start: 0.8168 (mtp-110) cc_final: 0.7964 (mtp-110) REVERT: C 69 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8347 (tm-30) REVERT: C 81 LYS cc_start: 0.8269 (ptpp) cc_final: 0.7979 (pptt) REVERT: C 84 MET cc_start: 0.7658 (ptp) cc_final: 0.7367 (ptp) REVERT: C 87 GLU cc_start: 0.8272 (pt0) cc_final: 0.7973 (pt0) REVERT: C 91 LYS cc_start: 0.8674 (tppt) cc_final: 0.7699 (tppt) REVERT: C 94 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8375 (ttpt) REVERT: C 95 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7680 (mt-10) REVERT: C 97 ARG cc_start: 0.8659 (mtm110) cc_final: 0.8261 (mtm110) REVERT: C 98 GLU cc_start: 0.7307 (tp30) cc_final: 0.6097 (tp30) REVERT: C 102 ASP cc_start: 0.8003 (m-30) cc_final: 0.7076 (m-30) REVERT: C 119 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8090 (mm-30) REVERT: C 125 LEU cc_start: 0.8242 (mt) cc_final: 0.7995 (mt) REVERT: C 126 LYS cc_start: 0.8744 (tttm) cc_final: 0.8393 (tttm) REVERT: C 127 MET cc_start: 0.8173 (mmm) cc_final: 0.7568 (mmp) REVERT: C 130 ASP cc_start: 0.7715 (m-30) cc_final: 0.7457 (m-30) REVERT: C 132 TYR cc_start: 0.8491 (m-80) cc_final: 0.7912 (m-80) REVERT: C 135 LEU cc_start: 0.8635 (mt) cc_final: 0.8382 (mt) REVERT: C 153 LYS cc_start: 0.8666 (tppt) cc_final: 0.7985 (tppt) REVERT: C 155 TYR cc_start: 0.7791 (m-10) cc_final: 0.7384 (m-80) REVERT: C 170 HIS cc_start: 0.8174 (t-90) cc_final: 0.7794 (t-90) REVERT: C 174 LEU cc_start: 0.8108 (mt) cc_final: 0.7787 (mt) REVERT: C 180 PHE cc_start: 0.8644 (m-80) cc_final: 0.7641 (m-80) REVERT: C 202 PHE cc_start: 0.9033 (t80) cc_final: 0.8814 (t80) REVERT: C 204 ASP cc_start: 0.8161 (t0) cc_final: 0.7879 (t0) REVERT: C 206 ILE cc_start: 0.8049 (mt) cc_final: 0.7827 (mt) REVERT: C 218 LYS cc_start: 0.7576 (mmpt) cc_final: 0.7324 (mmpt) REVERT: C 224 MET cc_start: 0.7433 (ptm) cc_final: 0.6494 (ptm) REVERT: C 225 GLN cc_start: 0.7433 (mm110) cc_final: 0.6638 (mm110) REVERT: D 6 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8203 (ttpt) REVERT: D 7 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8142 (mm-30) REVERT: D 9 LEU cc_start: 0.7967 (mt) cc_final: 0.7766 (mt) REVERT: D 14 LYS cc_start: 0.8737 (mttt) cc_final: 0.8339 (mttm) REVERT: D 20 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7190 (tm-30) REVERT: D 25 MET cc_start: 0.7706 (pmm) cc_final: 0.7323 (pmm) REVERT: D 29 MET cc_start: 0.8973 (tpp) cc_final: 0.8525 (mmm) REVERT: D 30 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7641 (mttt) REVERT: D 34 GLU cc_start: 0.7988 (pp20) cc_final: 0.7559 (pp20) REVERT: D 43 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8501 (mt-10) REVERT: D 52 LYS cc_start: 0.8629 (tptm) cc_final: 0.8248 (tptm) REVERT: D 59 ARG cc_start: 0.8338 (mtp-110) cc_final: 0.7934 (mtp180) REVERT: D 65 ILE cc_start: 0.8737 (pt) cc_final: 0.8458 (pt) REVERT: D 66 SER cc_start: 0.8067 (m) cc_final: 0.7657 (m) REVERT: D 84 MET cc_start: 0.7676 (ptp) cc_final: 0.7159 (ptp) REVERT: D 87 GLU cc_start: 0.8329 (pt0) cc_final: 0.7986 (pt0) REVERT: D 91 LYS cc_start: 0.8731 (tppt) cc_final: 0.8032 (tppt) REVERT: D 93 GLU cc_start: 0.8482 (tt0) cc_final: 0.8247 (tt0) REVERT: D 102 ASP cc_start: 0.7796 (m-30) cc_final: 0.7473 (m-30) REVERT: D 119 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7728 (tp30) REVERT: D 127 MET cc_start: 0.8332 (mmm) cc_final: 0.7681 (mmp) REVERT: D 128 LYS cc_start: 0.8053 (tttt) cc_final: 0.7656 (tttt) REVERT: D 130 ASP cc_start: 0.7555 (m-30) cc_final: 0.7256 (m-30) REVERT: D 133 ARG cc_start: 0.8684 (ttp-110) cc_final: 0.8247 (ttp-110) REVERT: D 153 LYS cc_start: 0.8450 (tppt) cc_final: 0.7731 (tppt) REVERT: D 155 TYR cc_start: 0.7947 (m-10) cc_final: 0.7343 (m-80) REVERT: D 170 HIS cc_start: 0.8463 (t-90) cc_final: 0.7879 (t-90) REVERT: D 174 LEU cc_start: 0.8088 (mt) cc_final: 0.7833 (mt) REVERT: D 192 ASP cc_start: 0.8088 (p0) cc_final: 0.7678 (p0) REVERT: D 195 CYS cc_start: 0.8415 (p) cc_final: 0.8121 (p) REVERT: D 220 SER cc_start: 0.7382 (m) cc_final: 0.7110 (m) REVERT: D 224 MET cc_start: 0.7749 (ptm) cc_final: 0.7487 (ptm) REVERT: E 96 ARG cc_start: 0.7545 (ptm160) cc_final: 0.6959 (ptm160) REVERT: E 121 CYS cc_start: 0.7545 (m) cc_final: 0.7134 (m) REVERT: E 125 TYR cc_start: 0.8045 (m-80) cc_final: 0.7178 (m-80) REVERT: E 160 ARG cc_start: 0.7300 (mpp80) cc_final: 0.6825 (mpt-90) REVERT: E 175 LYS cc_start: 0.8725 (ptmt) cc_final: 0.8201 (ptmt) REVERT: E 195 ASN cc_start: 0.8010 (t0) cc_final: 0.7749 (t0) REVERT: E 206 LEU cc_start: 0.6868 (tp) cc_final: 0.6319 (tp) REVERT: E 219 MET cc_start: 0.7914 (mtp) cc_final: 0.7570 (mtp) REVERT: E 227 ARG cc_start: 0.7695 (mtm180) cc_final: 0.7112 (mtm180) REVERT: E 235 LEU cc_start: 0.8660 (mt) cc_final: 0.8267 (mt) REVERT: E 253 LEU cc_start: 0.8788 (mt) cc_final: 0.8580 (mt) REVERT: E 256 MET cc_start: 0.7656 (ptm) cc_final: 0.7404 (ptm) REVERT: E 316 TYR cc_start: 0.8007 (t80) cc_final: 0.7560 (t80) REVERT: E 319 ASN cc_start: 0.8073 (t0) cc_final: 0.6814 (t0) REVERT: E 324 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7568 (mmtt) REVERT: E 334 PHE cc_start: 0.8505 (t80) cc_final: 0.8216 (t80) REVERT: E 344 LYS cc_start: 0.8574 (tmmt) cc_final: 0.8207 (mttt) REVERT: E 356 MET cc_start: 0.6921 (ppp) cc_final: 0.6524 (ppp) REVERT: E 360 PHE cc_start: 0.8412 (p90) cc_final: 0.8154 (p90) REVERT: E 371 PHE cc_start: 0.7565 (m-80) cc_final: 0.6960 (m-80) REVERT: F 88 LYS cc_start: 0.8496 (mmmt) cc_final: 0.7986 (mmmt) REVERT: F 110 GLN cc_start: 0.8315 (mm-40) cc_final: 0.8024 (mp10) REVERT: F 125 TYR cc_start: 0.8090 (m-80) cc_final: 0.7377 (m-80) REVERT: F 175 LYS cc_start: 0.8708 (ptmt) cc_final: 0.8199 (ptmt) REVERT: F 195 ASN cc_start: 0.8185 (m110) cc_final: 0.7385 (t0) REVERT: F 219 MET cc_start: 0.7735 (mtp) cc_final: 0.7504 (mtp) REVERT: F 227 ARG cc_start: 0.7713 (mtm180) cc_final: 0.7182 (mtm180) REVERT: F 233 GLU cc_start: 0.8128 (pt0) cc_final: 0.7853 (pt0) REVERT: F 249 MET cc_start: 0.8285 (ppp) cc_final: 0.8000 (ppp) REVERT: F 253 LEU cc_start: 0.8732 (mt) cc_final: 0.8529 (mt) REVERT: F 256 MET cc_start: 0.7782 (ptm) cc_final: 0.7408 (ptm) REVERT: F 316 TYR cc_start: 0.8005 (t80) cc_final: 0.7497 (t80) REVERT: F 319 ASN cc_start: 0.7913 (t0) cc_final: 0.6650 (t0) REVERT: F 320 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7642 (mm-30) REVERT: F 324 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7497 (mmtt) REVERT: F 334 PHE cc_start: 0.8393 (t80) cc_final: 0.8144 (t80) REVERT: F 356 MET cc_start: 0.6867 (ppp) cc_final: 0.6532 (ppp) REVERT: F 360 PHE cc_start: 0.8456 (p90) cc_final: 0.7942 (p90) outliers start: 0 outliers final: 0 residues processed: 674 average time/residue: 0.1355 time to fit residues: 125.3277 Evaluate side-chains 668 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 668 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.3980 chunk 134 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS A 388 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 200 GLN E 199 ASN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.132938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.107947 restraints weight = 27932.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.112248 restraints weight = 15261.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.115319 restraints weight = 9828.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.117477 restraints weight = 6989.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.119022 restraints weight = 5345.993| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12876 Z= 0.173 Angle : 0.691 11.862 17364 Z= 0.362 Chirality : 0.046 0.241 1918 Planarity : 0.005 0.049 2216 Dihedral : 5.573 39.017 1740 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.21), residues: 1538 helix: 0.45 (0.16), residues: 896 sheet: -2.74 (0.52), residues: 68 loop : -1.00 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 160 TYR 0.022 0.002 TYR C 131 PHE 0.021 0.002 PHE F 371 TRP 0.041 0.002 TRP B 368 HIS 0.016 0.001 HIS B 460 Details of bonding type rmsd covalent geometry : bond 0.00351 (12876) covalent geometry : angle 0.69138 (17364) hydrogen bonds : bond 0.03935 ( 710) hydrogen bonds : angle 4.87059 ( 2070) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 667 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.7487 (mtm) cc_final: 0.7090 (mtm) REVERT: A 362 THR cc_start: 0.8002 (m) cc_final: 0.7587 (m) REVERT: A 367 LYS cc_start: 0.7623 (mmtt) cc_final: 0.6771 (mmtt) REVERT: A 368 TRP cc_start: 0.8578 (t60) cc_final: 0.8237 (t60) REVERT: A 387 PHE cc_start: 0.8149 (t80) cc_final: 0.7180 (t80) REVERT: A 390 PHE cc_start: 0.8056 (t80) cc_final: 0.7430 (t80) REVERT: A 391 ARG cc_start: 0.8350 (mmt90) cc_final: 0.7688 (mmm-85) REVERT: A 393 GLU cc_start: 0.8077 (tp30) cc_final: 0.7625 (tp30) REVERT: A 399 LYS cc_start: 0.8367 (mmtp) cc_final: 0.7995 (mmtp) REVERT: A 402 HIS cc_start: 0.7613 (t-90) cc_final: 0.7118 (t-90) REVERT: A 408 PHE cc_start: 0.7269 (t80) cc_final: 0.7004 (t80) REVERT: A 409 MET cc_start: 0.7331 (mtt) cc_final: 0.7034 (mtt) REVERT: A 412 MET cc_start: 0.6045 (ppp) cc_final: 0.5445 (ppp) REVERT: A 417 LEU cc_start: 0.8027 (pt) cc_final: 0.7568 (pt) REVERT: A 419 ILE cc_start: 0.7254 (mm) cc_final: 0.6753 (mm) REVERT: A 422 GLN cc_start: 0.8223 (tt0) cc_final: 0.7164 (pt0) REVERT: A 425 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6967 (mm-30) REVERT: A 439 LYS cc_start: 0.8334 (mppt) cc_final: 0.7728 (mppt) REVERT: A 444 GLN cc_start: 0.7734 (mt0) cc_final: 0.7520 (mp10) REVERT: A 445 LEU cc_start: 0.8747 (tp) cc_final: 0.8528 (tp) REVERT: A 450 ARG cc_start: 0.8352 (ttp-170) cc_final: 0.7857 (ptm-80) REVERT: A 456 MET cc_start: 0.8266 (mmm) cc_final: 0.7029 (mmm) REVERT: A 457 ASP cc_start: 0.7917 (t0) cc_final: 0.7604 (t0) REVERT: A 458 TYR cc_start: 0.8528 (t80) cc_final: 0.8014 (t80) REVERT: A 460 HIS cc_start: 0.8466 (m170) cc_final: 0.7572 (m-70) REVERT: A 463 ASN cc_start: 0.7258 (m-40) cc_final: 0.7025 (m-40) REVERT: A 466 HIS cc_start: 0.8515 (t-90) cc_final: 0.8041 (t-90) REVERT: A 470 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7725 (mtpt) REVERT: A 477 HIS cc_start: 0.6468 (t70) cc_final: 0.6240 (t-90) REVERT: A 484 ILE cc_start: 0.7939 (mt) cc_final: 0.7679 (mt) REVERT: A 511 TRP cc_start: 0.7354 (m-90) cc_final: 0.7104 (m-90) REVERT: A 512 MET cc_start: 0.6146 (ttm) cc_final: 0.5595 (ttm) REVERT: A 517 ILE cc_start: 0.8700 (mt) cc_final: 0.8345 (mt) REVERT: A 518 ARG cc_start: 0.8233 (ptp-110) cc_final: 0.7574 (ptp-110) REVERT: A 528 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7234 (mm110) REVERT: A 532 TYR cc_start: 0.8055 (t80) cc_final: 0.7791 (t80) REVERT: A 534 TYR cc_start: 0.8480 (t80) cc_final: 0.7899 (t80) REVERT: A 541 LEU cc_start: 0.8683 (mt) cc_final: 0.8285 (mt) REVERT: A 545 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7398 (mt-10) REVERT: A 556 GLN cc_start: 0.8373 (tt0) cc_final: 0.7500 (tt0) REVERT: A 559 PHE cc_start: 0.8573 (t80) cc_final: 0.7537 (t80) REVERT: A 560 MET cc_start: 0.8400 (mmp) cc_final: 0.7618 (mmp) REVERT: A 563 ARG cc_start: 0.8710 (mmm-85) cc_final: 0.8075 (ttm-80) REVERT: A 572 LYS cc_start: 0.8285 (mmmm) cc_final: 0.7782 (mmmm) REVERT: A 574 TYR cc_start: 0.7851 (m-10) cc_final: 0.7414 (m-10) REVERT: A 581 MET cc_start: 0.7810 (mmm) cc_final: 0.7224 (mmm) REVERT: A 591 LYS cc_start: 0.8634 (ptpp) cc_final: 0.8411 (ptpp) REVERT: A 592 VAL cc_start: 0.7772 (t) cc_final: 0.7258 (m) REVERT: A 601 GLN cc_start: 0.8376 (tt0) cc_final: 0.8079 (tm-30) REVERT: A 622 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7180 (tm-30) REVERT: B 342 TRP cc_start: 0.8583 (m100) cc_final: 0.8044 (m100) REVERT: B 345 GLU cc_start: 0.7042 (mp0) cc_final: 0.6474 (mp0) REVERT: B 350 MET cc_start: 0.7506 (mtm) cc_final: 0.7067 (mtm) REVERT: B 362 THR cc_start: 0.7868 (m) cc_final: 0.7653 (m) REVERT: B 367 LYS cc_start: 0.7766 (mmtt) cc_final: 0.6856 (mmtt) REVERT: B 369 HIS cc_start: 0.8269 (m90) cc_final: 0.7987 (m-70) REVERT: B 387 PHE cc_start: 0.8254 (t80) cc_final: 0.7968 (t80) REVERT: B 393 GLU cc_start: 0.8092 (tp30) cc_final: 0.7445 (tp30) REVERT: B 399 LYS cc_start: 0.8416 (mmtp) cc_final: 0.7900 (mmtp) REVERT: B 402 HIS cc_start: 0.7745 (t-90) cc_final: 0.7427 (t-90) REVERT: B 409 MET cc_start: 0.7328 (mtm) cc_final: 0.6917 (mtm) REVERT: B 411 TYR cc_start: 0.7330 (p90) cc_final: 0.7078 (p90) REVERT: B 412 MET cc_start: 0.5862 (ppp) cc_final: 0.5436 (ppp) REVERT: B 417 LEU cc_start: 0.8249 (pt) cc_final: 0.7999 (pt) REVERT: B 419 ILE cc_start: 0.7194 (mm) cc_final: 0.6971 (mm) REVERT: B 429 LEU cc_start: 0.8340 (tp) cc_final: 0.8056 (tp) REVERT: B 431 LYS cc_start: 0.8302 (mptt) cc_final: 0.8006 (mptt) REVERT: B 439 LYS cc_start: 0.8568 (mppt) cc_final: 0.8094 (mppt) REVERT: B 442 MET cc_start: 0.7404 (mpp) cc_final: 0.7135 (mpp) REVERT: B 446 ILE cc_start: 0.8649 (mt) cc_final: 0.8431 (mt) REVERT: B 456 MET cc_start: 0.8044 (mmm) cc_final: 0.6899 (mmm) REVERT: B 457 ASP cc_start: 0.7882 (t70) cc_final: 0.7614 (t70) REVERT: B 458 TYR cc_start: 0.8528 (t80) cc_final: 0.7584 (t80) REVERT: B 463 ASN cc_start: 0.7378 (m-40) cc_final: 0.7083 (m-40) REVERT: B 466 HIS cc_start: 0.8517 (t-90) cc_final: 0.8132 (t70) REVERT: B 470 LYS cc_start: 0.8346 (mtpt) cc_final: 0.7935 (mtpt) REVERT: B 483 LYS cc_start: 0.8290 (mttp) cc_final: 0.7985 (mttp) REVERT: B 511 TRP cc_start: 0.7414 (m-90) cc_final: 0.7094 (m-90) REVERT: B 512 MET cc_start: 0.6056 (ttm) cc_final: 0.5805 (ttm) REVERT: B 517 ILE cc_start: 0.8621 (mt) cc_final: 0.8140 (mt) REVERT: B 518 ARG cc_start: 0.7820 (mtm-85) cc_final: 0.7402 (mtm-85) REVERT: B 528 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7055 (mm-40) REVERT: B 534 TYR cc_start: 0.8514 (t80) cc_final: 0.8126 (t80) REVERT: B 542 MET cc_start: 0.7500 (mtp) cc_final: 0.7116 (mtp) REVERT: B 545 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7219 (mt-10) REVERT: B 551 ILE cc_start: 0.8690 (mp) cc_final: 0.8417 (mp) REVERT: B 554 ARG cc_start: 0.7650 (tmm-80) cc_final: 0.7430 (tmm-80) REVERT: B 560 MET cc_start: 0.8283 (tpp) cc_final: 0.7500 (tpp) REVERT: B 563 ARG cc_start: 0.8399 (mmm-85) cc_final: 0.7852 (ttm-80) REVERT: B 572 LYS cc_start: 0.8410 (mmmm) cc_final: 0.8088 (mmmm) REVERT: B 583 ARG cc_start: 0.8598 (ptp-170) cc_final: 0.8007 (ptp-110) REVERT: B 591 LYS cc_start: 0.8703 (ptpp) cc_final: 0.8503 (ptpp) REVERT: B 594 GLU cc_start: 0.8000 (pm20) cc_final: 0.7680 (pm20) REVERT: B 601 GLN cc_start: 0.8560 (tt0) cc_final: 0.8285 (tt0) REVERT: B 618 ARG cc_start: 0.7934 (ptm160) cc_final: 0.7552 (ptm160) REVERT: B 622 GLU cc_start: 0.7432 (tm-30) cc_final: 0.6980 (tm-30) REVERT: C 25 MET cc_start: 0.7672 (pmm) cc_final: 0.7205 (pmm) REVERT: C 29 MET cc_start: 0.9119 (tpp) cc_final: 0.8613 (mmm) REVERT: C 32 VAL cc_start: 0.8743 (t) cc_final: 0.8539 (t) REVERT: C 34 GLU cc_start: 0.7923 (pp20) cc_final: 0.7446 (pp20) REVERT: C 52 LYS cc_start: 0.8620 (tttm) cc_final: 0.8326 (tttm) REVERT: C 59 ARG cc_start: 0.8145 (mtp-110) cc_final: 0.7938 (mtp-110) REVERT: C 69 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8344 (tm-30) REVERT: C 81 LYS cc_start: 0.8335 (ptpp) cc_final: 0.8019 (pptt) REVERT: C 84 MET cc_start: 0.7640 (ptp) cc_final: 0.7341 (ptp) REVERT: C 87 GLU cc_start: 0.8254 (pt0) cc_final: 0.7943 (pt0) REVERT: C 91 LYS cc_start: 0.8719 (tppt) cc_final: 0.7849 (tppt) REVERT: C 94 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8401 (ttpt) REVERT: C 95 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7695 (mt-10) REVERT: C 97 ARG cc_start: 0.8651 (mtm110) cc_final: 0.8273 (mtm110) REVERT: C 98 GLU cc_start: 0.7356 (tp30) cc_final: 0.6117 (tp30) REVERT: C 102 ASP cc_start: 0.8011 (m-30) cc_final: 0.7074 (m-30) REVERT: C 119 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7840 (tp30) REVERT: C 125 LEU cc_start: 0.8293 (mt) cc_final: 0.8051 (mt) REVERT: C 126 LYS cc_start: 0.8763 (tttm) cc_final: 0.8418 (tttm) REVERT: C 127 MET cc_start: 0.8219 (mmm) cc_final: 0.7602 (mmp) REVERT: C 130 ASP cc_start: 0.7680 (m-30) cc_final: 0.7269 (m-30) REVERT: C 132 TYR cc_start: 0.8495 (m-80) cc_final: 0.7914 (m-80) REVERT: C 135 LEU cc_start: 0.8684 (mt) cc_final: 0.8441 (mt) REVERT: C 149 GLU cc_start: 0.8297 (tp30) cc_final: 0.8080 (tp30) REVERT: C 153 LYS cc_start: 0.8671 (tppt) cc_final: 0.8017 (tppt) REVERT: C 170 HIS cc_start: 0.8133 (t-90) cc_final: 0.7629 (t70) REVERT: C 174 LEU cc_start: 0.8145 (mt) cc_final: 0.7832 (mt) REVERT: C 197 LEU cc_start: 0.8446 (mm) cc_final: 0.8207 (mm) REVERT: C 204 ASP cc_start: 0.8197 (t0) cc_final: 0.7920 (t0) REVERT: C 206 ILE cc_start: 0.8057 (mt) cc_final: 0.7856 (mt) REVERT: C 218 LYS cc_start: 0.7588 (mmpt) cc_final: 0.7323 (mmpt) REVERT: C 224 MET cc_start: 0.7465 (ptm) cc_final: 0.6515 (ptm) REVERT: C 225 GLN cc_start: 0.7437 (mm110) cc_final: 0.6674 (mm110) REVERT: D 6 LYS cc_start: 0.8495 (ttpt) cc_final: 0.8218 (ttpt) REVERT: D 7 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8164 (mm-30) REVERT: D 14 LYS cc_start: 0.8760 (mttt) cc_final: 0.8350 (mttm) REVERT: D 20 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7138 (tm-30) REVERT: D 25 MET cc_start: 0.7702 (pmm) cc_final: 0.7266 (pmm) REVERT: D 29 MET cc_start: 0.8991 (tpp) cc_final: 0.8457 (tpp) REVERT: D 30 LYS cc_start: 0.8075 (mtmt) cc_final: 0.7688 (mttt) REVERT: D 34 GLU cc_start: 0.8033 (pp20) cc_final: 0.7574 (pp20) REVERT: D 43 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8420 (mt-10) REVERT: D 52 LYS cc_start: 0.8642 (tptm) cc_final: 0.8265 (tptm) REVERT: D 59 ARG cc_start: 0.8318 (mtp-110) cc_final: 0.7943 (mtp180) REVERT: D 63 ARG cc_start: 0.8193 (tpp-160) cc_final: 0.7819 (tpp-160) REVERT: D 65 ILE cc_start: 0.8732 (pt) cc_final: 0.8454 (pt) REVERT: D 66 SER cc_start: 0.8031 (m) cc_final: 0.7544 (m) REVERT: D 84 MET cc_start: 0.7664 (ptp) cc_final: 0.7135 (ptp) REVERT: D 87 GLU cc_start: 0.8314 (pt0) cc_final: 0.7982 (pt0) REVERT: D 91 LYS cc_start: 0.8741 (tppt) cc_final: 0.8051 (tppt) REVERT: D 94 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8700 (ttpt) REVERT: D 102 ASP cc_start: 0.7802 (m-30) cc_final: 0.7445 (m-30) REVERT: D 119 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7734 (tp30) REVERT: D 127 MET cc_start: 0.8295 (mmm) cc_final: 0.7694 (mmp) REVERT: D 128 LYS cc_start: 0.8117 (tttt) cc_final: 0.7693 (tttt) REVERT: D 130 ASP cc_start: 0.7536 (m-30) cc_final: 0.7226 (m-30) REVERT: D 133 ARG cc_start: 0.8702 (ttp-110) cc_final: 0.8248 (ttp-110) REVERT: D 153 LYS cc_start: 0.8420 (tppt) cc_final: 0.7668 (tppt) REVERT: D 155 TYR cc_start: 0.8054 (m-10) cc_final: 0.7062 (m-80) REVERT: D 170 HIS cc_start: 0.8441 (t-90) cc_final: 0.7898 (t-90) REVERT: D 174 LEU cc_start: 0.8173 (mt) cc_final: 0.7926 (mt) REVERT: D 180 PHE cc_start: 0.8608 (m-80) cc_final: 0.7831 (m-80) REVERT: D 192 ASP cc_start: 0.8190 (p0) cc_final: 0.7765 (p0) REVERT: D 220 SER cc_start: 0.7339 (m) cc_final: 0.7041 (m) REVERT: D 224 MET cc_start: 0.7735 (ptm) cc_final: 0.7455 (ptm) REVERT: E 96 ARG cc_start: 0.7583 (ptm160) cc_final: 0.7040 (ptm160) REVERT: E 121 CYS cc_start: 0.7398 (m) cc_final: 0.7045 (m) REVERT: E 125 TYR cc_start: 0.8025 (m-80) cc_final: 0.7164 (m-80) REVERT: E 160 ARG cc_start: 0.7001 (mpp80) cc_final: 0.6742 (mpp80) REVERT: E 168 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7872 (ttmm) REVERT: E 175 LYS cc_start: 0.8738 (ptmt) cc_final: 0.8214 (ptmt) REVERT: E 187 MET cc_start: 0.6003 (mtt) cc_final: 0.5770 (mtt) REVERT: E 195 ASN cc_start: 0.8077 (t0) cc_final: 0.7805 (t0) REVERT: E 206 LEU cc_start: 0.6842 (tp) cc_final: 0.6290 (tp) REVERT: E 219 MET cc_start: 0.7892 (mtp) cc_final: 0.7563 (mtp) REVERT: E 227 ARG cc_start: 0.7702 (mtm180) cc_final: 0.7085 (mtm180) REVERT: E 235 LEU cc_start: 0.8678 (mt) cc_final: 0.8293 (mt) REVERT: E 249 MET cc_start: 0.8297 (ppp) cc_final: 0.8049 (ppp) REVERT: E 253 LEU cc_start: 0.8782 (mt) cc_final: 0.8518 (mt) REVERT: E 256 MET cc_start: 0.7713 (ptm) cc_final: 0.7359 (ptm) REVERT: E 316 TYR cc_start: 0.7971 (t80) cc_final: 0.7558 (t80) REVERT: E 319 ASN cc_start: 0.8125 (t0) cc_final: 0.6861 (t0) REVERT: E 320 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7645 (mm-30) REVERT: E 324 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7593 (mmtt) REVERT: E 334 PHE cc_start: 0.8478 (t80) cc_final: 0.8185 (t80) REVERT: E 340 LYS cc_start: 0.8798 (mttp) cc_final: 0.8285 (tptp) REVERT: E 344 LYS cc_start: 0.8593 (tmmt) cc_final: 0.8254 (mttt) REVERT: E 360 PHE cc_start: 0.8421 (p90) cc_final: 0.8207 (p90) REVERT: E 371 PHE cc_start: 0.7609 (m-80) cc_final: 0.7229 (m-80) REVERT: F 88 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8000 (mmmt) REVERT: F 96 ARG cc_start: 0.7619 (ptm160) cc_final: 0.6957 (ptm160) REVERT: F 110 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8062 (mp10) REVERT: F 125 TYR cc_start: 0.8092 (m-80) cc_final: 0.7381 (m-80) REVERT: F 175 LYS cc_start: 0.8701 (ptmt) cc_final: 0.8224 (ptmt) REVERT: F 195 ASN cc_start: 0.8282 (m110) cc_final: 0.7484 (t0) REVERT: F 219 MET cc_start: 0.7691 (mtp) cc_final: 0.7458 (mtp) REVERT: F 227 ARG cc_start: 0.7740 (mtm180) cc_final: 0.7156 (mtm180) REVERT: F 230 MET cc_start: 0.7281 (tpp) cc_final: 0.7074 (tpt) REVERT: F 233 GLU cc_start: 0.8217 (pt0) cc_final: 0.7979 (pt0) REVERT: F 249 MET cc_start: 0.8296 (ppp) cc_final: 0.8010 (ppp) REVERT: F 253 LEU cc_start: 0.8727 (mt) cc_final: 0.8516 (mt) REVERT: F 256 MET cc_start: 0.7771 (ptm) cc_final: 0.7379 (ptm) REVERT: F 316 TYR cc_start: 0.7966 (t80) cc_final: 0.7477 (t80) REVERT: F 319 ASN cc_start: 0.7908 (t0) cc_final: 0.6614 (t0) REVERT: F 320 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7656 (mm-30) REVERT: F 324 LYS cc_start: 0.7925 (mmtt) cc_final: 0.7474 (mmtt) REVERT: F 334 PHE cc_start: 0.8401 (t80) cc_final: 0.8141 (t80) REVERT: F 356 MET cc_start: 0.6810 (ppp) cc_final: 0.6436 (ppp) REVERT: F 360 PHE cc_start: 0.8515 (p90) cc_final: 0.8083 (p90) REVERT: F 371 PHE cc_start: 0.7498 (m-80) cc_final: 0.6921 (m-80) outliers start: 0 outliers final: 0 residues processed: 667 average time/residue: 0.1258 time to fit residues: 114.8526 Evaluate side-chains 660 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 121 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS A 388 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.134985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.109750 restraints weight = 27688.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.113932 restraints weight = 15265.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116922 restraints weight = 9936.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.119099 restraints weight = 7151.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.120667 restraints weight = 5489.032| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12876 Z= 0.196 Angle : 0.715 12.225 17364 Z= 0.374 Chirality : 0.048 0.453 1918 Planarity : 0.005 0.049 2216 Dihedral : 5.616 36.827 1740 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.21), residues: 1538 helix: 0.37 (0.16), residues: 896 sheet: -2.80 (0.51), residues: 68 loop : -1.06 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 160 TYR 0.068 0.002 TYR D 101 PHE 0.035 0.002 PHE C 202 TRP 0.045 0.002 TRP B 368 HIS 0.010 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00387 (12876) covalent geometry : angle 0.71518 (17364) hydrogen bonds : bond 0.04115 ( 710) hydrogen bonds : angle 4.89034 ( 2070) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 671 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.7527 (mtm) cc_final: 0.7136 (mtm) REVERT: A 362 THR cc_start: 0.8021 (m) cc_final: 0.7813 (m) REVERT: A 367 LYS cc_start: 0.7618 (mmtt) cc_final: 0.6769 (mmtt) REVERT: A 368 TRP cc_start: 0.8575 (t60) cc_final: 0.8211 (t60) REVERT: A 387 PHE cc_start: 0.8130 (t80) cc_final: 0.7150 (t80) REVERT: A 390 PHE cc_start: 0.8050 (t80) cc_final: 0.7409 (t80) REVERT: A 391 ARG cc_start: 0.8349 (mmt90) cc_final: 0.7690 (mmm-85) REVERT: A 393 GLU cc_start: 0.8078 (tp30) cc_final: 0.7604 (tp30) REVERT: A 399 LYS cc_start: 0.8355 (mmtp) cc_final: 0.7978 (mmtp) REVERT: A 402 HIS cc_start: 0.7606 (t-90) cc_final: 0.7204 (t-90) REVERT: A 408 PHE cc_start: 0.7277 (t80) cc_final: 0.7025 (t80) REVERT: A 409 MET cc_start: 0.7282 (mtt) cc_final: 0.7016 (mtt) REVERT: A 412 MET cc_start: 0.6033 (ppp) cc_final: 0.5415 (ppp) REVERT: A 417 LEU cc_start: 0.8027 (pt) cc_final: 0.7547 (pt) REVERT: A 419 ILE cc_start: 0.7273 (mm) cc_final: 0.6739 (mm) REVERT: A 422 GLN cc_start: 0.8188 (tt0) cc_final: 0.7072 (pt0) REVERT: A 425 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6929 (mm-30) REVERT: A 431 LYS cc_start: 0.8428 (mttp) cc_final: 0.8218 (mttp) REVERT: A 439 LYS cc_start: 0.8354 (mppt) cc_final: 0.7724 (mppt) REVERT: A 441 GLN cc_start: 0.7629 (mt0) cc_final: 0.7187 (mt0) REVERT: A 442 MET cc_start: 0.7537 (mpp) cc_final: 0.7115 (mpp) REVERT: A 444 GLN cc_start: 0.7724 (mt0) cc_final: 0.7165 (mt0) REVERT: A 445 LEU cc_start: 0.8741 (tp) cc_final: 0.8516 (tp) REVERT: A 456 MET cc_start: 0.8383 (mmm) cc_final: 0.8072 (mmm) REVERT: A 457 ASP cc_start: 0.7967 (t0) cc_final: 0.7621 (t0) REVERT: A 458 TYR cc_start: 0.8528 (t80) cc_final: 0.8017 (t80) REVERT: A 463 ASN cc_start: 0.7248 (m-40) cc_final: 0.7020 (m-40) REVERT: A 466 HIS cc_start: 0.8469 (t-90) cc_final: 0.8004 (t-90) REVERT: A 470 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7691 (mtpt) REVERT: A 483 LYS cc_start: 0.8254 (mttt) cc_final: 0.7806 (mttt) REVERT: A 484 ILE cc_start: 0.7917 (mt) cc_final: 0.7666 (mt) REVERT: A 511 TRP cc_start: 0.7317 (m-90) cc_final: 0.7073 (m-90) REVERT: A 512 MET cc_start: 0.6152 (ttm) cc_final: 0.5621 (ttm) REVERT: A 517 ILE cc_start: 0.8715 (mt) cc_final: 0.8326 (mt) REVERT: A 518 ARG cc_start: 0.8251 (ptp-110) cc_final: 0.7631 (ptp-110) REVERT: A 528 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7142 (mm110) REVERT: A 532 TYR cc_start: 0.8037 (t80) cc_final: 0.7793 (t80) REVERT: A 534 TYR cc_start: 0.8386 (t80) cc_final: 0.7865 (t80) REVERT: A 541 LEU cc_start: 0.8664 (mt) cc_final: 0.8270 (mt) REVERT: A 545 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7442 (mt-10) REVERT: A 556 GLN cc_start: 0.8363 (tt0) cc_final: 0.7527 (tt0) REVERT: A 560 MET cc_start: 0.8380 (mmp) cc_final: 0.7686 (mmp) REVERT: A 563 ARG cc_start: 0.8690 (mmm-85) cc_final: 0.8032 (ttm-80) REVERT: A 572 LYS cc_start: 0.8328 (mmmm) cc_final: 0.7834 (mmmm) REVERT: A 574 TYR cc_start: 0.7883 (m-10) cc_final: 0.7428 (m-10) REVERT: A 581 MET cc_start: 0.7775 (mmm) cc_final: 0.7188 (mmm) REVERT: A 591 LYS cc_start: 0.8631 (ptpp) cc_final: 0.8415 (ptpp) REVERT: A 592 VAL cc_start: 0.7768 (t) cc_final: 0.7283 (m) REVERT: A 601 GLN cc_start: 0.8399 (tt0) cc_final: 0.8128 (tm-30) REVERT: A 622 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7143 (tm-30) REVERT: B 342 TRP cc_start: 0.8509 (m100) cc_final: 0.8039 (m100) REVERT: B 350 MET cc_start: 0.7523 (mtm) cc_final: 0.7115 (mtm) REVERT: B 362 THR cc_start: 0.7870 (m) cc_final: 0.7593 (m) REVERT: B 367 LYS cc_start: 0.7758 (mmtt) cc_final: 0.6884 (mmtt) REVERT: B 369 HIS cc_start: 0.8250 (m90) cc_final: 0.7990 (m-70) REVERT: B 387 PHE cc_start: 0.8263 (t80) cc_final: 0.7967 (t80) REVERT: B 399 LYS cc_start: 0.8405 (mmtp) cc_final: 0.7900 (mmtp) REVERT: B 402 HIS cc_start: 0.7724 (t-90) cc_final: 0.7481 (t-90) REVERT: B 409 MET cc_start: 0.7379 (mtm) cc_final: 0.6993 (mtm) REVERT: B 411 TYR cc_start: 0.7316 (p90) cc_final: 0.7091 (p90) REVERT: B 412 MET cc_start: 0.5844 (ppp) cc_final: 0.5402 (ppp) REVERT: B 417 LEU cc_start: 0.8266 (pt) cc_final: 0.8015 (pt) REVERT: B 419 ILE cc_start: 0.7188 (mm) cc_final: 0.6962 (mm) REVERT: B 429 LEU cc_start: 0.8302 (tp) cc_final: 0.8037 (tp) REVERT: B 431 LYS cc_start: 0.8287 (mptt) cc_final: 0.7985 (mptt) REVERT: B 439 LYS cc_start: 0.8641 (mppt) cc_final: 0.8147 (mppt) REVERT: B 442 MET cc_start: 0.7363 (mpp) cc_final: 0.7142 (mpp) REVERT: B 456 MET cc_start: 0.7892 (mmm) cc_final: 0.6912 (mmm) REVERT: B 458 TYR cc_start: 0.8546 (t80) cc_final: 0.7509 (t80) REVERT: B 463 ASN cc_start: 0.7355 (m-40) cc_final: 0.7146 (m-40) REVERT: B 466 HIS cc_start: 0.8465 (t-90) cc_final: 0.8033 (t70) REVERT: B 470 LYS cc_start: 0.8404 (mtpt) cc_final: 0.7765 (mtpt) REVERT: B 473 ASN cc_start: 0.7596 (m110) cc_final: 0.7127 (m110) REVERT: B 477 HIS cc_start: 0.6719 (t-90) cc_final: 0.6517 (t-90) REVERT: B 483 LYS cc_start: 0.8257 (mttp) cc_final: 0.7759 (mttp) REVERT: B 511 TRP cc_start: 0.7414 (m-90) cc_final: 0.6974 (m-90) REVERT: B 512 MET cc_start: 0.6065 (ttm) cc_final: 0.5618 (ttm) REVERT: B 527 PHE cc_start: 0.8460 (m-80) cc_final: 0.8154 (m-80) REVERT: B 528 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7018 (mm-40) REVERT: B 534 TYR cc_start: 0.8508 (t80) cc_final: 0.8037 (t80) REVERT: B 539 TYR cc_start: 0.8240 (t80) cc_final: 0.7946 (t80) REVERT: B 542 MET cc_start: 0.7584 (mtp) cc_final: 0.7079 (mtp) REVERT: B 545 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7264 (mt-10) REVERT: B 551 ILE cc_start: 0.8771 (mp) cc_final: 0.8453 (mp) REVERT: B 560 MET cc_start: 0.8312 (tpp) cc_final: 0.7497 (tpp) REVERT: B 563 ARG cc_start: 0.8425 (mmm-85) cc_final: 0.7865 (ttm-80) REVERT: B 572 LYS cc_start: 0.8460 (mmmm) cc_final: 0.7993 (mmmm) REVERT: B 581 MET cc_start: 0.7957 (mmm) cc_final: 0.7540 (mmm) REVERT: B 583 ARG cc_start: 0.8677 (ptp-170) cc_final: 0.8195 (ptp-170) REVERT: B 591 LYS cc_start: 0.8686 (ptpp) cc_final: 0.8479 (ptpp) REVERT: B 601 GLN cc_start: 0.8562 (tt0) cc_final: 0.8303 (tt0) REVERT: B 618 ARG cc_start: 0.8051 (ptm160) cc_final: 0.7634 (ptm160) REVERT: C 10 VAL cc_start: 0.8908 (t) cc_final: 0.8580 (t) REVERT: C 14 LYS cc_start: 0.8683 (mttt) cc_final: 0.8305 (mtmm) REVERT: C 25 MET cc_start: 0.7747 (pmm) cc_final: 0.7257 (pmm) REVERT: C 29 MET cc_start: 0.9059 (mmt) cc_final: 0.8644 (mmm) REVERT: C 34 GLU cc_start: 0.7917 (pp20) cc_final: 0.7460 (pp20) REVERT: C 52 LYS cc_start: 0.8617 (tttm) cc_final: 0.8346 (tttm) REVERT: C 59 ARG cc_start: 0.8139 (mtp-110) cc_final: 0.7937 (mtp-110) REVERT: C 69 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8350 (tm-30) REVERT: C 81 LYS cc_start: 0.8394 (ptpp) cc_final: 0.8067 (pptt) REVERT: C 84 MET cc_start: 0.7681 (ptp) cc_final: 0.7396 (ptp) REVERT: C 87 GLU cc_start: 0.8252 (pt0) cc_final: 0.7946 (pt0) REVERT: C 91 LYS cc_start: 0.8699 (tppt) cc_final: 0.7806 (tppt) REVERT: C 92 VAL cc_start: 0.9091 (m) cc_final: 0.8749 (m) REVERT: C 94 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8378 (ttpt) REVERT: C 95 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7702 (mt-10) REVERT: C 97 ARG cc_start: 0.8632 (mtm110) cc_final: 0.8326 (mtm110) REVERT: C 98 GLU cc_start: 0.7348 (tp30) cc_final: 0.6116 (tp30) REVERT: C 102 ASP cc_start: 0.8039 (m-30) cc_final: 0.7091 (m-30) REVERT: C 103 VAL cc_start: 0.8645 (t) cc_final: 0.8356 (t) REVERT: C 119 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7891 (tp30) REVERT: C 125 LEU cc_start: 0.8356 (mt) cc_final: 0.8109 (mt) REVERT: C 126 LYS cc_start: 0.8779 (tttm) cc_final: 0.8428 (tttm) REVERT: C 127 MET cc_start: 0.8241 (mmm) cc_final: 0.7618 (mmp) REVERT: C 133 ARG cc_start: 0.8879 (ttp-110) cc_final: 0.8453 (ttp-110) REVERT: C 135 LEU cc_start: 0.8734 (mt) cc_final: 0.8507 (mt) REVERT: C 149 GLU cc_start: 0.8216 (tp30) cc_final: 0.8003 (tp30) REVERT: C 153 LYS cc_start: 0.8607 (tppt) cc_final: 0.7956 (tppt) REVERT: C 170 HIS cc_start: 0.8111 (t-90) cc_final: 0.7590 (t70) REVERT: C 174 LEU cc_start: 0.8174 (mt) cc_final: 0.7874 (mt) REVERT: C 197 LEU cc_start: 0.8374 (mm) cc_final: 0.8123 (mm) REVERT: C 204 ASP cc_start: 0.8227 (t0) cc_final: 0.7953 (t0) REVERT: C 218 LYS cc_start: 0.7604 (mmpt) cc_final: 0.7365 (mmpt) REVERT: C 224 MET cc_start: 0.7640 (ptm) cc_final: 0.6468 (ptm) REVERT: C 225 GLN cc_start: 0.7461 (mm110) cc_final: 0.6682 (mm110) REVERT: D 14 LYS cc_start: 0.8786 (mttt) cc_final: 0.8364 (mttm) REVERT: D 20 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7146 (tm-30) REVERT: D 25 MET cc_start: 0.7795 (pmm) cc_final: 0.7396 (pmm) REVERT: D 29 MET cc_start: 0.8987 (tpp) cc_final: 0.8493 (mmm) REVERT: D 30 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7719 (mttt) REVERT: D 34 GLU cc_start: 0.8083 (pp20) cc_final: 0.7655 (pp20) REVERT: D 43 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8374 (mt-10) REVERT: D 52 LYS cc_start: 0.8698 (tptm) cc_final: 0.8352 (tptm) REVERT: D 59 ARG cc_start: 0.8337 (mtp-110) cc_final: 0.7952 (mtp180) REVERT: D 63 ARG cc_start: 0.8198 (tpp-160) cc_final: 0.7838 (tpp-160) REVERT: D 65 ILE cc_start: 0.8746 (pt) cc_final: 0.8481 (pt) REVERT: D 66 SER cc_start: 0.8030 (m) cc_final: 0.7559 (m) REVERT: D 84 MET cc_start: 0.7657 (ptp) cc_final: 0.7115 (ptp) REVERT: D 87 GLU cc_start: 0.8282 (pt0) cc_final: 0.7940 (pt0) REVERT: D 91 LYS cc_start: 0.8748 (tppt) cc_final: 0.8051 (tppt) REVERT: D 93 GLU cc_start: 0.8677 (tt0) cc_final: 0.8272 (tt0) REVERT: D 97 ARG cc_start: 0.8742 (mtm110) cc_final: 0.8335 (ttm110) REVERT: D 102 ASP cc_start: 0.7807 (m-30) cc_final: 0.7478 (m-30) REVERT: D 119 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7732 (tp30) REVERT: D 123 PHE cc_start: 0.7909 (t80) cc_final: 0.7649 (t80) REVERT: D 127 MET cc_start: 0.8360 (mmm) cc_final: 0.7729 (mmp) REVERT: D 128 LYS cc_start: 0.8149 (tttt) cc_final: 0.7725 (tttt) REVERT: D 130 ASP cc_start: 0.7529 (m-30) cc_final: 0.7168 (m-30) REVERT: D 133 ARG cc_start: 0.8716 (ttp-110) cc_final: 0.8255 (ttp-110) REVERT: D 153 LYS cc_start: 0.8405 (tppt) cc_final: 0.7658 (tppt) REVERT: D 155 TYR cc_start: 0.8063 (m-10) cc_final: 0.7509 (m-80) REVERT: D 167 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7805 (tp-100) REVERT: D 170 HIS cc_start: 0.8446 (t-90) cc_final: 0.7882 (t-90) REVERT: D 174 LEU cc_start: 0.8197 (mt) cc_final: 0.7941 (mt) REVERT: D 192 ASP cc_start: 0.8114 (p0) cc_final: 0.7748 (p0) REVERT: D 195 CYS cc_start: 0.8437 (p) cc_final: 0.8205 (p) REVERT: D 220 SER cc_start: 0.7452 (m) cc_final: 0.7222 (m) REVERT: D 224 MET cc_start: 0.7765 (ptm) cc_final: 0.7501 (ptm) REVERT: E 96 ARG cc_start: 0.7607 (ptm160) cc_final: 0.7031 (ptm160) REVERT: E 121 CYS cc_start: 0.7395 (m) cc_final: 0.7067 (m) REVERT: E 125 TYR cc_start: 0.8015 (m-80) cc_final: 0.7146 (m-80) REVERT: E 160 ARG cc_start: 0.7043 (mpp80) cc_final: 0.6732 (mpp80) REVERT: E 175 LYS cc_start: 0.8756 (ptmt) cc_final: 0.8225 (ptmt) REVERT: E 187 MET cc_start: 0.6057 (mtt) cc_final: 0.5680 (mtt) REVERT: E 206 LEU cc_start: 0.6799 (tp) cc_final: 0.6338 (tp) REVERT: E 219 MET cc_start: 0.7849 (mtp) cc_final: 0.7526 (mtp) REVERT: E 227 ARG cc_start: 0.7707 (mtm180) cc_final: 0.7069 (mtm180) REVERT: E 235 LEU cc_start: 0.8741 (mt) cc_final: 0.8418 (mt) REVERT: E 249 MET cc_start: 0.8278 (ppp) cc_final: 0.8028 (ppp) REVERT: E 253 LEU cc_start: 0.8785 (mt) cc_final: 0.8545 (mt) REVERT: E 256 MET cc_start: 0.7708 (ptm) cc_final: 0.7355 (ptm) REVERT: E 313 LEU cc_start: 0.8216 (mt) cc_final: 0.8015 (mt) REVERT: E 316 TYR cc_start: 0.7965 (t80) cc_final: 0.7568 (t80) REVERT: E 319 ASN cc_start: 0.8137 (t0) cc_final: 0.6875 (t0) REVERT: E 320 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7687 (mm-30) REVERT: E 324 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7597 (mmtt) REVERT: E 340 LYS cc_start: 0.8797 (mttp) cc_final: 0.8193 (tptp) REVERT: E 344 LYS cc_start: 0.8597 (tmmt) cc_final: 0.8222 (mttt) REVERT: E 356 MET cc_start: 0.7028 (ppp) cc_final: 0.6636 (ppp) REVERT: E 362 LYS cc_start: 0.8889 (mppt) cc_final: 0.8613 (mmtt) REVERT: E 363 ARG cc_start: 0.8606 (mmp80) cc_final: 0.8271 (mmp80) REVERT: E 371 PHE cc_start: 0.7575 (m-80) cc_final: 0.7023 (m-80) REVERT: F 88 LYS cc_start: 0.8499 (mmmt) cc_final: 0.7998 (mmmt) REVERT: F 175 LYS cc_start: 0.8719 (ptmt) cc_final: 0.8202 (ptmt) REVERT: F 195 ASN cc_start: 0.8261 (m110) cc_final: 0.7476 (t0) REVERT: F 199 ASN cc_start: 0.7261 (t0) cc_final: 0.7017 (t0) REVERT: F 219 MET cc_start: 0.7660 (mtp) cc_final: 0.7314 (mtp) REVERT: F 227 ARG cc_start: 0.7733 (mtm180) cc_final: 0.7140 (mtm180) REVERT: F 233 GLU cc_start: 0.8204 (pt0) cc_final: 0.7988 (pt0) REVERT: F 249 MET cc_start: 0.8288 (ppp) cc_final: 0.7993 (ppp) REVERT: F 253 LEU cc_start: 0.8726 (mt) cc_final: 0.8514 (mt) REVERT: F 256 MET cc_start: 0.7792 (ptm) cc_final: 0.7498 (ptm) REVERT: F 316 TYR cc_start: 0.7968 (t80) cc_final: 0.7481 (t80) REVERT: F 319 ASN cc_start: 0.7919 (t0) cc_final: 0.6589 (t0) REVERT: F 320 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7693 (mm-30) REVERT: F 324 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7489 (mmtt) REVERT: F 334 PHE cc_start: 0.8401 (t80) cc_final: 0.8170 (t80) REVERT: F 356 MET cc_start: 0.6854 (ppp) cc_final: 0.6479 (ppp) REVERT: F 360 PHE cc_start: 0.8510 (p90) cc_final: 0.8061 (p90) REVERT: F 371 PHE cc_start: 0.7522 (m-80) cc_final: 0.7062 (m-80) outliers start: 0 outliers final: 0 residues processed: 671 average time/residue: 0.1331 time to fit residues: 122.8458 Evaluate side-chains 666 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 666 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 81 optimal weight: 0.0770 chunk 102 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS A 388 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.136405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.111075 restraints weight = 27706.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.115393 restraints weight = 15398.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.118475 restraints weight = 9990.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.120602 restraints weight = 7130.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.122234 restraints weight = 5464.929| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12876 Z= 0.144 Angle : 0.707 11.658 17364 Z= 0.363 Chirality : 0.046 0.211 1918 Planarity : 0.004 0.051 2216 Dihedral : 5.518 38.047 1740 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.21), residues: 1538 helix: 0.45 (0.16), residues: 896 sheet: -2.80 (0.50), residues: 68 loop : -1.02 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 349 TYR 0.051 0.002 TYR D 101 PHE 0.028 0.002 PHE C 202 TRP 0.037 0.002 TRP B 368 HIS 0.009 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00309 (12876) covalent geometry : angle 0.70731 (17364) hydrogen bonds : bond 0.03909 ( 710) hydrogen bonds : angle 4.72986 ( 2070) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 675 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.7516 (mtm) cc_final: 0.7116 (mtm) REVERT: A 367 LYS cc_start: 0.7647 (mmtt) cc_final: 0.6765 (mmtt) REVERT: A 368 TRP cc_start: 0.8519 (t60) cc_final: 0.8211 (t60) REVERT: A 386 GLN cc_start: 0.8665 (mt0) cc_final: 0.8374 (mt0) REVERT: A 387 PHE cc_start: 0.8114 (t80) cc_final: 0.7135 (t80) REVERT: A 390 PHE cc_start: 0.8049 (t80) cc_final: 0.7382 (t80) REVERT: A 391 ARG cc_start: 0.8371 (mmt90) cc_final: 0.7723 (mmm-85) REVERT: A 393 GLU cc_start: 0.8073 (tp30) cc_final: 0.7586 (tp30) REVERT: A 399 LYS cc_start: 0.8371 (mmtp) cc_final: 0.7967 (mmtp) REVERT: A 402 HIS cc_start: 0.7542 (t-90) cc_final: 0.7231 (t-90) REVERT: A 408 PHE cc_start: 0.7277 (t80) cc_final: 0.7072 (t80) REVERT: A 409 MET cc_start: 0.7308 (mtt) cc_final: 0.7021 (mtt) REVERT: A 412 MET cc_start: 0.6120 (ppp) cc_final: 0.5495 (ppp) REVERT: A 414 LYS cc_start: 0.8169 (tppt) cc_final: 0.7907 (tppt) REVERT: A 417 LEU cc_start: 0.8040 (pt) cc_final: 0.7575 (pt) REVERT: A 419 ILE cc_start: 0.7227 (mm) cc_final: 0.6712 (mm) REVERT: A 422 GLN cc_start: 0.8182 (tt0) cc_final: 0.7023 (pm20) REVERT: A 425 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6859 (mm-30) REVERT: A 431 LYS cc_start: 0.8391 (mttp) cc_final: 0.8173 (mttp) REVERT: A 439 LYS cc_start: 0.8250 (mppt) cc_final: 0.7602 (mppt) REVERT: A 442 MET cc_start: 0.7469 (mpp) cc_final: 0.7218 (mpp) REVERT: A 444 GLN cc_start: 0.7719 (mt0) cc_final: 0.7312 (mt0) REVERT: A 445 LEU cc_start: 0.8715 (tp) cc_final: 0.8494 (tp) REVERT: A 450 ARG cc_start: 0.8343 (ttp-170) cc_final: 0.8023 (ptm-80) REVERT: A 457 ASP cc_start: 0.7958 (t0) cc_final: 0.7544 (t0) REVERT: A 458 TYR cc_start: 0.8515 (t80) cc_final: 0.8210 (t80) REVERT: A 463 ASN cc_start: 0.7275 (m-40) cc_final: 0.7074 (m-40) REVERT: A 466 HIS cc_start: 0.8443 (t-90) cc_final: 0.8042 (t70) REVERT: A 470 LYS cc_start: 0.8310 (mtpt) cc_final: 0.7738 (mtpt) REVERT: A 477 HIS cc_start: 0.6576 (t-90) cc_final: 0.6331 (t-90) REVERT: A 483 LYS cc_start: 0.8245 (mttt) cc_final: 0.7990 (mttt) REVERT: A 484 ILE cc_start: 0.7949 (mt) cc_final: 0.7727 (mt) REVERT: A 504 GLN cc_start: 0.8118 (mt0) cc_final: 0.7872 (mt0) REVERT: A 511 TRP cc_start: 0.7230 (m-90) cc_final: 0.6981 (m-90) REVERT: A 512 MET cc_start: 0.6077 (ttm) cc_final: 0.5608 (ttm) REVERT: A 517 ILE cc_start: 0.8672 (mt) cc_final: 0.8290 (mt) REVERT: A 518 ARG cc_start: 0.8155 (ptp-110) cc_final: 0.7601 (ptp-110) REVERT: A 532 TYR cc_start: 0.7991 (t80) cc_final: 0.7767 (t80) REVERT: A 534 TYR cc_start: 0.8399 (t80) cc_final: 0.7819 (t80) REVERT: A 541 LEU cc_start: 0.8649 (mt) cc_final: 0.8249 (mt) REVERT: A 545 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7437 (mt-10) REVERT: A 559 PHE cc_start: 0.8554 (t80) cc_final: 0.7446 (t80) REVERT: A 560 MET cc_start: 0.8365 (mmp) cc_final: 0.7593 (mmp) REVERT: A 563 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8239 (ttm-80) REVERT: A 572 LYS cc_start: 0.8290 (mmmm) cc_final: 0.7783 (mmmm) REVERT: A 574 TYR cc_start: 0.7941 (m-10) cc_final: 0.7389 (m-10) REVERT: A 581 MET cc_start: 0.7714 (mmm) cc_final: 0.7189 (mmm) REVERT: A 591 LYS cc_start: 0.8615 (ptpp) cc_final: 0.8409 (ptpp) REVERT: A 592 VAL cc_start: 0.7768 (t) cc_final: 0.7265 (m) REVERT: A 601 GLN cc_start: 0.8396 (tt0) cc_final: 0.8094 (tm-30) REVERT: A 622 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7042 (tm-30) REVERT: B 342 TRP cc_start: 0.8499 (m100) cc_final: 0.7990 (m100) REVERT: B 345 GLU cc_start: 0.7025 (mp0) cc_final: 0.6410 (mp0) REVERT: B 350 MET cc_start: 0.7532 (mtm) cc_final: 0.7048 (mtm) REVERT: B 362 THR cc_start: 0.7831 (m) cc_final: 0.7619 (m) REVERT: B 367 LYS cc_start: 0.7780 (mmtt) cc_final: 0.6881 (mmtt) REVERT: B 369 HIS cc_start: 0.8129 (m90) cc_final: 0.7854 (m-70) REVERT: B 383 THR cc_start: 0.8421 (p) cc_final: 0.7996 (p) REVERT: B 385 GLU cc_start: 0.9031 (pm20) cc_final: 0.8760 (pm20) REVERT: B 386 GLN cc_start: 0.8651 (mt0) cc_final: 0.8344 (mt0) REVERT: B 387 PHE cc_start: 0.8254 (t80) cc_final: 0.7937 (t80) REVERT: B 393 GLU cc_start: 0.8082 (tp30) cc_final: 0.7455 (tp30) REVERT: B 399 LYS cc_start: 0.8370 (mmtp) cc_final: 0.7839 (mmtp) REVERT: B 402 HIS cc_start: 0.7699 (t-90) cc_final: 0.7375 (t-90) REVERT: B 409 MET cc_start: 0.7346 (mtm) cc_final: 0.7142 (mtm) REVERT: B 412 MET cc_start: 0.5976 (ppp) cc_final: 0.5455 (ppp) REVERT: B 417 LEU cc_start: 0.8107 (pt) cc_final: 0.7845 (pt) REVERT: B 419 ILE cc_start: 0.7115 (mm) cc_final: 0.6899 (mm) REVERT: B 422 GLN cc_start: 0.8354 (tt0) cc_final: 0.7548 (pt0) REVERT: B 429 LEU cc_start: 0.8342 (tp) cc_final: 0.8121 (tp) REVERT: B 431 LYS cc_start: 0.8336 (mptt) cc_final: 0.8007 (mptt) REVERT: B 439 LYS cc_start: 0.8538 (mppt) cc_final: 0.8029 (mppt) REVERT: B 441 GLN cc_start: 0.8392 (mt0) cc_final: 0.8147 (mt0) REVERT: B 442 MET cc_start: 0.7382 (mpp) cc_final: 0.6970 (mpp) REVERT: B 454 GLN cc_start: 0.8805 (mt0) cc_final: 0.8603 (mt0) REVERT: B 456 MET cc_start: 0.7832 (mmm) cc_final: 0.6840 (mmm) REVERT: B 458 TYR cc_start: 0.8562 (t80) cc_final: 0.7443 (t80) REVERT: B 463 ASN cc_start: 0.7383 (m-40) cc_final: 0.7162 (m-40) REVERT: B 466 HIS cc_start: 0.8470 (t-90) cc_final: 0.8075 (t70) REVERT: B 470 LYS cc_start: 0.8345 (mtpt) cc_final: 0.7678 (mtpt) REVERT: B 473 ASN cc_start: 0.7654 (m110) cc_final: 0.7153 (m110) REVERT: B 483 LYS cc_start: 0.8330 (mttp) cc_final: 0.7468 (mttp) REVERT: B 484 ILE cc_start: 0.7799 (mt) cc_final: 0.6798 (mt) REVERT: B 511 TRP cc_start: 0.7268 (m-90) cc_final: 0.6850 (m-90) REVERT: B 517 ILE cc_start: 0.8594 (mt) cc_final: 0.8102 (mt) REVERT: B 527 PHE cc_start: 0.8398 (m-80) cc_final: 0.8025 (m-80) REVERT: B 534 TYR cc_start: 0.8515 (t80) cc_final: 0.8039 (t80) REVERT: B 539 TYR cc_start: 0.8190 (t80) cc_final: 0.7932 (t80) REVERT: B 542 MET cc_start: 0.7316 (mtp) cc_final: 0.6934 (mtp) REVERT: B 545 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7341 (mt-10) REVERT: B 551 ILE cc_start: 0.8696 (mp) cc_final: 0.8408 (mp) REVERT: B 560 MET cc_start: 0.8254 (tpp) cc_final: 0.7501 (tpp) REVERT: B 563 ARG cc_start: 0.8344 (mmm-85) cc_final: 0.7796 (ttm-80) REVERT: B 572 LYS cc_start: 0.8400 (mmmm) cc_final: 0.7953 (mmmm) REVERT: B 581 MET cc_start: 0.7862 (mmm) cc_final: 0.7325 (mmm) REVERT: B 583 ARG cc_start: 0.8704 (ptp-170) cc_final: 0.8164 (ptp-110) REVERT: B 585 VAL cc_start: 0.8791 (p) cc_final: 0.8566 (m) REVERT: B 591 LYS cc_start: 0.8713 (ptpp) cc_final: 0.8507 (ptpp) REVERT: B 594 GLU cc_start: 0.7933 (pm20) cc_final: 0.7507 (pm20) REVERT: B 601 GLN cc_start: 0.8534 (tt0) cc_final: 0.8251 (tt0) REVERT: B 618 ARG cc_start: 0.8042 (ptm160) cc_final: 0.7557 (ptm160) REVERT: B 622 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7004 (tm-30) REVERT: C 25 MET cc_start: 0.7648 (pmm) cc_final: 0.7133 (pmm) REVERT: C 29 MET cc_start: 0.8935 (mmt) cc_final: 0.8553 (mmm) REVERT: C 30 LYS cc_start: 0.7882 (mtmm) cc_final: 0.7592 (mttt) REVERT: C 34 GLU cc_start: 0.7866 (pp20) cc_final: 0.7400 (pp20) REVERT: C 52 LYS cc_start: 0.8596 (tttm) cc_final: 0.8327 (tttm) REVERT: C 59 ARG cc_start: 0.8161 (mtp-110) cc_final: 0.7959 (mtp-110) REVERT: C 69 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8329 (tm-30) REVERT: C 84 MET cc_start: 0.7685 (ptp) cc_final: 0.7369 (ptp) REVERT: C 87 GLU cc_start: 0.8263 (pt0) cc_final: 0.7995 (pt0) REVERT: C 91 LYS cc_start: 0.8719 (tppt) cc_final: 0.7803 (tppt) REVERT: C 92 VAL cc_start: 0.9056 (m) cc_final: 0.8795 (m) REVERT: C 94 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8431 (ttpt) REVERT: C 95 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7607 (mt-10) REVERT: C 98 GLU cc_start: 0.7330 (tp30) cc_final: 0.6081 (tp30) REVERT: C 102 ASP cc_start: 0.7977 (m-30) cc_final: 0.7078 (m-30) REVERT: C 119 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7838 (tp30) REVERT: C 125 LEU cc_start: 0.8316 (mt) cc_final: 0.8067 (mt) REVERT: C 126 LYS cc_start: 0.8856 (tttm) cc_final: 0.8600 (tttm) REVERT: C 127 MET cc_start: 0.8208 (mmm) cc_final: 0.7589 (mmp) REVERT: C 133 ARG cc_start: 0.8862 (ttp-110) cc_final: 0.8344 (ttp-110) REVERT: C 135 LEU cc_start: 0.8660 (mt) cc_final: 0.8426 (mt) REVERT: C 149 GLU cc_start: 0.8174 (tp30) cc_final: 0.7763 (tp30) REVERT: C 153 LYS cc_start: 0.8569 (tppt) cc_final: 0.7927 (tppt) REVERT: C 155 TYR cc_start: 0.8053 (m-80) cc_final: 0.7124 (m-80) REVERT: C 170 HIS cc_start: 0.8073 (t-90) cc_final: 0.7631 (t70) REVERT: C 174 LEU cc_start: 0.8148 (mt) cc_final: 0.7845 (mt) REVERT: C 180 PHE cc_start: 0.8627 (m-80) cc_final: 0.7877 (m-80) REVERT: C 197 LEU cc_start: 0.8362 (mm) cc_final: 0.8112 (mm) REVERT: C 204 ASP cc_start: 0.8242 (t0) cc_final: 0.7963 (t0) REVERT: C 218 LYS cc_start: 0.7615 (mmpt) cc_final: 0.7374 (mmpt) REVERT: C 224 MET cc_start: 0.7610 (ptm) cc_final: 0.6510 (ptm) REVERT: C 225 GLN cc_start: 0.7430 (mm110) cc_final: 0.6662 (mm110) REVERT: D 10 VAL cc_start: 0.8959 (t) cc_final: 0.8731 (t) REVERT: D 14 LYS cc_start: 0.8763 (mttt) cc_final: 0.8344 (mttm) REVERT: D 25 MET cc_start: 0.7697 (pmm) cc_final: 0.7287 (pmm) REVERT: D 29 MET cc_start: 0.8996 (tpp) cc_final: 0.8555 (mmm) REVERT: D 30 LYS cc_start: 0.8075 (mtmt) cc_final: 0.7681 (mttt) REVERT: D 34 GLU cc_start: 0.8032 (pp20) cc_final: 0.7603 (pp20) REVERT: D 43 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8244 (mt-10) REVERT: D 52 LYS cc_start: 0.8648 (tptm) cc_final: 0.8299 (tptm) REVERT: D 59 ARG cc_start: 0.8336 (mtp-110) cc_final: 0.7910 (mtp180) REVERT: D 65 ILE cc_start: 0.8737 (pt) cc_final: 0.8465 (pt) REVERT: D 66 SER cc_start: 0.7994 (m) cc_final: 0.7653 (m) REVERT: D 84 MET cc_start: 0.7645 (ptp) cc_final: 0.7054 (ptp) REVERT: D 87 GLU cc_start: 0.8272 (pt0) cc_final: 0.7919 (pt0) REVERT: D 91 LYS cc_start: 0.8740 (tppt) cc_final: 0.8023 (tppt) REVERT: D 93 GLU cc_start: 0.8675 (tt0) cc_final: 0.8243 (tt0) REVERT: D 97 ARG cc_start: 0.8779 (mtm110) cc_final: 0.8337 (ttm110) REVERT: D 102 ASP cc_start: 0.7722 (m-30) cc_final: 0.7376 (m-30) REVERT: D 119 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7689 (tp30) REVERT: D 123 PHE cc_start: 0.7900 (t80) cc_final: 0.7641 (t80) REVERT: D 127 MET cc_start: 0.8367 (mmm) cc_final: 0.7749 (mmp) REVERT: D 128 LYS cc_start: 0.8148 (tttt) cc_final: 0.7716 (tttt) REVERT: D 130 ASP cc_start: 0.7442 (m-30) cc_final: 0.7138 (m-30) REVERT: D 133 ARG cc_start: 0.8620 (ttp-110) cc_final: 0.8208 (ttp-110) REVERT: D 155 TYR cc_start: 0.8073 (m-10) cc_final: 0.7415 (m-80) REVERT: D 170 HIS cc_start: 0.8413 (t-90) cc_final: 0.7889 (t-90) REVERT: D 174 LEU cc_start: 0.8160 (mt) cc_final: 0.7958 (mt) REVERT: D 192 ASP cc_start: 0.8054 (p0) cc_final: 0.7686 (p0) REVERT: D 195 CYS cc_start: 0.8422 (p) cc_final: 0.8181 (p) REVERT: D 220 SER cc_start: 0.7399 (m) cc_final: 0.7106 (m) REVERT: D 224 MET cc_start: 0.7742 (ptm) cc_final: 0.7466 (ptm) REVERT: E 96 ARG cc_start: 0.7575 (ptm160) cc_final: 0.7070 (ptm160) REVERT: E 121 CYS cc_start: 0.7394 (m) cc_final: 0.7059 (m) REVERT: E 125 TYR cc_start: 0.8028 (m-80) cc_final: 0.7159 (m-80) REVERT: E 160 ARG cc_start: 0.7064 (mpp80) cc_final: 0.6759 (mpp80) REVERT: E 175 LYS cc_start: 0.8731 (ptmt) cc_final: 0.8193 (ptmt) REVERT: E 187 MET cc_start: 0.5977 (mtt) cc_final: 0.5647 (mtt) REVERT: E 206 LEU cc_start: 0.6742 (tp) cc_final: 0.6388 (tp) REVERT: E 219 MET cc_start: 0.7860 (mtp) cc_final: 0.7534 (mtp) REVERT: E 227 ARG cc_start: 0.7675 (mtm180) cc_final: 0.6947 (mtm180) REVERT: E 235 LEU cc_start: 0.8711 (mt) cc_final: 0.8235 (mt) REVERT: E 249 MET cc_start: 0.8257 (ppp) cc_final: 0.7997 (ppp) REVERT: E 253 LEU cc_start: 0.8780 (mt) cc_final: 0.8552 (mt) REVERT: E 256 MET cc_start: 0.7680 (ptm) cc_final: 0.7402 (ptm) REVERT: E 316 TYR cc_start: 0.7955 (t80) cc_final: 0.7580 (t80) REVERT: E 319 ASN cc_start: 0.8118 (t0) cc_final: 0.6893 (t0) REVERT: E 320 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7619 (mm-30) REVERT: E 324 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7576 (mmtt) REVERT: E 340 LYS cc_start: 0.8812 (mttp) cc_final: 0.8208 (tptp) REVERT: E 344 LYS cc_start: 0.8513 (tmmt) cc_final: 0.8095 (mttt) REVERT: E 356 MET cc_start: 0.7058 (ppp) cc_final: 0.6655 (ppp) REVERT: E 362 LYS cc_start: 0.8890 (mppt) cc_final: 0.8532 (mmtt) REVERT: E 363 ARG cc_start: 0.8595 (mmp80) cc_final: 0.8328 (mmp80) REVERT: E 371 PHE cc_start: 0.7592 (m-80) cc_final: 0.7015 (m-80) REVERT: F 88 LYS cc_start: 0.8471 (mmmt) cc_final: 0.7977 (mmmt) REVERT: F 175 LYS cc_start: 0.8670 (ptmt) cc_final: 0.8189 (ptmt) REVERT: F 195 ASN cc_start: 0.8246 (m110) cc_final: 0.7337 (t0) REVERT: F 219 MET cc_start: 0.7638 (mtp) cc_final: 0.7353 (mtp) REVERT: F 227 ARG cc_start: 0.7570 (mtm180) cc_final: 0.6993 (mtm180) REVERT: F 233 GLU cc_start: 0.8202 (pt0) cc_final: 0.7966 (pt0) REVERT: F 249 MET cc_start: 0.8214 (ppp) cc_final: 0.7927 (ppp) REVERT: F 253 LEU cc_start: 0.8727 (mt) cc_final: 0.8510 (mt) REVERT: F 256 MET cc_start: 0.7771 (ptm) cc_final: 0.7374 (ptm) REVERT: F 316 TYR cc_start: 0.7973 (t80) cc_final: 0.7467 (t80) REVERT: F 319 ASN cc_start: 0.7898 (t0) cc_final: 0.6604 (t0) REVERT: F 320 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7626 (mm-30) REVERT: F 324 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7457 (mmtt) REVERT: F 334 PHE cc_start: 0.8406 (t80) cc_final: 0.8159 (t80) REVERT: F 360 PHE cc_start: 0.8489 (p90) cc_final: 0.8105 (p90) REVERT: F 371 PHE cc_start: 0.7510 (m-80) cc_final: 0.7061 (m-80) outliers start: 0 outliers final: 0 residues processed: 675 average time/residue: 0.1309 time to fit residues: 121.8893 Evaluate side-chains 667 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 667 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS A 388 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN C 200 GLN D 200 GLN E 195 ASN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.134176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.110205 restraints weight = 28356.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.114249 restraints weight = 16049.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.117142 restraints weight = 10530.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.119211 restraints weight = 7580.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.120667 restraints weight = 5814.935| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 12876 Z= 0.259 Angle : 0.814 19.769 17364 Z= 0.430 Chirality : 0.050 0.200 1918 Planarity : 0.005 0.086 2216 Dihedral : 5.786 38.313 1740 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.07 % Allowed : 0.58 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.21), residues: 1538 helix: 0.21 (0.16), residues: 892 sheet: -2.87 (0.49), residues: 68 loop : -1.07 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 181 TYR 0.055 0.003 TYR D 101 PHE 0.035 0.002 PHE C 180 TRP 0.058 0.003 TRP B 368 HIS 0.014 0.002 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00497 (12876) covalent geometry : angle 0.81429 (17364) hydrogen bonds : bond 0.04441 ( 710) hydrogen bonds : angle 5.10183 ( 2070) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3076 Ramachandran restraints generated. 1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 678 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.7600 (mtm) cc_final: 0.7200 (mtm) REVERT: A 362 THR cc_start: 0.8019 (m) cc_final: 0.7808 (m) REVERT: A 367 LYS cc_start: 0.7598 (mmtt) cc_final: 0.6770 (mmtt) REVERT: A 375 LYS cc_start: 0.7603 (ttpp) cc_final: 0.7270 (ttpp) REVERT: A 387 PHE cc_start: 0.8149 (t80) cc_final: 0.7170 (t80) REVERT: A 390 PHE cc_start: 0.8069 (t80) cc_final: 0.7413 (t80) REVERT: A 391 ARG cc_start: 0.8357 (mmt90) cc_final: 0.7721 (mmm-85) REVERT: A 399 LYS cc_start: 0.8400 (mmtp) cc_final: 0.8019 (mmtp) REVERT: A 404 ASN cc_start: 0.7904 (m110) cc_final: 0.7264 (m110) REVERT: A 408 PHE cc_start: 0.7325 (t80) cc_final: 0.7113 (t80) REVERT: A 409 MET cc_start: 0.7314 (mtt) cc_final: 0.6919 (mtt) REVERT: A 412 MET cc_start: 0.6077 (ppp) cc_final: 0.5485 (ppp) REVERT: A 414 LYS cc_start: 0.8255 (tppt) cc_final: 0.8024 (tppt) REVERT: A 417 LEU cc_start: 0.8007 (pt) cc_final: 0.7519 (pt) REVERT: A 419 ILE cc_start: 0.7319 (mm) cc_final: 0.6793 (mm) REVERT: A 422 GLN cc_start: 0.8212 (tt0) cc_final: 0.7297 (pt0) REVERT: A 425 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6653 (mm-30) REVERT: A 429 LEU cc_start: 0.8092 (tp) cc_final: 0.7826 (tp) REVERT: A 431 LYS cc_start: 0.8442 (mttp) cc_final: 0.7986 (mttp) REVERT: A 439 LYS cc_start: 0.8382 (mppt) cc_final: 0.7707 (mppt) REVERT: A 441 GLN cc_start: 0.8061 (pt0) cc_final: 0.7670 (pt0) REVERT: A 442 MET cc_start: 0.7567 (mpp) cc_final: 0.7172 (mpp) REVERT: A 444 GLN cc_start: 0.7978 (mt0) cc_final: 0.7538 (mt0) REVERT: A 445 LEU cc_start: 0.8667 (tp) cc_final: 0.8425 (tp) REVERT: A 446 ILE cc_start: 0.8726 (mt) cc_final: 0.8505 (mt) REVERT: A 450 ARG cc_start: 0.8396 (ttp-170) cc_final: 0.7999 (ptm-80) REVERT: A 458 TYR cc_start: 0.8526 (t80) cc_final: 0.7965 (t80) REVERT: A 463 ASN cc_start: 0.7184 (m-40) cc_final: 0.6980 (m-40) REVERT: A 466 HIS cc_start: 0.8395 (t-90) cc_final: 0.7971 (t-90) REVERT: A 470 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7712 (mtpt) REVERT: A 483 LYS cc_start: 0.8285 (mttt) cc_final: 0.7737 (mttt) REVERT: A 484 ILE cc_start: 0.7880 (mt) cc_final: 0.7491 (mt) REVERT: A 504 GLN cc_start: 0.8187 (mt0) cc_final: 0.7907 (mt0) REVERT: A 511 TRP cc_start: 0.7379 (m-90) cc_final: 0.7092 (m-90) REVERT: A 512 MET cc_start: 0.6294 (ttm) cc_final: 0.5664 (ttm) REVERT: A 517 ILE cc_start: 0.8740 (mt) cc_final: 0.8377 (mt) REVERT: A 518 ARG cc_start: 0.8270 (ptp-110) cc_final: 0.7767 (ptp-110) REVERT: A 532 TYR cc_start: 0.8112 (t80) cc_final: 0.7832 (t80) REVERT: A 534 TYR cc_start: 0.8391 (t80) cc_final: 0.7869 (t80) REVERT: A 541 LEU cc_start: 0.8641 (mt) cc_final: 0.8285 (mt) REVERT: A 542 MET cc_start: 0.7292 (mtp) cc_final: 0.7012 (mtp) REVERT: A 545 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7422 (mt-10) REVERT: A 560 MET cc_start: 0.8400 (mmp) cc_final: 0.7702 (mmp) REVERT: A 563 ARG cc_start: 0.8717 (mmm-85) cc_final: 0.8101 (ttm-80) REVERT: A 572 LYS cc_start: 0.8354 (mmmm) cc_final: 0.7940 (mmmm) REVERT: A 574 TYR cc_start: 0.7873 (m-10) cc_final: 0.7154 (m-10) REVERT: A 581 MET cc_start: 0.7680 (mmm) cc_final: 0.7146 (mmm) REVERT: A 601 GLN cc_start: 0.8405 (tt0) cc_final: 0.8095 (tm-30) REVERT: A 622 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7069 (tm-30) REVERT: B 342 TRP cc_start: 0.8458 (m100) cc_final: 0.8160 (m100) REVERT: B 350 MET cc_start: 0.7591 (mtm) cc_final: 0.7136 (mtm) REVERT: B 362 THR cc_start: 0.7860 (m) cc_final: 0.7628 (m) REVERT: B 367 LYS cc_start: 0.7705 (mmtt) cc_final: 0.6790 (mmtt) REVERT: B 375 LYS cc_start: 0.7648 (ttpp) cc_final: 0.7441 (ttpp) REVERT: B 383 THR cc_start: 0.8393 (p) cc_final: 0.7888 (p) REVERT: B 386 GLN cc_start: 0.8624 (mt0) cc_final: 0.8299 (mt0) REVERT: B 387 PHE cc_start: 0.8289 (t80) cc_final: 0.7964 (t80) REVERT: B 399 LYS cc_start: 0.8480 (mmtp) cc_final: 0.7994 (mmtp) REVERT: B 409 MET cc_start: 0.7455 (mtm) cc_final: 0.6936 (mtm) REVERT: B 412 MET cc_start: 0.5951 (ppp) cc_final: 0.5429 (ppp) REVERT: B 416 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7519 (p0) REVERT: B 417 LEU cc_start: 0.8203 (pt) cc_final: 0.7949 (pt) REVERT: B 419 ILE cc_start: 0.7242 (mm) cc_final: 0.6836 (mm) REVERT: B 422 GLN cc_start: 0.8268 (tt0) cc_final: 0.7453 (pt0) REVERT: B 424 CYS cc_start: 0.7816 (m) cc_final: 0.7443 (m) REVERT: B 429 LEU cc_start: 0.8305 (tp) cc_final: 0.8041 (tp) REVERT: B 431 LYS cc_start: 0.8324 (mptt) cc_final: 0.8004 (mptt) REVERT: B 439 LYS cc_start: 0.8641 (mppt) cc_final: 0.8215 (mppt) REVERT: B 442 MET cc_start: 0.7504 (mpp) cc_final: 0.7086 (mpp) REVERT: B 456 MET cc_start: 0.7868 (mmm) cc_final: 0.6828 (mmm) REVERT: B 458 TYR cc_start: 0.8553 (t80) cc_final: 0.7572 (t80) REVERT: B 463 ASN cc_start: 0.7389 (m-40) cc_final: 0.7147 (m-40) REVERT: B 466 HIS cc_start: 0.8423 (t-90) cc_final: 0.7370 (t70) REVERT: B 469 MET cc_start: 0.8017 (tpt) cc_final: 0.7705 (tpp) REVERT: B 470 LYS cc_start: 0.8424 (mtpt) cc_final: 0.7889 (mtpt) REVERT: B 473 ASN cc_start: 0.7671 (m110) cc_final: 0.7079 (m110) REVERT: B 483 LYS cc_start: 0.8382 (mttp) cc_final: 0.7614 (mttp) REVERT: B 484 ILE cc_start: 0.7896 (mt) cc_final: 0.6904 (mt) REVERT: B 511 TRP cc_start: 0.7356 (m-90) cc_final: 0.7093 (m-90) REVERT: B 518 ARG cc_start: 0.8039 (ptp-110) cc_final: 0.7667 (ptp-110) REVERT: B 527 PHE cc_start: 0.8469 (m-80) cc_final: 0.8212 (m-80) REVERT: B 528 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7323 (mm-40) REVERT: B 533 SER cc_start: 0.8660 (m) cc_final: 0.8326 (p) REVERT: B 534 TYR cc_start: 0.8501 (t80) cc_final: 0.8013 (t80) REVERT: B 536 ILE cc_start: 0.8546 (mm) cc_final: 0.8298 (mm) REVERT: B 539 TYR cc_start: 0.8215 (t80) cc_final: 0.7980 (t80) REVERT: B 542 MET cc_start: 0.7427 (mtp) cc_final: 0.7156 (mtp) REVERT: B 545 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7399 (mt-10) REVERT: B 551 ILE cc_start: 0.8763 (mp) cc_final: 0.8461 (mp) REVERT: B 560 MET cc_start: 0.8344 (tpp) cc_final: 0.7567 (tpp) REVERT: B 563 ARG cc_start: 0.8414 (mmm-85) cc_final: 0.7926 (ttm-80) REVERT: B 581 MET cc_start: 0.7936 (mmm) cc_final: 0.7336 (mmm) REVERT: B 583 ARG cc_start: 0.8745 (ptp-170) cc_final: 0.8182 (ptp-110) REVERT: B 585 VAL cc_start: 0.8800 (p) cc_final: 0.8555 (m) REVERT: B 601 GLN cc_start: 0.8561 (tt0) cc_final: 0.8326 (tt0) REVERT: B 618 ARG cc_start: 0.8144 (ptm160) cc_final: 0.7678 (ptm160) REVERT: C 6 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8470 (ttpt) REVERT: C 9 LEU cc_start: 0.8148 (mt) cc_final: 0.7924 (mt) REVERT: C 25 MET cc_start: 0.7610 (pmm) cc_final: 0.7136 (pmm) REVERT: C 29 MET cc_start: 0.8952 (mmt) cc_final: 0.8659 (mmm) REVERT: C 34 GLU cc_start: 0.7943 (pp20) cc_final: 0.7509 (pp20) REVERT: C 43 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8257 (mt-10) REVERT: C 52 LYS cc_start: 0.8607 (tttm) cc_final: 0.8374 (tttm) REVERT: C 59 ARG cc_start: 0.8135 (mtp-110) cc_final: 0.7900 (mtp-110) REVERT: C 69 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8318 (tm-30) REVERT: C 84 MET cc_start: 0.7792 (ptp) cc_final: 0.7469 (ptp) REVERT: C 87 GLU cc_start: 0.8283 (pt0) cc_final: 0.7963 (pt0) REVERT: C 91 LYS cc_start: 0.8733 (tppt) cc_final: 0.7849 (tppt) REVERT: C 92 VAL cc_start: 0.9108 (m) cc_final: 0.8763 (m) REVERT: C 94 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8401 (ttpt) REVERT: C 95 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7726 (mt-10) REVERT: C 97 ARG cc_start: 0.8629 (mtm110) cc_final: 0.8304 (mtm110) REVERT: C 98 GLU cc_start: 0.7368 (tp30) cc_final: 0.6134 (tp30) REVERT: C 102 ASP cc_start: 0.7994 (m-30) cc_final: 0.7021 (m-30) REVERT: C 119 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7864 (tp30) REVERT: C 126 LYS cc_start: 0.8871 (tttm) cc_final: 0.8351 (tttm) REVERT: C 127 MET cc_start: 0.8236 (mmm) cc_final: 0.7570 (mmp) REVERT: C 128 LYS cc_start: 0.8162 (tttt) cc_final: 0.7751 (tttt) REVERT: C 130 ASP cc_start: 0.7825 (m-30) cc_final: 0.7221 (m-30) REVERT: C 133 ARG cc_start: 0.8846 (ttp-110) cc_final: 0.8423 (ttp-110) REVERT: C 149 GLU cc_start: 0.8221 (tp30) cc_final: 0.7824 (tp30) REVERT: C 153 LYS cc_start: 0.8650 (tppt) cc_final: 0.7997 (tppt) REVERT: C 155 TYR cc_start: 0.7930 (m-80) cc_final: 0.6944 (m-80) REVERT: C 170 HIS cc_start: 0.8193 (t-90) cc_final: 0.7853 (t-90) REVERT: C 172 ILE cc_start: 0.8530 (tt) cc_final: 0.8158 (tt) REVERT: C 174 LEU cc_start: 0.8140 (mt) cc_final: 0.7832 (mt) REVERT: C 180 PHE cc_start: 0.8717 (m-80) cc_final: 0.7909 (m-80) REVERT: C 204 ASP cc_start: 0.8266 (t0) cc_final: 0.8005 (t0) REVERT: C 218 LYS cc_start: 0.7666 (mmpt) cc_final: 0.7412 (mmpt) REVERT: C 224 MET cc_start: 0.7734 (ptm) cc_final: 0.6562 (ptm) REVERT: C 225 GLN cc_start: 0.7444 (mm110) cc_final: 0.6693 (mm110) REVERT: D 6 LYS cc_start: 0.8652 (pttp) cc_final: 0.8192 (pttp) REVERT: D 7 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7973 (mm-30) REVERT: D 14 LYS cc_start: 0.8765 (mttt) cc_final: 0.8346 (mttm) REVERT: D 20 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7145 (tm-30) REVERT: D 25 MET cc_start: 0.7861 (pmm) cc_final: 0.7405 (pmm) REVERT: D 29 MET cc_start: 0.9003 (tpp) cc_final: 0.8534 (mmm) REVERT: D 34 GLU cc_start: 0.8067 (pp20) cc_final: 0.7646 (pp20) REVERT: D 52 LYS cc_start: 0.8749 (tptm) cc_final: 0.8421 (tptm) REVERT: D 59 ARG cc_start: 0.8326 (mtp-110) cc_final: 0.7978 (mtp180) REVERT: D 63 ARG cc_start: 0.8226 (tpp-160) cc_final: 0.7802 (tpp-160) REVERT: D 65 ILE cc_start: 0.8752 (pt) cc_final: 0.8499 (pt) REVERT: D 66 SER cc_start: 0.8032 (m) cc_final: 0.7590 (m) REVERT: D 84 MET cc_start: 0.7697 (ptp) cc_final: 0.7091 (ptp) REVERT: D 87 GLU cc_start: 0.8291 (pt0) cc_final: 0.7995 (pt0) REVERT: D 91 LYS cc_start: 0.8767 (tppt) cc_final: 0.8038 (tppt) REVERT: D 93 GLU cc_start: 0.8729 (tt0) cc_final: 0.8327 (tt0) REVERT: D 97 ARG cc_start: 0.8796 (mtm110) cc_final: 0.8361 (ttm110) REVERT: D 102 ASP cc_start: 0.7710 (m-30) cc_final: 0.7371 (m-30) REVERT: D 119 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7808 (tp30) REVERT: D 123 PHE cc_start: 0.7992 (t80) cc_final: 0.7572 (t80) REVERT: D 127 MET cc_start: 0.8348 (mmm) cc_final: 0.8090 (mmm) REVERT: D 128 LYS cc_start: 0.8191 (tttt) cc_final: 0.7808 (tttt) REVERT: D 130 ASP cc_start: 0.7422 (m-30) cc_final: 0.7074 (m-30) REVERT: D 133 ARG cc_start: 0.8666 (ttp-110) cc_final: 0.8233 (ttp-110) REVERT: D 155 TYR cc_start: 0.8147 (m-10) cc_final: 0.7582 (m-80) REVERT: D 167 GLN cc_start: 0.7978 (tp-100) cc_final: 0.7734 (tp-100) REVERT: D 170 HIS cc_start: 0.8450 (t-90) cc_final: 0.7919 (t-90) REVERT: D 174 LEU cc_start: 0.8208 (mt) cc_final: 0.7946 (mt) REVERT: D 192 ASP cc_start: 0.8222 (p0) cc_final: 0.7821 (p0) REVERT: D 195 CYS cc_start: 0.8488 (p) cc_final: 0.8284 (p) REVERT: D 220 SER cc_start: 0.7612 (m) cc_final: 0.7361 (m) REVERT: D 224 MET cc_start: 0.7840 (ptm) cc_final: 0.7576 (ptm) REVERT: D 229 ASP cc_start: 0.8175 (t70) cc_final: 0.7925 (t70) REVERT: E 96 ARG cc_start: 0.7557 (ptm160) cc_final: 0.7159 (ptm160) REVERT: E 125 TYR cc_start: 0.8102 (m-80) cc_final: 0.7262 (m-80) REVERT: E 144 GLU cc_start: 0.7875 (pp20) cc_final: 0.7224 (pp20) REVERT: E 160 ARG cc_start: 0.7103 (mpp80) cc_final: 0.6685 (mpp80) REVERT: E 175 LYS cc_start: 0.8789 (ptmt) cc_final: 0.8258 (ptmt) REVERT: E 180 LEU cc_start: 0.9090 (tp) cc_final: 0.8764 (tp) REVERT: E 187 MET cc_start: 0.6074 (mtt) cc_final: 0.5772 (mtt) REVERT: E 192 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7621 (ttpt) REVERT: E 206 LEU cc_start: 0.6748 (tp) cc_final: 0.6276 (tp) REVERT: E 219 MET cc_start: 0.7782 (mtp) cc_final: 0.7420 (mtp) REVERT: E 227 ARG cc_start: 0.7853 (mtm180) cc_final: 0.6755 (mtm180) REVERT: E 235 LEU cc_start: 0.8818 (mt) cc_final: 0.8522 (mt) REVERT: E 249 MET cc_start: 0.8291 (ppp) cc_final: 0.8025 (ppp) REVERT: E 253 LEU cc_start: 0.8773 (mt) cc_final: 0.8514 (mt) REVERT: E 256 MET cc_start: 0.7721 (ptm) cc_final: 0.7348 (ptm) REVERT: E 313 LEU cc_start: 0.8222 (mt) cc_final: 0.7952 (mt) REVERT: E 316 TYR cc_start: 0.7999 (t80) cc_final: 0.7616 (t80) REVERT: E 319 ASN cc_start: 0.8216 (t0) cc_final: 0.7004 (t0) REVERT: E 320 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7686 (mm-30) REVERT: E 324 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7583 (mmtt) REVERT: E 340 LYS cc_start: 0.8869 (mttp) cc_final: 0.8253 (tptp) REVERT: E 344 LYS cc_start: 0.8549 (tmmt) cc_final: 0.8123 (mttt) REVERT: E 363 ARG cc_start: 0.8585 (mmp80) cc_final: 0.8312 (mmp80) REVERT: E 371 PHE cc_start: 0.7662 (m-80) cc_final: 0.7110 (m-80) REVERT: F 88 LYS cc_start: 0.8484 (mmmt) cc_final: 0.8004 (mmmt) REVERT: F 96 ARG cc_start: 0.7693 (ptm160) cc_final: 0.7399 (ptm160) REVERT: F 175 LYS cc_start: 0.8757 (ptmt) cc_final: 0.8259 (ptmt) REVERT: F 195 ASN cc_start: 0.8353 (m110) cc_final: 0.7489 (t0) REVERT: F 219 MET cc_start: 0.7586 (mtp) cc_final: 0.7294 (mtp) REVERT: F 227 ARG cc_start: 0.7650 (mtm180) cc_final: 0.7043 (mtm180) REVERT: F 249 MET cc_start: 0.8328 (ppp) cc_final: 0.8008 (ppp) REVERT: F 253 LEU cc_start: 0.8706 (mt) cc_final: 0.8490 (mt) REVERT: F 256 MET cc_start: 0.7753 (ptm) cc_final: 0.7467 (ptm) REVERT: F 263 ILE cc_start: 0.8875 (tp) cc_final: 0.8449 (mp) REVERT: F 316 TYR cc_start: 0.7997 (t80) cc_final: 0.7511 (t80) REVERT: F 319 ASN cc_start: 0.7978 (t0) cc_final: 0.6659 (t0) REVERT: F 320 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7575 (mm-30) REVERT: F 324 LYS cc_start: 0.7931 (mmtt) cc_final: 0.7482 (mmtt) REVERT: F 334 PHE cc_start: 0.8346 (t80) cc_final: 0.8145 (t80) REVERT: F 360 PHE cc_start: 0.8498 (p90) cc_final: 0.8063 (p90) REVERT: F 371 PHE cc_start: 0.7520 (m-80) cc_final: 0.7081 (m-80) outliers start: 1 outliers final: 0 residues processed: 678 average time/residue: 0.1244 time to fit residues: 116.2968 Evaluate side-chains 664 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 663 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 125 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS B 369 HIS ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 243 GLN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.127591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.104157 restraints weight = 28793.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.108394 restraints weight = 16009.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.111448 restraints weight = 10270.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.113548 restraints weight = 7175.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.115008 restraints weight = 5349.405| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 12876 Z= 0.208 Angle : 0.774 16.904 17364 Z= 0.403 Chirality : 0.049 0.236 1918 Planarity : 0.005 0.079 2216 Dihedral : 5.797 38.675 1740 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.20), residues: 1538 helix: 0.18 (0.16), residues: 896 sheet: -2.89 (0.49), residues: 68 loop : -1.08 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 181 TYR 0.051 0.002 TYR D 101 PHE 0.025 0.002 PHE C 202 TRP 0.050 0.004 TRP A 368 HIS 0.014 0.002 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00425 (12876) covalent geometry : angle 0.77448 (17364) hydrogen bonds : bond 0.04255 ( 710) hydrogen bonds : angle 5.05436 ( 2070) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2835.46 seconds wall clock time: 49 minutes 39.40 seconds (2979.40 seconds total)