Starting phenix.real_space_refine on Wed Jul 30 15:56:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8chf_16660/07_2025/8chf_16660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8chf_16660/07_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_16660/07_2025/8chf_16660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8chf_16660/07_2025/8chf_16660.map" model { file = "/net/cci-nas-00/data/ceres_data/8chf_16660/07_2025/8chf_16660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8chf_16660/07_2025/8chf_16660.cif" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.50, per 1000 atoms: 0.59 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: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.24 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: 3.36 Time building geometry restraints manager: 3.67 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: 0.06 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.440 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.710 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), 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 TRP 0.024 0.003 TRP D 234 HIS 0.009 0.002 HIS D 170 PHE 0.032 0.002 PHE D 180 TYR 0.033 0.002 TYR D 185 ARG 0.005 0.001 ARG C 228 Details of bonding type rmsd hydrogen bonds : bond 0.12629 ( 710) hydrogen bonds : angle 5.77320 ( 2070) covalent geometry : bond 0.00564 (12876) covalent geometry : angle 0.81298 (17364) *********************** 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 : 1.310 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: A 387 PHE cc_start: 0.7830 (t80) cc_final: 0.6730 (t80) REVERT: A 392 ASN cc_start: 0.8091 (m-40) cc_final: 0.7822 (m-40) REVERT: A 399 LYS cc_start: 0.8208 (mmtp) cc_final: 0.7758 (mmtp) REVERT: A 412 MET cc_start: 0.6490 (ppp) cc_final: 0.6144 (ppp) REVERT: A 421 THR cc_start: 0.7766 (p) cc_final: 0.7518 (t) REVERT: A 431 LYS cc_start: 0.8085 (mppt) cc_final: 0.7807 (mppt) REVERT: A 439 LYS cc_start: 0.8126 (mppt) cc_final: 0.7569 (mppt) REVERT: A 442 MET cc_start: 0.6933 (mpp) cc_final: 0.6474 (mpp) REVERT: A 451 GLN cc_start: 0.7937 (mt0) cc_final: 0.6616 (tt0) REVERT: A 456 MET cc_start: 0.6524 (mmm) cc_final: 0.6150 (mmm) REVERT: A 460 HIS cc_start: 0.7686 (m170) cc_final: 0.7288 (m90) REVERT: A 463 ASN cc_start: 0.6322 (m-40) cc_final: 0.6098 (m-40) REVERT: A 470 LYS cc_start: 0.8051 (mtpt) cc_final: 0.7545 (mtpt) REVERT: A 516 VAL cc_start: 0.8865 (t) cc_final: 0.8467 (t) REVERT: A 517 ILE cc_start: 0.8731 (mt) cc_final: 0.8516 (mt) REVERT: A 528 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7565 (mm110) REVERT: A 541 LEU cc_start: 0.8164 (mt) cc_final: 0.7539 (mt) REVERT: A 542 MET cc_start: 0.6231 (mtp) cc_final: 0.6016 (mtp) REVERT: A 554 ARG cc_start: 0.7415 (tmm-80) cc_final: 0.6979 (tmm-80) REVERT: A 590 LYS cc_start: 0.7746 (mmtm) cc_final: 0.7314 (mmtm) REVERT: A 592 VAL cc_start: 0.8335 (t) cc_final: 0.7890 (m) REVERT: A 601 GLN cc_start: 0.7965 (tt0) cc_final: 0.7670 (tm-30) REVERT: A 609 LEU cc_start: 0.8494 (tp) cc_final: 0.7760 (tt) REVERT: A 610 GLN cc_start: 0.8015 (mm110) cc_final: 0.7730 (mm110) REVERT: B 351 LEU cc_start: 0.8234 (mp) cc_final: 0.7952 (mt) REVERT: B 365 LYS cc_start: 0.7472 (tttt) cc_final: 0.6811 (tttt) REVERT: B 367 LYS cc_start: 0.7555 (mmtt) cc_final: 0.6716 (mmtt) REVERT: B 393 GLU cc_start: 0.6785 (tp30) cc_final: 0.6319 (tp30) REVERT: B 399 LYS cc_start: 0.8298 (mmtp) cc_final: 0.7786 (mmtp) REVERT: B 412 MET cc_start: 0.6493 (ppp) cc_final: 0.5955 (ppp) REVERT: B 419 ILE cc_start: 0.7133 (mm) cc_final: 0.6844 (mm) REVERT: B 421 THR cc_start: 0.7815 (p) cc_final: 0.7402 (t) REVERT: B 432 HIS cc_start: 0.7013 (m90) cc_final: 0.6309 (m90) REVERT: B 439 LYS cc_start: 0.8352 (mppt) cc_final: 0.7854 (mppt) REVERT: B 441 GLN cc_start: 0.7276 (mt0) cc_final: 0.6699 (mt0) REVERT: B 442 MET cc_start: 0.6918 (mpp) cc_final: 0.6558 (mpp) REVERT: B 450 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.7816 (ttp-170) REVERT: B 458 TYR cc_start: 0.7973 (t80) cc_final: 0.7685 (t80) REVERT: B 470 LYS cc_start: 0.8018 (mtpt) cc_final: 0.7460 (mtpt) REVERT: B 492 VAL cc_start: 0.7925 (t) cc_final: 0.7649 (t) REVERT: B 516 VAL cc_start: 0.8821 (t) cc_final: 0.8506 (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: 0.7532 (mm110) REVERT: B 541 LEU cc_start: 0.8177 (mt) cc_final: 0.7887 (mt) REVERT: B 542 MET cc_start: 0.6488 (mtp) cc_final: 0.6256 (mtp) REVERT: B 545 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7244 (mt-10) REVERT: B 554 ARG cc_start: 0.7418 (tmm-80) cc_final: 0.6914 (tmm-80) REVERT: B 560 MET cc_start: 0.7617 (mmp) cc_final: 0.7059 (mmp) REVERT: B 581 MET cc_start: 0.6798 (tpt) cc_final: 0.6546 (tpt) REVERT: B 583 ARG cc_start: 0.8214 (ptp-170) cc_final: 0.7921 (ptp-110) REVERT: B 590 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7371 (mmtm) REVERT: B 592 VAL cc_start: 0.8199 (t) cc_final: 0.7710 (m) REVERT: B 613 LEU cc_start: 0.8573 (mt) cc_final: 0.8222 (mt) REVERT: B 615 LYS cc_start: 0.7633 (mttm) cc_final: 0.7343 (mttm) REVERT: B 622 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6968 (tm-30) REVERT: C 20 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7007 (tm-30) REVERT: C 29 MET cc_start: 0.8854 (tpp) cc_final: 0.8522 (mmm) REVERT: C 43 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8247 (mt-10) REVERT: C 49 VAL cc_start: 0.7897 (t) cc_final: 0.7412 (t) REVERT: C 51 TYR cc_start: 0.7798 (m-10) cc_final: 0.7588 (m-10) REVERT: C 53 ASN cc_start: 0.7965 (m-40) cc_final: 0.7575 (m-40) REVERT: C 87 GLU cc_start: 0.8098 (pt0) cc_final: 0.7866 (pt0) REVERT: C 91 LYS cc_start: 0.8529 (tppt) cc_final: 0.7706 (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: 0.7847 (mtm110) REVERT: C 98 GLU cc_start: 0.6698 (tp30) cc_final: 0.5797 (tp30) REVERT: C 102 ASP cc_start: 0.7639 (m-30) cc_final: 0.6887 (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: 0.7798 (mt) REVERT: C 126 LYS cc_start: 0.8561 (tttm) cc_final: 0.8354 (tttm) REVERT: C 127 MET cc_start: 0.8016 (mmm) cc_final: 0.7562 (mmp) REVERT: C 132 TYR cc_start: 0.7918 (m-80) cc_final: 0.7238 (m-80) REVERT: C 134 TYR cc_start: 0.8001 (m-10) cc_final: 0.7759 (m-80) REVERT: C 150 ASP cc_start: 0.8065 (m-30) cc_final: 0.7753 (m-30) REVERT: C 153 LYS cc_start: 0.8760 (tppt) cc_final: 0.7975 (tppt) REVERT: C 157 ASP cc_start: 0.7359 (t0) cc_final: 0.7070 (t0) REVERT: C 159 PHE cc_start: 0.8056 (t80) cc_final: 0.7817 (t80) REVERT: C 176 LEU cc_start: 0.8745 (tt) cc_final: 0.8133 (tt) REVERT: C 180 PHE cc_start: 0.8064 (m-80) cc_final: 0.7406 (m-80) REVERT: C 195 CYS cc_start: 0.8070 (m) cc_final: 0.7818 (m) REVERT: C 224 MET cc_start: 0.7304 (ptm) cc_final: 0.6593 (ptm) REVERT: C 225 GLN cc_start: 0.7477 (mm110) cc_final: 0.6815 (mm110) REVERT: D 14 LYS cc_start: 0.8789 (mttt) cc_final: 0.8545 (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: 0.8037 (t) REVERT: D 34 GLU cc_start: 0.7845 (pp20) cc_final: 0.7464 (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: 0.7472 (mtp85) REVERT: D 65 ILE cc_start: 0.8688 (pt) cc_final: 0.8238 (pt) REVERT: D 66 SER cc_start: 0.8004 (m) cc_final: 0.7334 (m) REVERT: D 91 LYS cc_start: 0.8545 (tppt) cc_final: 0.7602 (tppt) REVERT: D 93 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7946 (mt-10) REVERT: D 95 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7416 (mt-10) REVERT: D 119 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7803 (tp30) REVERT: D 128 LYS cc_start: 0.8076 (tttt) cc_final: 0.7637 (tttt) REVERT: D 133 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.7855 (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: 0.7734 (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: 0.7250 (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: 0.7778 (mptt) REVERT: D 195 CYS cc_start: 0.7952 (m) cc_final: 0.7662 (m) REVERT: D 197 LEU cc_start: 0.8455 (mm) cc_final: 0.8221 (mm) REVERT: D 220 SER cc_start: 0.7058 (m) cc_final: 0.6805 (m) REVERT: D 224 MET cc_start: 0.7170 (ptm) cc_final: 0.6370 (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: 0.7288 (m) REVERT: E 160 ARG cc_start: 0.7508 (mpp80) cc_final: 0.6224 (mtt90) REVERT: E 175 LYS cc_start: 0.8653 (ptmt) cc_final: 0.8129 (ptmt) REVERT: E 187 MET cc_start: 0.6403 (mtt) cc_final: 0.6139 (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: 0.7168 (tm-30) REVERT: E 253 LEU cc_start: 0.8769 (mt) cc_final: 0.8562 (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: 0.5681 (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: 0.7250 (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: 0.7503 (mm-30) REVERT: E 333 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8320 (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: 0.7163 (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: 0.8172 (ptmt) REVERT: F 195 ASN cc_start: 0.7088 (t0) cc_final: 0.6870 (t0) REVERT: F 206 LEU cc_start: 0.6739 (tp) cc_final: 0.6420 (tp) REVERT: F 219 MET cc_start: 0.7549 (mtp) cc_final: 0.7324 (mtp) REVERT: F 270 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7605 (mt-10) REVERT: F 316 TYR cc_start: 0.7743 (t80) cc_final: 0.7210 (t80) REVERT: F 318 VAL cc_start: 0.8492 (p) cc_final: 0.8213 (m) REVERT: F 319 ASN cc_start: 0.7733 (t0) cc_final: 0.6510 (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: 0.2805 time to fit residues: 259.1792 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 : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 120 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.128912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.106072 restraints weight = 28782.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.110351 restraints weight = 15761.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.113252 restraints weight = 10000.176| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 12876 Z= 0.168 Angle : 0.675 12.772 17364 Z= 0.354 Chirality : 0.045 0.187 1918 Planarity : 0.005 0.066 2216 Dihedral : 6.512 114.456 1740 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.07 % Allowed : 5.69 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1538 helix: 0.52 (0.16), residues: 892 sheet: -2.95 (0.46), residues: 88 loop : -1.04 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 368 HIS 0.007 0.002 HIS A 466 PHE 0.020 0.002 PHE A 387 TYR 0.040 0.003 TYR C 101 ARG 0.014 0.001 ARG F 181 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 710) hydrogen bonds : angle 4.97512 ( 2070) covalent geometry : bond 0.00350 (12876) covalent geometry : angle 0.67512 (17364) *********************** 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 673 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 672 time to evaluate : 1.293 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: A 343 GLU cc_start: 0.7950 (tt0) cc_final: 0.7661 (tt0) REVERT: A 350 MET cc_start: 0.7530 (mtm) cc_final: 0.7097 (mtm) REVERT: A 351 LEU cc_start: 0.8571 (mt) cc_final: 0.8371 (mt) REVERT: A 359 SER cc_start: 0.8296 (m) cc_final: 0.7841 (p) REVERT: A 387 PHE cc_start: 0.8207 (t80) cc_final: 0.7477 (t80) REVERT: A 391 ARG cc_start: 0.8388 (mmt90) cc_final: 0.7810 (mmm-85) REVERT: A 392 ASN cc_start: 0.8310 (m-40) cc_final: 0.7938 (m-40) REVERT: A 399 LYS cc_start: 0.8331 (mmtp) cc_final: 0.7822 (mmtp) REVERT: A 402 HIS cc_start: 0.7964 (t-90) cc_final: 0.7485 (t-90) REVERT: A 409 MET cc_start: 0.7430 (mtt) cc_final: 0.7035 (mtt) REVERT: A 412 MET cc_start: 0.6399 (ppp) cc_final: 0.5730 (ppp) REVERT: A 416 ASN cc_start: 0.7502 (p0) cc_final: 0.7042 (p0) REVERT: A 422 GLN cc_start: 0.8371 (tt0) cc_final: 0.7538 (pt0) REVERT: A 423 TRP cc_start: 0.8017 (t-100) cc_final: 0.7503 (t60) REVERT: A 425 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6631 (mm-30) REVERT: A 431 LYS cc_start: 0.8244 (mppt) cc_final: 0.7881 (mppt) REVERT: A 439 LYS cc_start: 0.8203 (mppt) cc_final: 0.7641 (mppt) REVERT: A 444 GLN cc_start: 0.7974 (mt0) cc_final: 0.7712 (mp10) REVERT: A 450 ARG cc_start: 0.8404 (ttp-170) cc_final: 0.7767 (ttp-170) REVERT: A 451 GLN cc_start: 0.8102 (mt0) cc_final: 0.6851 (tt0) REVERT: A 456 MET cc_start: 0.8192 (mmm) cc_final: 0.7658 (mmm) REVERT: A 458 TYR cc_start: 0.8587 (t80) cc_final: 0.8133 (t80) REVERT: A 460 HIS cc_start: 0.8407 (m170) cc_final: 0.8146 (m90) REVERT: A 466 HIS cc_start: 0.8635 (t-90) cc_final: 0.8134 (t-90) REVERT: A 512 MET cc_start: 0.5824 (ttm) cc_final: 0.5467 (ttm) REVERT: A 516 VAL cc_start: 0.8656 (t) cc_final: 0.8240 (t) REVERT: A 518 ARG cc_start: 0.8210 (ptp-110) cc_final: 0.7263 (ptp-110) REVERT: A 528 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7239 (mm110) REVERT: A 534 TYR cc_start: 0.8500 (t80) cc_final: 0.8260 (t80) REVERT: A 541 LEU cc_start: 0.8643 (mt) cc_final: 0.8263 (mt) REVERT: A 542 MET cc_start: 0.7257 (mtp) cc_final: 0.6862 (mtp) REVERT: A 560 MET cc_start: 0.8328 (mmp) cc_final: 0.8096 (mmt) REVERT: A 581 MET cc_start: 0.7727 (mmm) cc_final: 0.7095 (mmm) REVERT: A 590 LYS cc_start: 0.7746 (mmtm) cc_final: 0.7453 (mmtm) REVERT: A 592 VAL cc_start: 0.7902 (t) cc_final: 0.7501 (m) REVERT: A 601 GLN cc_start: 0.8476 (tt0) cc_final: 0.8192 (tm-30) REVERT: A 609 LEU cc_start: 0.8323 (tp) cc_final: 0.7837 (tt) REVERT: A 622 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7346 (tm-30) REVERT: B 350 MET cc_start: 0.7520 (mtm) cc_final: 0.7096 (mtm) REVERT: B 367 LYS cc_start: 0.7746 (mmtt) cc_final: 0.6812 (mmtt) REVERT: B 383 THR cc_start: 0.8339 (p) cc_final: 0.7998 (p) REVERT: B 386 GLN cc_start: 0.8707 (mt0) cc_final: 0.8428 (mt0) REVERT: B 387 PHE cc_start: 0.8309 (t80) cc_final: 0.8035 (t80) REVERT: B 393 GLU cc_start: 0.7808 (tp30) cc_final: 0.7237 (tp30) REVERT: B 399 LYS cc_start: 0.8339 (mmtp) cc_final: 0.7764 (mmtp) REVERT: B 402 HIS cc_start: 0.8050 (t-90) cc_final: 0.7551 (t-90) REVERT: B 409 MET cc_start: 0.7382 (mtm) cc_final: 0.6696 (mtm) REVERT: B 412 MET cc_start: 0.6408 (ppp) cc_final: 0.5819 (ppp) REVERT: B 416 ASN cc_start: 0.7749 (p0) cc_final: 0.7308 (p0) REVERT: B 419 ILE cc_start: 0.7563 (mm) cc_final: 0.7263 (mm) REVERT: B 422 GLN cc_start: 0.8435 (tt0) cc_final: 0.7367 (pm20) REVERT: B 432 HIS cc_start: 0.7593 (m90) cc_final: 0.6497 (m90) REVERT: B 439 LYS cc_start: 0.8415 (mppt) cc_final: 0.7928 (mppt) REVERT: B 442 MET cc_start: 0.7665 (mpp) cc_final: 0.7428 (mpp) REVERT: B 450 ARG cc_start: 0.8462 (ttp-170) cc_final: 0.7856 (ttp-170) REVERT: B 458 TYR cc_start: 0.8468 (t80) cc_final: 0.7396 (t80) REVERT: B 460 HIS cc_start: 0.8226 (m170) cc_final: 0.7973 (m-70) REVERT: B 466 HIS cc_start: 0.8563 (t-90) cc_final: 0.8213 (t-90) REVERT: B 470 LYS cc_start: 0.8284 (mtpt) cc_final: 0.8063 (mtpt) REVERT: B 484 ILE cc_start: 0.8076 (mt) cc_final: 0.7806 (mt) REVERT: B 512 MET cc_start: 0.5801 (ttm) cc_final: 0.5430 (ttm) REVERT: B 516 VAL cc_start: 0.8764 (t) cc_final: 0.8509 (t) REVERT: B 528 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7249 (mm110) REVERT: B 534 TYR cc_start: 0.8479 (t80) cc_final: 0.8149 (t80) REVERT: B 541 LEU cc_start: 0.8654 (mt) cc_final: 0.8304 (mt) REVERT: B 545 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7212 (mt-10) REVERT: B 551 ILE cc_start: 0.8798 (mp) cc_final: 0.8529 (mp) REVERT: B 556 GLN cc_start: 0.8272 (tt0) cc_final: 0.7911 (tp40) REVERT: B 563 ARG cc_start: 0.8433 (mmm-85) cc_final: 0.7689 (ttm-80) REVERT: B 574 TYR cc_start: 0.7763 (m-80) cc_final: 0.7472 (m-10) REVERT: B 583 ARG cc_start: 0.8546 (ptp-170) cc_final: 0.8059 (ptp-110) REVERT: B 592 VAL cc_start: 0.7734 (t) cc_final: 0.7319 (m) REVERT: B 601 GLN cc_start: 0.8603 (tt0) cc_final: 0.8260 (tt0) REVERT: B 615 LYS cc_start: 0.7887 (mttm) cc_final: 0.7592 (mttm) REVERT: B 622 GLU cc_start: 0.7562 (tm-30) cc_final: 0.6928 (tm-30) REVERT: C 20 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7239 (tm-30) REVERT: C 25 MET cc_start: 0.7785 (pmm) cc_final: 0.7206 (pmm) REVERT: C 29 MET cc_start: 0.9084 (tpp) cc_final: 0.8725 (mmm) REVERT: C 43 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8480 (mt-10) REVERT: C 49 VAL cc_start: 0.8105 (t) cc_final: 0.7682 (m) REVERT: C 52 LYS cc_start: 0.8653 (tptm) cc_final: 0.8355 (tptm) REVERT: C 53 ASN cc_start: 0.8208 (m-40) cc_final: 0.7892 (m-40) REVERT: C 59 ARG cc_start: 0.8427 (mtp-110) cc_final: 0.8223 (mtp-110) REVERT: C 69 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8302 (tm-30) REVERT: C 81 LYS cc_start: 0.8027 (ptpp) cc_final: 0.7775 (pptt) REVERT: C 87 GLU cc_start: 0.8319 (pt0) cc_final: 0.8080 (pt0) REVERT: C 91 LYS cc_start: 0.8681 (tppt) cc_final: 0.7746 (tppt) REVERT: C 93 GLU cc_start: 0.8272 (tt0) cc_final: 0.8009 (tt0) REVERT: C 94 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8400 (ttpt) REVERT: C 95 GLU cc_start: 0.8491 (mt-10) cc_final: 0.7562 (mt-10) REVERT: C 98 GLU cc_start: 0.7198 (tp30) cc_final: 0.6132 (tp30) REVERT: C 102 ASP cc_start: 0.7894 (m-30) cc_final: 0.7094 (m-30) REVERT: C 119 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7963 (tp30) REVERT: C 127 MET cc_start: 0.8362 (mmm) cc_final: 0.7645 (mmm) REVERT: C 132 TYR cc_start: 0.8311 (m-80) cc_final: 0.7528 (m-80) REVERT: C 133 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8188 (ttp-110) REVERT: C 149 GLU cc_start: 0.8344 (tp30) cc_final: 0.7999 (tp30) REVERT: C 150 ASP cc_start: 0.8372 (m-30) cc_final: 0.8142 (m-30) REVERT: C 155 TYR cc_start: 0.7830 (m-10) cc_final: 0.7294 (m-80) REVERT: C 159 PHE cc_start: 0.8500 (t80) cc_final: 0.8294 (t80) REVERT: C 167 GLN cc_start: 0.8212 (tp-100) cc_final: 0.8000 (tp-100) REVERT: C 170 HIS cc_start: 0.8140 (t-90) cc_final: 0.7689 (t-90) REVERT: C 196 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8018 (pp30) REVERT: C 200 GLN cc_start: 0.8760 (pt0) cc_final: 0.8493 (pt0) REVERT: C 224 MET cc_start: 0.7327 (ptm) cc_final: 0.6558 (ptm) REVERT: C 225 GLN cc_start: 0.7479 (mm110) cc_final: 0.6796 (mm110) REVERT: D 7 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8228 (mm-30) REVERT: D 14 LYS cc_start: 0.8695 (mttt) cc_final: 0.8398 (mttt) REVERT: D 20 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7525 (tm-30) REVERT: D 25 MET cc_start: 0.7861 (pmm) cc_final: 0.7386 (pmm) REVERT: D 29 MET cc_start: 0.9001 (tpp) cc_final: 0.8687 (mmm) REVERT: D 34 GLU cc_start: 0.8047 (pp20) cc_final: 0.7735 (pp20) REVERT: D 43 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8619 (mt-10) REVERT: D 59 ARG cc_start: 0.8518 (mtp-110) cc_final: 0.7821 (mtp85) REVERT: D 65 ILE cc_start: 0.8788 (pt) cc_final: 0.8531 (pt) REVERT: D 66 SER cc_start: 0.8016 (m) cc_final: 0.7540 (m) REVERT: D 87 GLU cc_start: 0.8337 (pt0) cc_final: 0.8089 (pt0) REVERT: D 91 LYS cc_start: 0.8712 (tppt) cc_final: 0.7964 (tppt) REVERT: D 93 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8316 (mt-10) REVERT: D 94 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8705 (ttpt) REVERT: D 97 ARG cc_start: 0.8849 (mtm110) cc_final: 0.8470 (mtm110) REVERT: D 119 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7880 (tp30) REVERT: D 125 LEU cc_start: 0.8235 (mt) cc_final: 0.8006 (mt) REVERT: D 127 MET cc_start: 0.8435 (mmm) cc_final: 0.7691 (mmp) REVERT: D 130 ASP cc_start: 0.7940 (m-30) cc_final: 0.6992 (m-30) REVERT: D 132 TYR cc_start: 0.8417 (m-80) cc_final: 0.7279 (m-80) REVERT: D 133 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.7945 (ttp80) REVERT: D 150 ASP cc_start: 0.8231 (m-30) cc_final: 0.7911 (p0) REVERT: D 153 LYS cc_start: 0.8619 (tppt) cc_final: 0.7953 (tppt) REVERT: D 155 TYR cc_start: 0.7683 (m-10) cc_final: 0.7014 (m-80) REVERT: D 170 HIS cc_start: 0.8303 (t-90) cc_final: 0.7990 (t-90) REVERT: D 180 PHE cc_start: 0.8590 (m-80) cc_final: 0.7789 (m-80) REVERT: D 192 ASP cc_start: 0.8399 (p0) cc_final: 0.7792 (p0) REVERT: D 193 LYS cc_start: 0.8257 (mttt) cc_final: 0.7813 (mptt) REVERT: D 206 ILE cc_start: 0.7765 (mt) cc_final: 0.7542 (mt) REVERT: D 220 SER cc_start: 0.7336 (m) cc_final: 0.6610 (p) REVERT: D 224 MET cc_start: 0.7380 (ptm) cc_final: 0.6653 (ptm) REVERT: D 225 GLN cc_start: 0.7452 (mm110) cc_final: 0.6773 (mm110) REVERT: E 88 LYS cc_start: 0.8428 (mmmt) cc_final: 0.7970 (mmmt) REVERT: E 121 CYS cc_start: 0.7679 (m) cc_final: 0.7411 (m) REVERT: E 160 ARG cc_start: 0.7724 (mpp80) cc_final: 0.6250 (mtt180) REVERT: E 175 LYS cc_start: 0.8537 (ptmt) cc_final: 0.7984 (ptmt) REVERT: E 187 MET cc_start: 0.6519 (mtt) cc_final: 0.5759 (mtm) REVERT: E 195 ASN cc_start: 0.7562 (t0) cc_final: 0.7347 (t0) REVERT: E 206 LEU cc_start: 0.6864 (tp) cc_final: 0.6456 (tp) REVERT: E 219 MET cc_start: 0.7888 (mtp) cc_final: 0.7657 (mtp) REVERT: E 227 ARG cc_start: 0.7525 (mtm180) cc_final: 0.7092 (mtm180) REVERT: E 236 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7839 (tm-30) REVERT: E 249 MET cc_start: 0.8340 (ppp) cc_final: 0.8051 (ppp) REVERT: E 253 LEU cc_start: 0.8796 (mt) cc_final: 0.8535 (mt) REVERT: E 256 MET cc_start: 0.7698 (ptm) cc_final: 0.7308 (ptm) REVERT: E 267 ASP cc_start: 0.7573 (p0) cc_final: 0.7083 (p0) REVERT: E 310 ILE cc_start: 0.8667 (mp) cc_final: 0.8436 (mt) REVERT: E 311 PHE cc_start: 0.7178 (t80) cc_final: 0.6608 (t80) REVERT: E 312 GLU cc_start: 0.7827 (pp20) cc_final: 0.7483 (pp20) REVERT: E 313 LEU cc_start: 0.8256 (mt) cc_final: 0.7989 (mt) REVERT: E 316 TYR cc_start: 0.8128 (t80) cc_final: 0.7575 (t80) REVERT: E 319 ASN cc_start: 0.7937 (t0) cc_final: 0.6767 (t0) REVERT: E 320 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7641 (mm-30) REVERT: E 333 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8361 (mt-10) REVERT: E 344 LYS cc_start: 0.8404 (tttt) cc_final: 0.7975 (mttt) REVERT: F 88 LYS cc_start: 0.8523 (mmmt) cc_final: 0.7989 (mmmt) REVERT: F 96 ARG cc_start: 0.7617 (ptm160) cc_final: 0.6898 (ptm160) REVERT: F 125 TYR cc_start: 0.8136 (m-80) cc_final: 0.7243 (m-80) REVERT: F 168 LYS cc_start: 0.8394 (ttmm) cc_final: 0.7847 (ttmm) REVERT: F 175 LYS cc_start: 0.8569 (ptmt) cc_final: 0.8083 (ptmt) REVERT: F 187 MET cc_start: 0.6324 (mtm) cc_final: 0.5744 (mtm) REVERT: F 195 ASN cc_start: 0.7436 (t0) cc_final: 0.7147 (t0) REVERT: F 206 LEU cc_start: 0.6835 (tp) cc_final: 0.6344 (tp) REVERT: F 219 MET cc_start: 0.7775 (mtp) cc_final: 0.7479 (mtp) REVERT: F 249 MET cc_start: 0.8310 (ppp) cc_final: 0.8015 (ppp) REVERT: F 256 MET cc_start: 0.7693 (ptm) cc_final: 0.7419 (ptm) REVERT: F 267 ASP cc_start: 0.7214 (p0) cc_final: 0.6418 (p0) REVERT: F 270 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7600 (mt-10) REVERT: F 316 TYR cc_start: 0.8118 (t80) cc_final: 0.7488 (t80) REVERT: F 318 VAL cc_start: 0.8531 (p) cc_final: 0.8247 (m) REVERT: F 319 ASN cc_start: 0.7791 (t0) cc_final: 0.6530 (t0) REVERT: F 320 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7561 (mm-30) REVERT: F 333 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8256 (mt-10) REVERT: F 334 PHE cc_start: 0.8612 (t80) cc_final: 0.8402 (t80) REVERT: F 356 MET cc_start: 0.6957 (ppp) cc_final: 0.6658 (ppp) outliers start: 1 outliers final: 0 residues processed: 673 average time/residue: 0.2823 time to fit residues: 259.0841 Evaluate side-chains 670 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 669 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 35 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 109 ASN ** E 335 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.134328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.109752 restraints weight = 28433.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.114164 restraints weight = 15705.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.117214 restraints weight = 10168.223| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 12876 Z= 0.145 Angle : 0.633 10.630 17364 Z= 0.333 Chirality : 0.044 0.190 1918 Planarity : 0.005 0.073 2216 Dihedral : 6.118 96.890 1740 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1538 helix: 0.57 (0.17), residues: 892 sheet: -2.72 (0.45), residues: 96 loop : -1.02 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 368 HIS 0.009 0.001 HIS B 460 PHE 0.012 0.002 PHE E 360 TYR 0.025 0.002 TYR C 101 ARG 0.009 0.001 ARG E 181 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 710) hydrogen bonds : angle 4.86059 ( 2070) covalent geometry : bond 0.00305 (12876) covalent geometry : angle 0.63329 (17364) *********************** 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: 0 poor density : 676 time to evaluate : 1.480 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: A 350 MET cc_start: 0.7503 (mtm) cc_final: 0.7086 (mtm) REVERT: A 359 SER cc_start: 0.8296 (m) cc_final: 0.7816 (p) REVERT: A 387 PHE cc_start: 0.8136 (t80) cc_final: 0.7308 (t80) REVERT: A 391 ARG cc_start: 0.8328 (mmt90) cc_final: 0.7777 (mmm-85) REVERT: A 392 ASN cc_start: 0.8279 (m-40) cc_final: 0.7905 (m-40) REVERT: A 399 LYS cc_start: 0.8376 (mmtp) cc_final: 0.7817 (mmtp) REVERT: A 402 HIS cc_start: 0.7898 (t-90) cc_final: 0.7464 (t-90) REVERT: A 409 MET cc_start: 0.7407 (mtt) cc_final: 0.7112 (mtt) REVERT: A 411 TYR cc_start: 0.7143 (p90) cc_final: 0.6884 (p90) REVERT: A 412 MET cc_start: 0.6095 (ppp) cc_final: 0.5531 (ppp) REVERT: A 413 THR cc_start: 0.8025 (p) cc_final: 0.7818 (p) REVERT: A 414 LYS cc_start: 0.8171 (tppt) cc_final: 0.7782 (mmmt) REVERT: A 416 ASN cc_start: 0.7420 (p0) cc_final: 0.7016 (p0) REVERT: A 417 LEU cc_start: 0.8058 (pt) cc_final: 0.7837 (pt) REVERT: A 422 GLN cc_start: 0.8304 (tt0) cc_final: 0.7369 (pt0) REVERT: A 423 TRP cc_start: 0.8018 (t-100) cc_final: 0.7449 (t60) REVERT: A 425 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6689 (mm-30) REVERT: A 431 LYS cc_start: 0.8277 (mppt) cc_final: 0.7916 (mppt) REVERT: A 439 LYS cc_start: 0.8221 (mppt) cc_final: 0.7621 (mppt) REVERT: A 444 GLN cc_start: 0.7953 (mt0) cc_final: 0.7682 (mp10) REVERT: A 450 ARG cc_start: 0.8358 (ttp-170) cc_final: 0.7718 (ttp-170) REVERT: A 451 GLN cc_start: 0.8098 (mt0) cc_final: 0.6868 (tt0) REVERT: A 456 MET cc_start: 0.8204 (mmm) cc_final: 0.7605 (mmm) REVERT: A 458 TYR cc_start: 0.8559 (t80) cc_final: 0.8106 (t80) REVERT: A 460 HIS cc_start: 0.8440 (m170) cc_final: 0.8075 (m90) REVERT: A 463 ASN cc_start: 0.7253 (m-40) cc_final: 0.6994 (m-40) REVERT: A 466 HIS cc_start: 0.8610 (t-90) cc_final: 0.7966 (t-90) REVERT: A 512 MET cc_start: 0.5844 (ttm) cc_final: 0.5494 (ttm) REVERT: A 516 VAL cc_start: 0.8640 (t) cc_final: 0.8187 (t) REVERT: A 518 ARG cc_start: 0.8181 (ptp-110) cc_final: 0.7278 (ptp-110) REVERT: A 528 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7476 (mm-40) REVERT: A 534 TYR cc_start: 0.8536 (t80) cc_final: 0.8277 (t80) REVERT: A 541 LEU cc_start: 0.8544 (mt) cc_final: 0.8278 (mt) REVERT: A 559 PHE cc_start: 0.8560 (t80) cc_final: 0.8311 (t80) REVERT: A 560 MET cc_start: 0.8418 (mmp) cc_final: 0.8148 (mmt) REVERT: A 574 TYR cc_start: 0.7614 (m-10) cc_final: 0.7392 (m-10) REVERT: A 576 ASN cc_start: 0.7831 (t0) cc_final: 0.7470 (t0) REVERT: A 581 MET cc_start: 0.7725 (mmm) cc_final: 0.7179 (mmm) REVERT: A 590 LYS cc_start: 0.7701 (mmtm) cc_final: 0.7413 (mmtm) REVERT: A 591 LYS cc_start: 0.8596 (ptpp) cc_final: 0.8380 (ptpp) REVERT: A 592 VAL cc_start: 0.7872 (t) cc_final: 0.7426 (m) REVERT: A 601 GLN cc_start: 0.8424 (tt0) cc_final: 0.8130 (tm-30) REVERT: A 606 ILE cc_start: 0.8994 (mm) cc_final: 0.8661 (tp) REVERT: A 622 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7318 (tm-30) REVERT: B 350 MET cc_start: 0.7483 (mtm) cc_final: 0.7045 (mtm) REVERT: B 367 LYS cc_start: 0.7714 (mmtt) cc_final: 0.6779 (mmtt) REVERT: B 387 PHE cc_start: 0.8199 (t80) cc_final: 0.7942 (t80) REVERT: B 393 GLU cc_start: 0.7793 (tp30) cc_final: 0.7174 (tp30) REVERT: B 399 LYS cc_start: 0.8335 (mmtp) cc_final: 0.7796 (mmtp) REVERT: B 402 HIS cc_start: 0.7973 (t-90) cc_final: 0.7539 (t-90) REVERT: B 409 MET cc_start: 0.7448 (mtm) cc_final: 0.6754 (mtm) REVERT: B 412 MET cc_start: 0.5967 (ppp) cc_final: 0.5476 (ppp) REVERT: B 414 LYS cc_start: 0.8252 (tppt) cc_final: 0.8004 (mmmt) REVERT: B 416 ASN cc_start: 0.7666 (p0) cc_final: 0.7308 (p0) REVERT: B 419 ILE cc_start: 0.7481 (mm) cc_final: 0.7107 (mm) REVERT: B 422 GLN cc_start: 0.8290 (tt0) cc_final: 0.7498 (pt0) REVERT: B 429 LEU cc_start: 0.8361 (tp) cc_final: 0.8019 (tp) REVERT: B 432 HIS cc_start: 0.7660 (m90) cc_final: 0.6589 (m90) REVERT: B 433 LEU cc_start: 0.8378 (mt) cc_final: 0.8115 (mt) REVERT: B 439 LYS cc_start: 0.8407 (mppt) cc_final: 0.7899 (mppt) REVERT: B 442 MET cc_start: 0.7616 (mpp) cc_final: 0.7265 (mpp) REVERT: B 450 ARG cc_start: 0.8431 (ttp-170) cc_final: 0.7830 (ttp-170) REVERT: B 456 MET cc_start: 0.8081 (mmm) cc_final: 0.7745 (mmm) REVERT: B 466 HIS cc_start: 0.8513 (t-90) cc_final: 0.8188 (t-90) REVERT: B 470 LYS cc_start: 0.8292 (mtpt) cc_final: 0.8030 (mtpt) REVERT: B 483 LYS cc_start: 0.8298 (mttm) cc_final: 0.7426 (mttm) REVERT: B 492 VAL cc_start: 0.7825 (t) cc_final: 0.7581 (p) REVERT: B 512 MET cc_start: 0.5780 (ttm) cc_final: 0.5459 (ttm) REVERT: B 516 VAL cc_start: 0.8789 (t) cc_final: 0.8454 (t) REVERT: B 528 GLN cc_start: 0.7739 (mm-40) cc_final: 0.6727 (mm-40) REVERT: B 534 TYR cc_start: 0.8452 (t80) cc_final: 0.8107 (t80) REVERT: B 541 LEU cc_start: 0.8740 (mt) cc_final: 0.8458 (mt) REVERT: B 542 MET cc_start: 0.7387 (mtp) cc_final: 0.7182 (mtp) REVERT: B 545 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7219 (mt-10) REVERT: B 551 ILE cc_start: 0.8764 (mp) cc_final: 0.8519 (mp) REVERT: B 554 ARG cc_start: 0.7575 (tmm-80) cc_final: 0.7296 (tmm-80) REVERT: B 556 GLN cc_start: 0.8302 (tt0) cc_final: 0.7937 (tp40) REVERT: B 563 ARG cc_start: 0.8420 (mmm-85) cc_final: 0.7728 (ttm-80) REVERT: B 574 TYR cc_start: 0.7820 (m-80) cc_final: 0.7589 (m-10) REVERT: B 583 ARG cc_start: 0.8519 (ptp-170) cc_final: 0.8053 (ptp-110) REVERT: B 592 VAL cc_start: 0.7712 (t) cc_final: 0.7266 (m) REVERT: B 601 GLN cc_start: 0.8613 (tt0) cc_final: 0.8249 (tt0) REVERT: B 615 LYS cc_start: 0.7940 (mttm) cc_final: 0.7681 (mttm) REVERT: B 618 ARG cc_start: 0.6968 (ptm160) cc_final: 0.6714 (ptm160) REVERT: B 622 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7062 (tm-30) REVERT: C 25 MET cc_start: 0.7817 (pmm) cc_final: 0.7270 (pmm) REVERT: C 29 MET cc_start: 0.9141 (tpp) cc_final: 0.8657 (mmm) REVERT: C 34 GLU cc_start: 0.7706 (pp20) cc_final: 0.7193 (pp20) REVERT: C 43 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8504 (mt-10) REVERT: C 49 VAL cc_start: 0.8108 (t) cc_final: 0.7696 (m) REVERT: C 52 LYS cc_start: 0.8603 (tptm) cc_final: 0.8322 (tptm) REVERT: C 53 ASN cc_start: 0.8174 (m-40) cc_final: 0.7928 (m-40) REVERT: C 81 LYS cc_start: 0.8055 (ptpp) cc_final: 0.7816 (pptt) REVERT: C 87 GLU cc_start: 0.8338 (pt0) cc_final: 0.8107 (pt0) REVERT: C 91 LYS cc_start: 0.8690 (tppt) cc_final: 0.7677 (tppt) REVERT: C 93 GLU cc_start: 0.8388 (tt0) cc_final: 0.8066 (tt0) REVERT: C 94 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8425 (ttpt) REVERT: C 95 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7572 (mt-10) REVERT: C 98 GLU cc_start: 0.7173 (tp30) cc_final: 0.6004 (tp30) REVERT: C 102 ASP cc_start: 0.7907 (m-30) cc_final: 0.7054 (m-30) REVERT: C 119 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7950 (tp30) REVERT: C 126 LYS cc_start: 0.8773 (ttpp) cc_final: 0.8541 (ttpp) REVERT: C 132 TYR cc_start: 0.8306 (m-80) cc_final: 0.7504 (m-80) REVERT: C 133 ARG cc_start: 0.8609 (ttp-110) cc_final: 0.8147 (ttp-110) REVERT: C 149 GLU cc_start: 0.8371 (tp30) cc_final: 0.8052 (tp30) REVERT: C 150 ASP cc_start: 0.8363 (m-30) cc_final: 0.8130 (m-30) REVERT: C 153 LYS cc_start: 0.8824 (tppt) cc_final: 0.8166 (tppt) REVERT: C 155 TYR cc_start: 0.7854 (m-10) cc_final: 0.7273 (m-80) REVERT: C 166 MET cc_start: 0.6937 (tpt) cc_final: 0.6615 (tpt) REVERT: C 167 GLN cc_start: 0.8232 (tp-100) cc_final: 0.7924 (tp-100) REVERT: C 170 HIS cc_start: 0.8196 (t-90) cc_final: 0.7857 (t-90) REVERT: C 174 LEU cc_start: 0.8096 (mt) cc_final: 0.7782 (mt) REVERT: C 193 LYS cc_start: 0.8638 (tttt) cc_final: 0.7915 (tppp) REVERT: C 197 LEU cc_start: 0.8572 (mm) cc_final: 0.7992 (mm) REVERT: C 224 MET cc_start: 0.7296 (ptm) cc_final: 0.6400 (ptm) REVERT: C 225 GLN cc_start: 0.7506 (mm110) cc_final: 0.6772 (mm110) REVERT: D 7 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8257 (mm-30) REVERT: D 14 LYS cc_start: 0.8694 (mttt) cc_final: 0.8371 (mttt) REVERT: D 20 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7419 (tm-30) REVERT: D 25 MET cc_start: 0.7841 (pmm) cc_final: 0.7437 (pmm) REVERT: D 29 MET cc_start: 0.9001 (tpp) cc_final: 0.8714 (mmm) REVERT: D 34 GLU cc_start: 0.8029 (pp20) cc_final: 0.7730 (pp20) REVERT: D 43 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8608 (mt-10) REVERT: D 52 LYS cc_start: 0.8603 (tptm) cc_final: 0.8184 (tptm) REVERT: D 58 ARG cc_start: 0.8836 (mpt180) cc_final: 0.8502 (mmt90) REVERT: D 59 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.7853 (mtp85) REVERT: D 65 ILE cc_start: 0.8780 (pt) cc_final: 0.8520 (pt) REVERT: D 66 SER cc_start: 0.8042 (m) cc_final: 0.7579 (m) REVERT: D 87 GLU cc_start: 0.8355 (pt0) cc_final: 0.8074 (pt0) REVERT: D 91 LYS cc_start: 0.8714 (tppt) cc_final: 0.8063 (tppt) REVERT: D 93 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8271 (mt-10) REVERT: D 94 LYS cc_start: 0.8913 (ttpt) cc_final: 0.8711 (ttpt) REVERT: D 97 ARG cc_start: 0.8845 (mtm110) cc_final: 0.8405 (mtm110) REVERT: D 119 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7802 (tp30) REVERT: D 125 LEU cc_start: 0.8201 (mt) cc_final: 0.7999 (mt) REVERT: D 127 MET cc_start: 0.8443 (mmm) cc_final: 0.7702 (mmp) REVERT: D 130 ASP cc_start: 0.7785 (m-30) cc_final: 0.7419 (m-30) REVERT: D 132 TYR cc_start: 0.8449 (m-80) cc_final: 0.7341 (m-80) REVERT: D 133 ARG cc_start: 0.8567 (ttp-110) cc_final: 0.8366 (ttp-110) REVERT: D 150 ASP cc_start: 0.8219 (m-30) cc_final: 0.7947 (p0) REVERT: D 153 LYS cc_start: 0.8587 (tppt) cc_final: 0.7889 (tppt) REVERT: D 155 TYR cc_start: 0.7791 (m-10) cc_final: 0.7340 (m-80) REVERT: D 170 HIS cc_start: 0.8371 (t-90) cc_final: 0.8076 (t-90) REVERT: D 174 LEU cc_start: 0.8129 (mt) cc_final: 0.7849 (mt) REVERT: D 192 ASP cc_start: 0.8430 (p0) cc_final: 0.7859 (p0) REVERT: D 193 LYS cc_start: 0.8281 (mttt) cc_final: 0.7877 (mptt) REVERT: D 206 ILE cc_start: 0.7818 (mt) cc_final: 0.7587 (mt) REVERT: D 220 SER cc_start: 0.7340 (m) cc_final: 0.6996 (m) REVERT: D 224 MET cc_start: 0.7394 (ptm) cc_final: 0.6609 (ptm) REVERT: D 225 GLN cc_start: 0.7500 (mm110) cc_final: 0.6710 (mm110) REVERT: E 88 LYS cc_start: 0.8393 (mmmt) cc_final: 0.7937 (mmmt) REVERT: E 121 CYS cc_start: 0.7608 (m) cc_final: 0.7333 (m) REVERT: E 125 TYR cc_start: 0.7961 (m-80) cc_final: 0.6973 (m-80) REVERT: E 146 MET cc_start: 0.6636 (tpp) cc_final: 0.6146 (tpp) REVERT: E 168 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7737 (ttmm) REVERT: E 175 LYS cc_start: 0.8552 (ptmt) cc_final: 0.8024 (ptmt) REVERT: E 187 MET cc_start: 0.6032 (mtt) cc_final: 0.5598 (mtm) REVERT: E 189 ARG cc_start: 0.7954 (tpp-160) cc_final: 0.7177 (tpp-160) REVERT: E 195 ASN cc_start: 0.7488 (t0) cc_final: 0.7258 (t0) REVERT: E 206 LEU cc_start: 0.6811 (tp) cc_final: 0.6362 (tp) REVERT: E 219 MET cc_start: 0.7930 (mtp) cc_final: 0.7693 (mtp) REVERT: E 227 ARG cc_start: 0.7482 (mtm180) cc_final: 0.7054 (mtm180) REVERT: E 236 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7804 (tm-30) REVERT: E 249 MET cc_start: 0.8261 (ppp) cc_final: 0.7993 (ppp) REVERT: E 253 LEU cc_start: 0.8801 (mt) cc_final: 0.8537 (mt) REVERT: E 256 MET cc_start: 0.7717 (ptm) cc_final: 0.7332 (ptm) REVERT: E 267 ASP cc_start: 0.7717 (p0) cc_final: 0.7174 (p0) REVERT: E 311 PHE cc_start: 0.7226 (t80) cc_final: 0.6622 (t80) REVERT: E 312 GLU cc_start: 0.7809 (pp20) cc_final: 0.7378 (pp20) REVERT: E 313 LEU cc_start: 0.8274 (mt) cc_final: 0.8000 (mt) REVERT: E 316 TYR cc_start: 0.8078 (t80) cc_final: 0.7575 (t80) REVERT: E 319 ASN cc_start: 0.8043 (t0) cc_final: 0.6876 (t0) REVERT: E 320 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7612 (mm-30) REVERT: E 333 GLU cc_start: 0.8647 (mt-10) cc_final: 0.7979 (mt-10) REVERT: E 334 PHE cc_start: 0.8522 (t80) cc_final: 0.8256 (t80) REVERT: E 344 LYS cc_start: 0.8418 (tttt) cc_final: 0.7953 (mttm) REVERT: E 356 MET cc_start: 0.7003 (ppp) cc_final: 0.6669 (ppp) REVERT: E 360 PHE cc_start: 0.8246 (p90) cc_final: 0.8032 (p90) REVERT: F 88 LYS cc_start: 0.8524 (mmmt) cc_final: 0.7996 (mmmt) REVERT: F 96 ARG cc_start: 0.7630 (ptm160) cc_final: 0.6968 (ptm160) REVERT: F 125 TYR cc_start: 0.8107 (m-80) cc_final: 0.7220 (m-80) REVERT: F 146 MET cc_start: 0.6609 (tpp) cc_final: 0.6063 (tpp) REVERT: F 175 LYS cc_start: 0.8582 (ptmt) cc_final: 0.8071 (ptmt) REVERT: F 195 ASN cc_start: 0.7502 (t0) cc_final: 0.7147 (t0) REVERT: F 206 LEU cc_start: 0.6715 (tp) cc_final: 0.6235 (tp) REVERT: F 219 MET cc_start: 0.7766 (mtp) cc_final: 0.7468 (mtp) REVERT: F 249 MET cc_start: 0.8276 (ppp) cc_final: 0.7997 (ppp) REVERT: F 256 MET cc_start: 0.7771 (ptm) cc_final: 0.7397 (ptm) REVERT: F 267 ASP cc_start: 0.7407 (p0) cc_final: 0.6675 (p0) REVERT: F 316 TYR cc_start: 0.8078 (t80) cc_final: 0.7466 (t80) REVERT: F 318 VAL cc_start: 0.8532 (p) cc_final: 0.8243 (m) REVERT: F 319 ASN cc_start: 0.7771 (t0) cc_final: 0.6503 (t0) REVERT: F 320 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7486 (mm-30) REVERT: F 330 PHE cc_start: 0.8314 (m-80) cc_final: 0.8044 (m-80) outliers start: 0 outliers final: 0 residues processed: 676 average time/residue: 0.3908 time to fit residues: 360.2866 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 : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 31 optimal weight: 0.0870 chunk 138 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 119 optimal weight: 0.0770 chunk 36 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 146 optimal weight: 0.0570 chunk 62 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 4 optimal weight: 0.0980 chunk 137 optimal weight: 4.9990 overall best weight: 0.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN C 200 GLN D 11 GLN D 200 GLN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** 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 = 0.3968 r_free = 0.3968 target = 0.135123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.111083 restraints weight = 28107.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.115497 restraints weight = 15588.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.118567 restraints weight = 10042.243| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12876 Z= 0.125 Angle : 0.617 8.766 17364 Z= 0.323 Chirality : 0.043 0.179 1918 Planarity : 0.005 0.074 2216 Dihedral : 5.747 84.473 1740 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.22 % Allowed : 2.81 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1538 helix: 0.64 (0.17), residues: 894 sheet: -2.74 (0.44), residues: 96 loop : -0.99 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 368 HIS 0.009 0.001 HIS F 358 PHE 0.018 0.002 PHE B 599 TYR 0.023 0.002 TYR B 532 ARG 0.008 0.000 ARG F 181 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 710) hydrogen bonds : angle 4.71966 ( 2070) covalent geometry : bond 0.00260 (12876) covalent geometry : angle 0.61677 (17364) *********************** 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 662 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 659 time to evaluate : 2.468 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 345 GLU cc_start: 0.6907 (mp0) cc_final: 0.6357 (mp0) REVERT: A 350 MET cc_start: 0.7441 (mtm) cc_final: 0.7005 (mtm) REVERT: A 386 GLN cc_start: 0.8675 (mt0) cc_final: 0.8445 (mt0) REVERT: A 387 PHE cc_start: 0.8090 (t80) cc_final: 0.7233 (t80) REVERT: A 391 ARG cc_start: 0.8337 (mmt90) cc_final: 0.7733 (mmm-85) REVERT: A 392 ASN cc_start: 0.8279 (m-40) cc_final: 0.7898 (m-40) REVERT: A 399 LYS cc_start: 0.8298 (mmtp) cc_final: 0.7787 (mmtp) REVERT: A 402 HIS cc_start: 0.7845 (t-90) cc_final: 0.7581 (t-90) REVERT: A 409 MET cc_start: 0.7396 (mtt) cc_final: 0.7070 (mtt) REVERT: A 411 TYR cc_start: 0.7162 (p90) cc_final: 0.6887 (p90) REVERT: A 412 MET cc_start: 0.6060 (ppp) cc_final: 0.5461 (ppp) REVERT: A 414 LYS cc_start: 0.8225 (tppt) cc_final: 0.7959 (tppt) REVERT: A 416 ASN cc_start: 0.7403 (p0) cc_final: 0.7063 (p0) REVERT: A 417 LEU cc_start: 0.8055 (pt) cc_final: 0.7834 (pt) REVERT: A 422 GLN cc_start: 0.8285 (tt0) cc_final: 0.7377 (pt0) REVERT: A 423 TRP cc_start: 0.7960 (t-100) cc_final: 0.7497 (t60) REVERT: A 431 LYS cc_start: 0.8255 (mppt) cc_final: 0.7839 (mppt) REVERT: A 439 LYS cc_start: 0.8127 (mppt) cc_final: 0.7476 (mppt) REVERT: A 444 GLN cc_start: 0.7955 (mt0) cc_final: 0.7706 (mp10) REVERT: A 454 GLN cc_start: 0.8715 (mt0) cc_final: 0.8493 (mt0) REVERT: A 456 MET cc_start: 0.8238 (mmm) cc_final: 0.6759 (mmm) REVERT: A 458 TYR cc_start: 0.8542 (t80) cc_final: 0.8104 (t80) REVERT: A 460 HIS cc_start: 0.8143 (m170) cc_final: 0.7734 (m90) REVERT: A 463 ASN cc_start: 0.7225 (m-40) cc_final: 0.6997 (m-40) REVERT: A 466 HIS cc_start: 0.8591 (t-90) cc_final: 0.7969 (t-90) REVERT: A 512 MET cc_start: 0.5796 (ttm) cc_final: 0.5555 (ttm) REVERT: A 518 ARG cc_start: 0.8109 (ptp-110) cc_final: 0.7384 (ptp-110) REVERT: A 528 GLN cc_start: 0.7692 (mm-40) cc_final: 0.6669 (mm110) REVERT: A 532 TYR cc_start: 0.7838 (t80) cc_final: 0.7554 (t80) REVERT: A 534 TYR cc_start: 0.8492 (t80) cc_final: 0.8133 (t80) REVERT: A 536 ILE cc_start: 0.8539 (mm) cc_final: 0.8138 (mm) REVERT: A 541 LEU cc_start: 0.8572 (mt) cc_final: 0.8339 (mt) REVERT: A 560 MET cc_start: 0.8354 (mmp) cc_final: 0.8079 (mmp) REVERT: A 563 ARG cc_start: 0.8691 (mmm-85) cc_final: 0.8065 (ttm-80) REVERT: A 576 ASN cc_start: 0.7845 (t0) cc_final: 0.7482 (t0) REVERT: A 581 MET cc_start: 0.7783 (mmm) cc_final: 0.7086 (mmm) REVERT: A 590 LYS cc_start: 0.7705 (mmtm) cc_final: 0.7382 (mmtm) REVERT: A 592 VAL cc_start: 0.7765 (t) cc_final: 0.7338 (m) REVERT: A 601 GLN cc_start: 0.8443 (tt0) cc_final: 0.8066 (tm-30) REVERT: A 609 LEU cc_start: 0.8331 (tp) cc_final: 0.7879 (tt) REVERT: B 350 MET cc_start: 0.7451 (mtm) cc_final: 0.7005 (mtm) REVERT: B 362 THR cc_start: 0.7671 (m) cc_final: 0.7415 (m) REVERT: B 367 LYS cc_start: 0.7671 (mmtt) cc_final: 0.6689 (mmtt) REVERT: B 387 PHE cc_start: 0.8211 (t80) cc_final: 0.7929 (t80) REVERT: B 393 GLU cc_start: 0.7942 (tp30) cc_final: 0.7372 (tp30) REVERT: B 399 LYS cc_start: 0.8319 (mmtp) cc_final: 0.7871 (mmtp) REVERT: B 402 HIS cc_start: 0.7927 (t-90) cc_final: 0.7587 (t-90) REVERT: B 409 MET cc_start: 0.7477 (mtm) cc_final: 0.6735 (mtm) REVERT: B 412 MET cc_start: 0.6048 (ppp) cc_final: 0.5515 (ppp) REVERT: B 414 LYS cc_start: 0.8265 (tppt) cc_final: 0.7932 (mmmt) REVERT: B 416 ASN cc_start: 0.7623 (p0) cc_final: 0.7286 (p0) REVERT: B 419 ILE cc_start: 0.7489 (mm) cc_final: 0.7023 (mm) REVERT: B 432 HIS cc_start: 0.7643 (m90) cc_final: 0.6604 (m90) REVERT: B 433 LEU cc_start: 0.8369 (mt) cc_final: 0.8130 (mt) REVERT: B 439 LYS cc_start: 0.8337 (mppt) cc_final: 0.7818 (mppt) REVERT: B 442 MET cc_start: 0.7425 (mpp) cc_final: 0.7186 (mpp) REVERT: B 450 ARG cc_start: 0.8456 (ttp-170) cc_final: 0.7824 (ttp-170) REVERT: B 456 MET cc_start: 0.8092 (mmm) cc_final: 0.7872 (mmm) REVERT: B 466 HIS cc_start: 0.8542 (t-90) cc_final: 0.8212 (t-90) REVERT: B 470 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7981 (mtpt) REVERT: B 484 ILE cc_start: 0.8137 (mt) cc_final: 0.7781 (mt) REVERT: B 493 LYS cc_start: 0.7236 (mmtm) cc_final: 0.6860 (mmtm) REVERT: B 512 MET cc_start: 0.5847 (ttm) cc_final: 0.5368 (ttm) REVERT: B 516 VAL cc_start: 0.8762 (t) cc_final: 0.8411 (t) REVERT: B 528 GLN cc_start: 0.7664 (mm-40) cc_final: 0.6936 (mm110) REVERT: B 534 TYR cc_start: 0.8431 (t80) cc_final: 0.8156 (t80) REVERT: B 541 LEU cc_start: 0.8756 (mt) cc_final: 0.8467 (mt) REVERT: B 551 ILE cc_start: 0.8758 (mp) cc_final: 0.8435 (mp) REVERT: B 554 ARG cc_start: 0.7455 (tmm-80) cc_final: 0.7095 (tmm-80) REVERT: B 563 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.7756 (ttm-80) REVERT: B 581 MET cc_start: 0.7793 (tpt) cc_final: 0.7532 (tpt) REVERT: B 583 ARG cc_start: 0.8632 (ptp-170) cc_final: 0.8107 (ptp-110) REVERT: B 592 VAL cc_start: 0.7644 (t) cc_final: 0.7204 (m) REVERT: B 601 GLN cc_start: 0.8579 (tt0) cc_final: 0.8188 (tt0) REVERT: B 615 LYS cc_start: 0.7997 (mttm) cc_final: 0.7762 (mttm) REVERT: B 622 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7084 (tm-30) REVERT: C 9 LEU cc_start: 0.8196 (mt) cc_final: 0.7991 (mt) REVERT: C 25 MET cc_start: 0.7770 (pmm) cc_final: 0.7244 (pmm) REVERT: C 29 MET cc_start: 0.9121 (tpp) cc_final: 0.8648 (mmm) REVERT: C 34 GLU cc_start: 0.7669 (pp20) cc_final: 0.7150 (pp20) REVERT: C 43 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8474 (mt-10) REVERT: C 52 LYS cc_start: 0.8595 (tptm) cc_final: 0.8374 (tptm) REVERT: C 59 ARG cc_start: 0.8385 (mtp-110) cc_final: 0.7944 (mtp180) REVERT: C 69 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8328 (tm-30) REVERT: C 81 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7833 (pptt) REVERT: C 87 GLU cc_start: 0.8325 (pt0) cc_final: 0.8073 (pt0) REVERT: C 91 LYS cc_start: 0.8681 (tppt) cc_final: 0.7835 (tppt) REVERT: C 93 GLU cc_start: 0.8555 (tt0) cc_final: 0.8108 (tt0) REVERT: C 94 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8421 (ttpt) REVERT: C 95 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7702 (mt-10) REVERT: C 97 ARG cc_start: 0.8701 (mtm110) cc_final: 0.8264 (mtm110) REVERT: C 98 GLU cc_start: 0.7172 (tp30) cc_final: 0.5988 (tp30) REVERT: C 102 ASP cc_start: 0.7916 (m-30) cc_final: 0.7061 (m-30) REVERT: C 126 LYS cc_start: 0.8745 (ttpp) cc_final: 0.8456 (ttpp) REVERT: C 130 ASP cc_start: 0.7632 (m-30) cc_final: 0.6837 (m-30) REVERT: C 132 TYR cc_start: 0.8267 (m-80) cc_final: 0.7440 (m-80) REVERT: C 133 ARG cc_start: 0.8612 (ttp-110) cc_final: 0.7816 (ttp80) REVERT: C 149 GLU cc_start: 0.8330 (tp30) cc_final: 0.8005 (tp30) REVERT: C 150 ASP cc_start: 0.8343 (m-30) cc_final: 0.8118 (m-30) REVERT: C 153 LYS cc_start: 0.8759 (tppt) cc_final: 0.8108 (tppt) REVERT: C 155 TYR cc_start: 0.7881 (m-10) cc_final: 0.7464 (m-80) REVERT: C 167 GLN cc_start: 0.8235 (tp-100) cc_final: 0.7976 (tp-100) REVERT: C 170 HIS cc_start: 0.8198 (t-90) cc_final: 0.7794 (t-90) REVERT: C 174 LEU cc_start: 0.8077 (mt) cc_final: 0.7767 (mt) REVERT: C 193 LYS cc_start: 0.8650 (tttt) cc_final: 0.7926 (tppp) REVERT: C 197 LEU cc_start: 0.8534 (mm) cc_final: 0.7978 (mm) REVERT: C 204 ASP cc_start: 0.8247 (t0) cc_final: 0.7952 (t0) REVERT: C 218 LYS cc_start: 0.7499 (mmpt) cc_final: 0.7291 (mmpt) REVERT: C 224 MET cc_start: 0.7203 (ptm) cc_final: 0.6258 (ptm) REVERT: C 225 GLN cc_start: 0.7459 (mm110) cc_final: 0.6597 (mm110) REVERT: D 7 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8209 (mm-30) REVERT: D 14 LYS cc_start: 0.8685 (mttt) cc_final: 0.8363 (mttt) REVERT: D 20 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7203 (tm-30) REVERT: D 25 MET cc_start: 0.7695 (pmm) cc_final: 0.7280 (pmm) REVERT: D 29 MET cc_start: 0.8965 (tpp) cc_final: 0.8600 (mmm) REVERT: D 34 GLU cc_start: 0.8000 (pp20) cc_final: 0.7682 (pp20) REVERT: D 43 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8552 (mt-10) REVERT: D 52 LYS cc_start: 0.8567 (tptm) cc_final: 0.8187 (tptm) REVERT: D 59 ARG cc_start: 0.8457 (mtp-110) cc_final: 0.7882 (mtp85) REVERT: D 65 ILE cc_start: 0.8775 (pt) cc_final: 0.8489 (pt) REVERT: D 66 SER cc_start: 0.8045 (m) cc_final: 0.7594 (m) REVERT: D 84 MET cc_start: 0.7668 (ptp) cc_final: 0.7466 (ptp) REVERT: D 87 GLU cc_start: 0.8350 (pt0) cc_final: 0.8050 (pt0) REVERT: D 91 LYS cc_start: 0.8726 (tppt) cc_final: 0.7993 (tppt) REVERT: D 93 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8288 (mt-10) REVERT: D 119 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7738 (tp30) REVERT: D 125 LEU cc_start: 0.8178 (mt) cc_final: 0.7975 (mt) REVERT: D 127 MET cc_start: 0.8414 (mmm) cc_final: 0.7768 (mmp) REVERT: D 130 ASP cc_start: 0.7713 (m-30) cc_final: 0.7347 (m-30) REVERT: D 132 TYR cc_start: 0.8365 (m-80) cc_final: 0.7273 (m-80) REVERT: D 133 ARG cc_start: 0.8525 (ttp-110) cc_final: 0.8293 (ttp-110) REVERT: D 150 ASP cc_start: 0.8195 (m-30) cc_final: 0.7933 (p0) REVERT: D 153 LYS cc_start: 0.8518 (tppt) cc_final: 0.7818 (tppt) REVERT: D 155 TYR cc_start: 0.7811 (m-10) cc_final: 0.7011 (m-80) REVERT: D 167 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7929 (tp-100) REVERT: D 170 HIS cc_start: 0.8379 (t-90) cc_final: 0.7921 (t-90) REVERT: D 174 LEU cc_start: 0.8051 (mt) cc_final: 0.7788 (mt) REVERT: D 176 LEU cc_start: 0.8816 (tt) cc_final: 0.8160 (tt) REVERT: D 180 PHE cc_start: 0.8533 (m-80) cc_final: 0.7835 (m-80) REVERT: D 192 ASP cc_start: 0.8415 (p0) cc_final: 0.7691 (p0) REVERT: D 193 LYS cc_start: 0.8267 (mttt) cc_final: 0.7823 (mptt) REVERT: D 220 SER cc_start: 0.7332 (m) cc_final: 0.7014 (m) REVERT: D 224 MET cc_start: 0.7337 (ptm) cc_final: 0.6539 (ptm) REVERT: D 225 GLN cc_start: 0.7486 (mm110) cc_final: 0.6646 (mm110) REVERT: E 88 LYS cc_start: 0.8392 (mmmt) cc_final: 0.7950 (mmmt) REVERT: E 121 CYS cc_start: 0.7624 (m) cc_final: 0.7363 (m) REVERT: E 125 TYR cc_start: 0.7842 (m-80) cc_final: 0.6838 (m-80) REVERT: E 144 GLU cc_start: 0.7021 (pt0) cc_final: 0.6784 (pt0) REVERT: E 146 MET cc_start: 0.6545 (tpp) cc_final: 0.6068 (tpp) REVERT: E 168 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7695 (ttmm) REVERT: E 175 LYS cc_start: 0.8511 (ptmt) cc_final: 0.7964 (ptmt) REVERT: E 181 ARG cc_start: 0.8327 (tpm170) cc_final: 0.7907 (tpm170) REVERT: E 187 MET cc_start: 0.6079 (mtt) cc_final: 0.5547 (mtm) REVERT: E 189 ARG cc_start: 0.7909 (tpp-160) cc_final: 0.7334 (tpp-160) REVERT: E 206 LEU cc_start: 0.6810 (tp) cc_final: 0.6468 (tp) REVERT: E 219 MET cc_start: 0.7892 (mtp) cc_final: 0.7635 (mtp) REVERT: E 227 ARG cc_start: 0.7457 (mtm180) cc_final: 0.7055 (mtp180) REVERT: E 236 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7840 (tm-30) REVERT: E 249 MET cc_start: 0.8224 (ppp) cc_final: 0.7951 (ppp) REVERT: E 253 LEU cc_start: 0.8759 (mt) cc_final: 0.8514 (mt) REVERT: E 256 MET cc_start: 0.7675 (ptm) cc_final: 0.7279 (ptm) REVERT: E 267 ASP cc_start: 0.7815 (p0) cc_final: 0.7254 (p0) REVERT: E 316 TYR cc_start: 0.8097 (t80) cc_final: 0.7580 (t80) REVERT: E 318 VAL cc_start: 0.8690 (p) cc_final: 0.8381 (m) REVERT: E 319 ASN cc_start: 0.8031 (t0) cc_final: 0.6892 (t0) REVERT: E 320 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7630 (mm-30) REVERT: E 334 PHE cc_start: 0.8491 (t80) cc_final: 0.8279 (t80) REVERT: F 88 LYS cc_start: 0.8517 (mmmt) cc_final: 0.7976 (mmmt) REVERT: F 96 ARG cc_start: 0.7622 (ptm160) cc_final: 0.6974 (ptm160) REVERT: F 110 GLN cc_start: 0.8441 (mm110) cc_final: 0.8193 (mp10) REVERT: F 125 TYR cc_start: 0.8060 (m-80) cc_final: 0.7168 (m-80) REVERT: F 146 MET cc_start: 0.6549 (tpp) cc_final: 0.5928 (tpp) REVERT: F 175 LYS cc_start: 0.8542 (ptmt) cc_final: 0.8046 (ptmt) REVERT: F 187 MET cc_start: 0.5939 (mtm) cc_final: 0.5711 (mtm) REVERT: F 195 ASN cc_start: 0.7525 (t0) cc_final: 0.7234 (t0) REVERT: F 206 LEU cc_start: 0.6665 (tp) cc_final: 0.6171 (tp) REVERT: F 219 MET cc_start: 0.7787 (mtp) cc_final: 0.7491 (mtp) REVERT: F 249 MET cc_start: 0.8241 (ppp) cc_final: 0.7931 (ppp) REVERT: F 256 MET cc_start: 0.7753 (ptm) cc_final: 0.7396 (ptm) REVERT: F 267 ASP cc_start: 0.7487 (p0) cc_final: 0.6712 (p0) REVERT: F 316 TYR cc_start: 0.8108 (t80) cc_final: 0.7501 (t80) REVERT: F 318 VAL cc_start: 0.8507 (p) cc_final: 0.8227 (m) REVERT: F 324 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7609 (mmtt) REVERT: F 333 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8225 (mt-10) REVERT: F 356 MET cc_start: 0.7055 (ppp) cc_final: 0.6813 (ppp) outliers start: 3 outliers final: 0 residues processed: 661 average time/residue: 0.4190 time to fit residues: 385.8527 Evaluate side-chains 656 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 656 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 114 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 144 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 117 ASN D 200 GLN ** E 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 ASN ** 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 = 0.3956 r_free = 0.3956 target = 0.133724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.109920 restraints weight = 28293.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.114341 restraints weight = 15639.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.117435 restraints weight = 10026.916| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12876 Z= 0.129 Angle : 0.626 13.905 17364 Z= 0.327 Chirality : 0.044 0.173 1918 Planarity : 0.004 0.047 2216 Dihedral : 5.459 71.824 1740 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.07 % Allowed : 3.53 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1538 helix: 0.65 (0.17), residues: 896 sheet: -2.81 (0.44), residues: 98 loop : -1.02 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 368 HIS 0.013 0.001 HIS F 358 PHE 0.036 0.002 PHE D 180 TYR 0.022 0.002 TYR D 51 ARG 0.010 0.000 ARG E 96 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 710) hydrogen bonds : angle 4.67954 ( 2070) covalent geometry : bond 0.00271 (12876) covalent geometry : angle 0.62593 (17364) *********************** 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 654 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 653 time to evaluate : 2.201 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: A 350 MET cc_start: 0.7432 (mtm) cc_final: 0.7025 (mtm) REVERT: A 387 PHE cc_start: 0.8079 (t80) cc_final: 0.7209 (t80) REVERT: A 391 ARG cc_start: 0.8367 (mmt90) cc_final: 0.7731 (mmm-85) REVERT: A 399 LYS cc_start: 0.8410 (mmtp) cc_final: 0.7853 (mmtp) REVERT: A 402 HIS cc_start: 0.7811 (t-90) cc_final: 0.7589 (t-90) REVERT: A 409 MET cc_start: 0.7414 (mtt) cc_final: 0.7128 (mtt) REVERT: A 411 TYR cc_start: 0.7248 (p90) cc_final: 0.7017 (p90) REVERT: A 412 MET cc_start: 0.6230 (ppp) cc_final: 0.5593 (ppp) REVERT: A 414 LYS cc_start: 0.8233 (tppt) cc_final: 0.7953 (tppt) REVERT: A 416 ASN cc_start: 0.7385 (p0) cc_final: 0.7042 (p0) REVERT: A 417 LEU cc_start: 0.8043 (pt) cc_final: 0.7830 (pt) REVERT: A 423 TRP cc_start: 0.7978 (t-100) cc_final: 0.7569 (t60) REVERT: A 439 LYS cc_start: 0.8164 (mppt) cc_final: 0.7502 (mppt) REVERT: A 444 GLN cc_start: 0.7938 (mt0) cc_final: 0.7726 (mp10) REVERT: A 454 GLN cc_start: 0.8695 (mt0) cc_final: 0.8470 (mt0) REVERT: A 456 MET cc_start: 0.8250 (mmm) cc_final: 0.6852 (mmm) REVERT: A 458 TYR cc_start: 0.8530 (t80) cc_final: 0.7975 (t80) REVERT: A 460 HIS cc_start: 0.8239 (m170) cc_final: 0.7589 (m90) REVERT: A 463 ASN cc_start: 0.7318 (m-40) cc_final: 0.7071 (m-40) REVERT: A 466 HIS cc_start: 0.8548 (t-90) cc_final: 0.8175 (t-90) REVERT: A 470 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7776 (mtmt) REVERT: A 477 HIS cc_start: 0.6575 (t-90) cc_final: 0.6340 (t-90) REVERT: A 512 MET cc_start: 0.5987 (ttm) cc_final: 0.5743 (ttm) REVERT: A 518 ARG cc_start: 0.8134 (ptp-110) cc_final: 0.7466 (ptp-110) REVERT: A 528 GLN cc_start: 0.7656 (mm-40) cc_final: 0.6906 (mm-40) REVERT: A 532 TYR cc_start: 0.7857 (t80) cc_final: 0.7505 (t80) REVERT: A 534 TYR cc_start: 0.8484 (t80) cc_final: 0.8134 (t80) REVERT: A 536 ILE cc_start: 0.8577 (mm) cc_final: 0.8150 (mm) REVERT: A 541 LEU cc_start: 0.8619 (mt) cc_final: 0.8401 (mt) REVERT: A 560 MET cc_start: 0.8323 (mmp) cc_final: 0.7972 (mmp) REVERT: A 563 ARG cc_start: 0.8710 (mmm-85) cc_final: 0.8058 (ttm-80) REVERT: A 581 MET cc_start: 0.7761 (mmm) cc_final: 0.7172 (mmm) REVERT: A 590 LYS cc_start: 0.7701 (mmtm) cc_final: 0.7367 (mmtm) REVERT: A 591 LYS cc_start: 0.8596 (ptpp) cc_final: 0.8382 (ptpp) REVERT: A 592 VAL cc_start: 0.7805 (t) cc_final: 0.7357 (m) REVERT: A 601 GLN cc_start: 0.8455 (tt0) cc_final: 0.8133 (tm-30) REVERT: B 350 MET cc_start: 0.7440 (mtm) cc_final: 0.6992 (mtm) REVERT: B 362 THR cc_start: 0.7685 (m) cc_final: 0.7434 (m) REVERT: B 367 LYS cc_start: 0.7692 (mmtt) cc_final: 0.6726 (mmtt) REVERT: B 387 PHE cc_start: 0.8220 (t80) cc_final: 0.7921 (t80) REVERT: B 393 GLU cc_start: 0.7975 (tp30) cc_final: 0.7412 (tp30) REVERT: B 399 LYS cc_start: 0.8434 (mmtp) cc_final: 0.7893 (mmtp) REVERT: B 402 HIS cc_start: 0.7881 (t-90) cc_final: 0.7519 (t-90) REVERT: B 407 LEU cc_start: 0.7375 (mp) cc_final: 0.7020 (mp) REVERT: B 409 MET cc_start: 0.7368 (mtm) cc_final: 0.6704 (mtm) REVERT: B 411 TYR cc_start: 0.7347 (p90) cc_final: 0.7135 (p90) REVERT: B 412 MET cc_start: 0.6001 (ppp) cc_final: 0.5481 (ppp) REVERT: B 414 LYS cc_start: 0.8308 (tppt) cc_final: 0.8066 (mmmt) REVERT: B 416 ASN cc_start: 0.7633 (p0) cc_final: 0.7262 (p0) REVERT: B 419 ILE cc_start: 0.7486 (mm) cc_final: 0.6996 (mm) REVERT: B 422 GLN cc_start: 0.8363 (tt0) cc_final: 0.7162 (pt0) REVERT: B 425 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7119 (mm-30) REVERT: B 432 HIS cc_start: 0.7673 (m90) cc_final: 0.6701 (m90) REVERT: B 433 LEU cc_start: 0.8369 (mt) cc_final: 0.8133 (mt) REVERT: B 439 LYS cc_start: 0.8322 (mppt) cc_final: 0.7750 (mppt) REVERT: B 442 MET cc_start: 0.7517 (mpp) cc_final: 0.7147 (mpp) REVERT: B 450 ARG cc_start: 0.8501 (ttp-170) cc_final: 0.7869 (ttp-170) REVERT: B 456 MET cc_start: 0.8146 (mmm) cc_final: 0.7842 (mmm) REVERT: B 458 TYR cc_start: 0.8533 (t80) cc_final: 0.7448 (t80) REVERT: B 466 HIS cc_start: 0.8533 (t-90) cc_final: 0.7930 (t70) REVERT: B 483 LYS cc_start: 0.8307 (mttp) cc_final: 0.7030 (mttp) REVERT: B 484 ILE cc_start: 0.8120 (mt) cc_final: 0.7843 (mt) REVERT: B 493 LYS cc_start: 0.7047 (mmtm) cc_final: 0.6791 (mmtm) REVERT: B 512 MET cc_start: 0.5962 (ttm) cc_final: 0.5514 (ttm) REVERT: B 516 VAL cc_start: 0.8762 (t) cc_final: 0.8397 (t) REVERT: B 528 GLN cc_start: 0.7605 (mm-40) cc_final: 0.6854 (mm-40) REVERT: B 534 TYR cc_start: 0.8451 (t80) cc_final: 0.8142 (t80) REVERT: B 541 LEU cc_start: 0.8754 (mt) cc_final: 0.8446 (mt) REVERT: B 545 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7364 (mt-10) REVERT: B 551 ILE cc_start: 0.8674 (mp) cc_final: 0.8361 (mp) REVERT: B 554 ARG cc_start: 0.7478 (tmm-80) cc_final: 0.7092 (tmm-80) REVERT: B 563 ARG cc_start: 0.8412 (mmm-85) cc_final: 0.7822 (ttm-80) REVERT: B 574 TYR cc_start: 0.7961 (m-80) cc_final: 0.7610 (m-10) REVERT: B 581 MET cc_start: 0.7761 (tpt) cc_final: 0.7535 (tpt) REVERT: B 583 ARG cc_start: 0.8627 (ptp-170) cc_final: 0.8081 (ptp-110) REVERT: B 601 GLN cc_start: 0.8606 (tt0) cc_final: 0.8256 (tt0) REVERT: B 622 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7081 (tm-30) REVERT: C 25 MET cc_start: 0.7624 (pmm) cc_final: 0.7226 (pmm) REVERT: C 43 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8449 (mt-10) REVERT: C 51 TYR cc_start: 0.8374 (m-10) cc_final: 0.8087 (m-10) REVERT: C 52 LYS cc_start: 0.8604 (tptm) cc_final: 0.8389 (tptm) REVERT: C 59 ARG cc_start: 0.8358 (mtp-110) cc_final: 0.7691 (mtp85) REVERT: C 69 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8347 (tm-30) REVERT: C 81 LYS cc_start: 0.8165 (ptpp) cc_final: 0.7890 (pptt) REVERT: C 84 MET cc_start: 0.7726 (ptp) cc_final: 0.7396 (ptp) REVERT: C 87 GLU cc_start: 0.8317 (pt0) cc_final: 0.8044 (pt0) REVERT: C 91 LYS cc_start: 0.8703 (tppt) cc_final: 0.7871 (tppt) REVERT: C 93 GLU cc_start: 0.8624 (tt0) cc_final: 0.8157 (tt0) REVERT: C 94 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8428 (ttpt) REVERT: C 95 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7813 (mt-10) REVERT: C 97 ARG cc_start: 0.8690 (mtm110) cc_final: 0.8265 (mtm110) REVERT: C 98 GLU cc_start: 0.7218 (tp30) cc_final: 0.6081 (tp30) REVERT: C 102 ASP cc_start: 0.7922 (m-30) cc_final: 0.7129 (m-30) REVERT: C 126 LYS cc_start: 0.8759 (ttpp) cc_final: 0.8471 (ttpp) REVERT: C 130 ASP cc_start: 0.7605 (m-30) cc_final: 0.7175 (m-30) REVERT: C 132 TYR cc_start: 0.8369 (m-80) cc_final: 0.7604 (m-80) REVERT: C 133 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8289 (ttp-110) REVERT: C 149 GLU cc_start: 0.8346 (tp30) cc_final: 0.8027 (tp30) REVERT: C 150 ASP cc_start: 0.8386 (m-30) cc_final: 0.8155 (m-30) REVERT: C 153 LYS cc_start: 0.8741 (tppt) cc_final: 0.8074 (tppt) REVERT: C 155 TYR cc_start: 0.7909 (m-10) cc_final: 0.7415 (m-80) REVERT: C 170 HIS cc_start: 0.8150 (t-90) cc_final: 0.7920 (t-90) REVERT: C 174 LEU cc_start: 0.8076 (mt) cc_final: 0.7754 (mt) REVERT: C 202 PHE cc_start: 0.9029 (t80) cc_final: 0.8804 (t80) REVERT: C 204 ASP cc_start: 0.8219 (t0) cc_final: 0.7928 (t0) REVERT: C 206 ILE cc_start: 0.7970 (mt) cc_final: 0.7717 (mt) REVERT: C 218 LYS cc_start: 0.7505 (mmpt) cc_final: 0.7272 (mmpt) REVERT: C 224 MET cc_start: 0.7226 (ptm) cc_final: 0.6403 (ptm) REVERT: C 225 GLN cc_start: 0.7459 (mm110) cc_final: 0.6645 (mm110) REVERT: D 7 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8197 (mm-30) REVERT: D 14 LYS cc_start: 0.8737 (mttt) cc_final: 0.8385 (mttm) REVERT: D 20 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7232 (tm-30) REVERT: D 25 MET cc_start: 0.7677 (pmm) cc_final: 0.7198 (pmm) REVERT: D 29 MET cc_start: 0.8954 (tpp) cc_final: 0.8417 (tpp) REVERT: D 34 GLU cc_start: 0.7998 (pp20) cc_final: 0.7662 (pp20) REVERT: D 43 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8540 (mt-10) REVERT: D 52 LYS cc_start: 0.8600 (tptm) cc_final: 0.8209 (tptm) REVERT: D 59 ARG cc_start: 0.8444 (mtp-110) cc_final: 0.8164 (mtp180) REVERT: D 65 ILE cc_start: 0.8762 (pt) cc_final: 0.8500 (pt) REVERT: D 66 SER cc_start: 0.8004 (m) cc_final: 0.7584 (m) REVERT: D 84 MET cc_start: 0.7849 (ptp) cc_final: 0.7370 (ptp) REVERT: D 87 GLU cc_start: 0.8363 (pt0) cc_final: 0.8032 (pt0) REVERT: D 91 LYS cc_start: 0.8749 (tppt) cc_final: 0.8196 (tppt) REVERT: D 93 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8306 (mt-10) REVERT: D 101 TYR cc_start: 0.8152 (m-80) cc_final: 0.7870 (m-80) REVERT: D 119 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7773 (tp30) REVERT: D 125 LEU cc_start: 0.8214 (mt) cc_final: 0.8007 (mt) REVERT: D 127 MET cc_start: 0.8392 (mmm) cc_final: 0.7744 (mmp) REVERT: D 130 ASP cc_start: 0.7708 (m-30) cc_final: 0.7348 (m-30) REVERT: D 133 ARG cc_start: 0.8571 (ttp-110) cc_final: 0.8289 (ttp-110) REVERT: D 153 LYS cc_start: 0.8524 (tppt) cc_final: 0.7818 (tppt) REVERT: D 155 TYR cc_start: 0.7719 (m-10) cc_final: 0.7269 (m-80) REVERT: D 170 HIS cc_start: 0.8380 (t-90) cc_final: 0.7972 (t-90) REVERT: D 174 LEU cc_start: 0.8075 (mt) cc_final: 0.7842 (mt) REVERT: D 192 ASP cc_start: 0.8294 (p0) cc_final: 0.7738 (p0) REVERT: D 193 LYS cc_start: 0.8247 (mttt) cc_final: 0.7723 (mptt) REVERT: D 220 SER cc_start: 0.7381 (m) cc_final: 0.7087 (m) REVERT: D 224 MET cc_start: 0.7377 (ptm) cc_final: 0.6388 (ptm) REVERT: D 225 GLN cc_start: 0.7489 (mm110) cc_final: 0.6646 (mm110) REVERT: E 121 CYS cc_start: 0.7612 (m) cc_final: 0.7328 (m) REVERT: E 125 TYR cc_start: 0.7870 (m-80) cc_final: 0.6917 (m-80) REVERT: E 144 GLU cc_start: 0.7070 (pt0) cc_final: 0.6831 (pt0) REVERT: E 146 MET cc_start: 0.6581 (tpp) cc_final: 0.6104 (tpp) REVERT: E 160 ARG cc_start: 0.7576 (mpp80) cc_final: 0.7135 (mpp80) REVERT: E 168 LYS cc_start: 0.8237 (ttmm) cc_final: 0.7715 (ttmm) REVERT: E 175 LYS cc_start: 0.8554 (ptmt) cc_final: 0.8006 (ptmt) REVERT: E 181 ARG cc_start: 0.8397 (tpm170) cc_final: 0.8158 (tpm170) REVERT: E 187 MET cc_start: 0.6143 (mtt) cc_final: 0.5515 (mtm) REVERT: E 189 ARG cc_start: 0.7931 (tpp-160) cc_final: 0.7519 (tpp80) REVERT: E 206 LEU cc_start: 0.6746 (tp) cc_final: 0.6510 (tp) REVERT: E 219 MET cc_start: 0.7924 (mtp) cc_final: 0.7656 (mtp) REVERT: E 227 ARG cc_start: 0.7495 (mtm180) cc_final: 0.7160 (mtp85) REVERT: E 236 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7820 (tm-30) REVERT: E 249 MET cc_start: 0.8247 (ppp) cc_final: 0.7986 (ppp) REVERT: E 253 LEU cc_start: 0.8763 (mt) cc_final: 0.8502 (mt) REVERT: E 256 MET cc_start: 0.7683 (ptm) cc_final: 0.7299 (ptm) REVERT: E 316 TYR cc_start: 0.8085 (t80) cc_final: 0.7591 (t80) REVERT: E 318 VAL cc_start: 0.8586 (p) cc_final: 0.8274 (m) REVERT: E 319 ASN cc_start: 0.8030 (t0) cc_final: 0.6897 (t0) REVERT: E 320 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7638 (mm-30) REVERT: E 334 PHE cc_start: 0.8497 (t80) cc_final: 0.8287 (t80) REVERT: E 356 MET cc_start: 0.7030 (ppp) cc_final: 0.6707 (ppp) REVERT: E 360 PHE cc_start: 0.8306 (p90) cc_final: 0.8071 (p90) REVERT: F 88 LYS cc_start: 0.8507 (mmmt) cc_final: 0.7977 (mmmt) REVERT: F 96 ARG cc_start: 0.7615 (ptm160) cc_final: 0.7028 (ptm160) REVERT: F 110 GLN cc_start: 0.8389 (mm110) cc_final: 0.8152 (mp10) REVERT: F 125 TYR cc_start: 0.8070 (m-80) cc_final: 0.7272 (m-80) REVERT: F 146 MET cc_start: 0.6615 (tpp) cc_final: 0.5938 (tpp) REVERT: F 175 LYS cc_start: 0.8568 (ptmt) cc_final: 0.8076 (ptmt) REVERT: F 189 ARG cc_start: 0.7756 (tpp-160) cc_final: 0.7419 (tpp-160) REVERT: F 195 ASN cc_start: 0.7611 (t0) cc_final: 0.7316 (t0) REVERT: F 206 LEU cc_start: 0.6650 (tp) cc_final: 0.6187 (tp) REVERT: F 219 MET cc_start: 0.7789 (mtp) cc_final: 0.7492 (mtp) REVERT: F 249 MET cc_start: 0.8299 (ppp) cc_final: 0.8002 (ppp) REVERT: F 256 MET cc_start: 0.7771 (ptm) cc_final: 0.7397 (ptm) REVERT: F 267 ASP cc_start: 0.7549 (p0) cc_final: 0.6890 (p0) REVERT: F 316 TYR cc_start: 0.8086 (t80) cc_final: 0.7508 (t80) REVERT: F 318 VAL cc_start: 0.8471 (p) cc_final: 0.8195 (m) REVERT: F 320 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7743 (mm-30) REVERT: F 324 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7598 (mmtt) REVERT: F 356 MET cc_start: 0.7087 (ppp) cc_final: 0.6831 (ppp) outliers start: 1 outliers final: 0 residues processed: 653 average time/residue: 0.3075 time to fit residues: 272.8168 Evaluate side-chains 651 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 651 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 22 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 128 optimal weight: 0.0030 chunk 136 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 E 109 ASN ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** 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 = 0.3856 r_free = 0.3856 target = 0.123482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101065 restraints weight = 29483.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.105270 restraints weight = 15911.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.108234 restraints weight = 9990.821| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12876 Z= 0.224 Angle : 0.691 9.698 17364 Z= 0.371 Chirality : 0.046 0.175 1918 Planarity : 0.005 0.048 2216 Dihedral : 5.515 53.394 1740 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1538 helix: 0.51 (0.16), residues: 894 sheet: -2.25 (0.52), residues: 78 loop : -1.15 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 368 HIS 0.014 0.002 HIS F 188 PHE 0.024 0.002 PHE D 180 TYR 0.020 0.002 TYR D 131 ARG 0.009 0.001 ARG E 96 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 710) hydrogen bonds : angle 4.88895 ( 2070) covalent geometry : bond 0.00423 (12876) covalent geometry : angle 0.69058 (17364) *********************** 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 659 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 658 time to evaluate : 1.484 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: 0.7472 (mtm) cc_final: 0.7130 (mtm) REVERT: A 367 LYS cc_start: 0.7582 (mmtt) cc_final: 0.6741 (mmtt) REVERT: A 375 LYS cc_start: 0.7562 (ttpp) cc_final: 0.7181 (ttpp) REVERT: A 387 PHE cc_start: 0.8141 (t80) cc_final: 0.7229 (t80) REVERT: A 391 ARG cc_start: 0.8417 (mmt90) cc_final: 0.7771 (mmm-85) REVERT: A 399 LYS cc_start: 0.8425 (mmtp) cc_final: 0.7895 (mmtp) REVERT: A 404 ASN cc_start: 0.7985 (m110) cc_final: 0.7365 (m110) REVERT: A 412 MET cc_start: 0.6347 (ppp) cc_final: 0.5643 (ppp) REVERT: A 414 LYS cc_start: 0.8276 (tppt) cc_final: 0.7967 (tppt) REVERT: A 416 ASN cc_start: 0.7559 (p0) cc_final: 0.7273 (p0) REVERT: A 417 LEU cc_start: 0.7998 (pt) cc_final: 0.7783 (pt) REVERT: A 422 GLN cc_start: 0.8202 (tt0) cc_final: 0.7410 (pt0) REVERT: A 423 TRP cc_start: 0.8136 (t-100) cc_final: 0.7791 (t60) REVERT: A 425 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6692 (mm-30) REVERT: A 429 LEU cc_start: 0.8210 (tp) cc_final: 0.7930 (tp) REVERT: A 439 LYS cc_start: 0.8315 (mppt) cc_final: 0.7647 (mppt) REVERT: A 444 GLN cc_start: 0.7861 (mt0) cc_final: 0.7636 (mp10) REVERT: A 456 MET cc_start: 0.8338 (mmm) cc_final: 0.7821 (mmm) REVERT: A 457 ASP cc_start: 0.7948 (t0) cc_final: 0.7600 (t0) REVERT: A 458 TYR cc_start: 0.8566 (t80) cc_final: 0.8054 (t80) REVERT: A 463 ASN cc_start: 0.7272 (m-40) cc_final: 0.7037 (m-40) REVERT: A 466 HIS cc_start: 0.8562 (t-90) cc_final: 0.7985 (t-90) REVERT: A 470 LYS cc_start: 0.8351 (mtmt) cc_final: 0.7522 (mtmt) REVERT: A 484 ILE cc_start: 0.8026 (mt) cc_final: 0.7685 (mt) REVERT: A 512 MET cc_start: 0.6156 (ttm) cc_final: 0.5721 (ttm) REVERT: A 518 ARG cc_start: 0.8233 (ptp-110) cc_final: 0.7543 (ptp-110) REVERT: A 528 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7159 (mm110) REVERT: A 532 TYR cc_start: 0.7952 (t80) cc_final: 0.7630 (t80) REVERT: A 534 TYR cc_start: 0.8446 (t80) cc_final: 0.7888 (t80) REVERT: A 536 ILE cc_start: 0.8599 (mm) cc_final: 0.8244 (mm) REVERT: A 541 LEU cc_start: 0.8657 (mt) cc_final: 0.8287 (mt) REVERT: A 560 MET cc_start: 0.8459 (mmp) cc_final: 0.7671 (mmp) REVERT: A 563 ARG cc_start: 0.8754 (mmm-85) cc_final: 0.8065 (ttm-80) REVERT: A 572 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7666 (mmmm) REVERT: A 574 TYR cc_start: 0.7718 (m-10) cc_final: 0.7342 (m-10) REVERT: A 581 MET cc_start: 0.7863 (mmm) cc_final: 0.7286 (mmm) REVERT: A 591 LYS cc_start: 0.8674 (ptpp) cc_final: 0.8454 (ptpp) REVERT: A 592 VAL cc_start: 0.7845 (t) cc_final: 0.7336 (m) REVERT: A 601 GLN cc_start: 0.8462 (tt0) cc_final: 0.8148 (tm-30) REVERT: A 622 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7252 (tm-30) REVERT: B 350 MET cc_start: 0.7530 (mtm) cc_final: 0.7115 (mtm) REVERT: B 362 THR cc_start: 0.7786 (m) cc_final: 0.7537 (m) REVERT: B 367 LYS cc_start: 0.7691 (mmtt) cc_final: 0.6814 (mmtt) REVERT: B 383 THR cc_start: 0.8412 (p) cc_final: 0.7945 (p) REVERT: B 386 GLN cc_start: 0.8656 (mt0) cc_final: 0.8391 (mt0) REVERT: B 387 PHE cc_start: 0.8265 (t80) cc_final: 0.7958 (t80) REVERT: B 398 ARG cc_start: 0.8276 (ttm170) cc_final: 0.7639 (ttm170) REVERT: B 399 LYS cc_start: 0.8389 (mmtp) cc_final: 0.7860 (mmtp) REVERT: B 402 HIS cc_start: 0.7722 (t-90) cc_final: 0.7309 (t-90) REVERT: B 409 MET cc_start: 0.7443 (mtm) cc_final: 0.6809 (mtm) REVERT: B 412 MET cc_start: 0.6106 (ppp) cc_final: 0.5585 (ppp) REVERT: B 414 LYS cc_start: 0.8324 (tppt) cc_final: 0.8077 (mmmt) REVERT: B 416 ASN cc_start: 0.7671 (p0) cc_final: 0.7411 (p0) REVERT: B 419 ILE cc_start: 0.7533 (mm) cc_final: 0.7138 (mm) REVERT: B 422 GLN cc_start: 0.8268 (tt0) cc_final: 0.7458 (pt0) REVERT: B 429 LEU cc_start: 0.8354 (tp) cc_final: 0.8141 (tp) REVERT: B 432 HIS cc_start: 0.7693 (m90) cc_final: 0.6897 (m90) REVERT: B 439 LYS cc_start: 0.8502 (mppt) cc_final: 0.7952 (mppt) REVERT: B 450 ARG cc_start: 0.8510 (ttp-170) cc_final: 0.7874 (ttp-170) REVERT: B 456 MET cc_start: 0.8149 (mmm) cc_final: 0.7833 (mmm) REVERT: B 457 ASP cc_start: 0.7953 (t70) cc_final: 0.7604 (t70) REVERT: B 458 TYR cc_start: 0.8548 (t80) cc_final: 0.7621 (t80) REVERT: B 466 HIS cc_start: 0.8506 (t-90) cc_final: 0.8071 (t-90) REVERT: B 470 LYS cc_start: 0.8386 (mtpt) cc_final: 0.7831 (mtpt) REVERT: B 483 LYS cc_start: 0.8324 (mttp) cc_final: 0.7559 (mttp) REVERT: B 484 ILE cc_start: 0.8057 (mt) cc_final: 0.7744 (mt) REVERT: B 492 VAL cc_start: 0.7801 (t) cc_final: 0.7524 (m) REVERT: B 493 LYS cc_start: 0.7415 (mmtm) cc_final: 0.6854 (mmtm) REVERT: B 511 TRP cc_start: 0.7425 (m-90) cc_final: 0.7104 (m-90) REVERT: B 512 MET cc_start: 0.6091 (ttm) cc_final: 0.5833 (ttm) REVERT: B 518 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7119 (mtm-85) REVERT: B 528 GLN cc_start: 0.7700 (mm-40) cc_final: 0.6986 (mm-40) REVERT: B 532 TYR cc_start: 0.8251 (t80) cc_final: 0.7979 (t80) REVERT: B 534 TYR cc_start: 0.8478 (t80) cc_final: 0.8202 (t80) REVERT: B 541 LEU cc_start: 0.8758 (mt) cc_final: 0.8532 (mt) REVERT: B 545 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7323 (mt-10) REVERT: B 551 ILE cc_start: 0.8754 (mp) cc_final: 0.8437 (mp) REVERT: B 554 ARG cc_start: 0.7662 (tmm-80) cc_final: 0.7368 (tmm-80) REVERT: B 563 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.7901 (ttm-80) REVERT: B 574 TYR cc_start: 0.8170 (m-80) cc_final: 0.7797 (m-10) REVERT: B 583 ARG cc_start: 0.8660 (ptp-170) cc_final: 0.8154 (ptp-110) REVERT: B 591 LYS cc_start: 0.8665 (ptpp) cc_final: 0.8461 (ptpp) REVERT: B 601 GLN cc_start: 0.8594 (tt0) cc_final: 0.8286 (tt0) REVERT: C 25 MET cc_start: 0.7324 (pmm) cc_final: 0.6858 (pmm) REVERT: C 51 TYR cc_start: 0.8396 (m-10) cc_final: 0.8139 (m-10) REVERT: C 69 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8349 (tm-30) REVERT: C 81 LYS cc_start: 0.8286 (ptpp) cc_final: 0.7985 (pptt) REVERT: C 84 MET cc_start: 0.7760 (ptp) cc_final: 0.7431 (ptp) REVERT: C 87 GLU cc_start: 0.8301 (pt0) cc_final: 0.8005 (pt0) REVERT: C 91 LYS cc_start: 0.8710 (tppt) cc_final: 0.7843 (tppt) REVERT: C 92 VAL cc_start: 0.9086 (m) cc_final: 0.8864 (m) REVERT: C 93 GLU cc_start: 0.8635 (tt0) cc_final: 0.8170 (tt0) REVERT: C 94 LYS cc_start: 0.8810 (ttpt) cc_final: 0.8472 (ttpt) REVERT: C 95 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7791 (mt-10) REVERT: C 97 ARG cc_start: 0.8699 (mtm110) cc_final: 0.8318 (mtm110) REVERT: C 98 GLU cc_start: 0.7358 (tp30) cc_final: 0.6151 (tp30) REVERT: C 102 ASP cc_start: 0.7960 (m-30) cc_final: 0.7045 (m-30) REVERT: C 103 VAL cc_start: 0.8599 (t) cc_final: 0.8209 (t) REVERT: C 126 LYS cc_start: 0.8696 (ttpp) cc_final: 0.8342 (ttpp) REVERT: C 132 TYR cc_start: 0.8566 (m-80) cc_final: 0.7848 (m-80) REVERT: C 134 TYR cc_start: 0.8412 (m-10) cc_final: 0.7792 (m-80) REVERT: C 149 GLU cc_start: 0.8401 (tp30) cc_final: 0.8097 (tp30) REVERT: C 150 ASP cc_start: 0.8423 (m-30) cc_final: 0.8202 (m-30) REVERT: C 153 LYS cc_start: 0.8724 (tppt) cc_final: 0.8033 (tppt) REVERT: C 155 TYR cc_start: 0.8006 (m-10) cc_final: 0.7643 (m-80) REVERT: C 170 HIS cc_start: 0.8201 (t-90) cc_final: 0.7942 (t-90) REVERT: C 174 LEU cc_start: 0.8241 (mt) cc_final: 0.7887 (mt) REVERT: C 197 LEU cc_start: 0.8537 (mm) cc_final: 0.8299 (mm) REVERT: C 202 PHE cc_start: 0.9049 (t80) cc_final: 0.8793 (t80) REVERT: C 204 ASP cc_start: 0.8219 (t0) cc_final: 0.7949 (t0) REVERT: C 206 ILE cc_start: 0.8002 (mt) cc_final: 0.7780 (mt) REVERT: C 218 LYS cc_start: 0.7620 (mmpt) cc_final: 0.7346 (mmpt) REVERT: C 224 MET cc_start: 0.7354 (ptm) cc_final: 0.6511 (ptm) REVERT: C 225 GLN cc_start: 0.7462 (mm110) cc_final: 0.6670 (mm110) REVERT: D 7 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8163 (mm-30) REVERT: D 14 LYS cc_start: 0.8750 (mttt) cc_final: 0.8340 (mttm) REVERT: D 20 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7269 (tm-30) REVERT: D 25 MET cc_start: 0.7838 (pmm) cc_final: 0.7419 (pmm) REVERT: D 29 MET cc_start: 0.8957 (tpp) cc_final: 0.8565 (mmm) REVERT: D 34 GLU cc_start: 0.8065 (pp20) cc_final: 0.7736 (pp20) REVERT: D 43 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8512 (mt-10) REVERT: D 52 LYS cc_start: 0.8671 (tptm) cc_final: 0.8291 (tptm) REVERT: D 59 ARG cc_start: 0.8346 (mtp-110) cc_final: 0.8039 (mtp180) REVERT: D 63 ARG cc_start: 0.8193 (tpp-160) cc_final: 0.7745 (tpp-160) REVERT: D 65 ILE cc_start: 0.8754 (pt) cc_final: 0.8492 (pt) REVERT: D 66 SER cc_start: 0.8093 (m) cc_final: 0.7514 (m) REVERT: D 84 MET cc_start: 0.7822 (ptp) cc_final: 0.7298 (ptp) REVERT: D 87 GLU cc_start: 0.8349 (pt0) cc_final: 0.8044 (pt0) REVERT: D 91 LYS cc_start: 0.8776 (tppt) cc_final: 0.7760 (tppt) REVERT: D 92 VAL cc_start: 0.9117 (m) cc_final: 0.8806 (m) REVERT: D 93 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8383 (mt-10) REVERT: D 95 GLU cc_start: 0.8604 (mt-10) cc_final: 0.7787 (mt-10) REVERT: D 102 ASP cc_start: 0.7725 (m-30) cc_final: 0.7381 (m-30) REVERT: D 119 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7833 (tp30) REVERT: D 125 LEU cc_start: 0.8294 (mt) cc_final: 0.8086 (mt) REVERT: D 127 MET cc_start: 0.8401 (mmm) cc_final: 0.7756 (mmp) REVERT: D 130 ASP cc_start: 0.7580 (m-30) cc_final: 0.7261 (m-30) REVERT: D 133 ARG cc_start: 0.8521 (ttp-110) cc_final: 0.8257 (ttp-110) REVERT: D 153 LYS cc_start: 0.8492 (tppt) cc_final: 0.7753 (tppt) REVERT: D 155 TYR cc_start: 0.7971 (m-10) cc_final: 0.7427 (m-80) REVERT: D 170 HIS cc_start: 0.8388 (t-90) cc_final: 0.7948 (t-90) REVERT: D 172 ILE cc_start: 0.8720 (tt) cc_final: 0.8255 (tt) REVERT: D 174 LEU cc_start: 0.8187 (mt) cc_final: 0.7955 (mt) REVERT: D 192 ASP cc_start: 0.8363 (p0) cc_final: 0.7986 (p0) REVERT: D 195 CYS cc_start: 0.8394 (p) cc_final: 0.8139 (p) REVERT: D 220 SER cc_start: 0.7380 (m) cc_final: 0.7109 (m) REVERT: D 224 MET cc_start: 0.7566 (ptm) cc_final: 0.7346 (ptm) REVERT: E 121 CYS cc_start: 0.7354 (m) cc_final: 0.6985 (m) REVERT: E 125 TYR cc_start: 0.8090 (m-80) cc_final: 0.7256 (m-80) REVERT: E 144 GLU cc_start: 0.7332 (pt0) cc_final: 0.6725 (pt0) REVERT: E 160 ARG cc_start: 0.7527 (mpp80) cc_final: 0.6974 (mpt-90) REVERT: E 175 LYS cc_start: 0.8707 (ptmt) cc_final: 0.8186 (ptmt) REVERT: E 206 LEU cc_start: 0.6718 (tp) cc_final: 0.6408 (tp) REVERT: E 215 LEU cc_start: 0.5354 (tp) cc_final: 0.5076 (tt) REVERT: E 219 MET cc_start: 0.7837 (mtp) cc_final: 0.7460 (mtp) REVERT: E 227 ARG cc_start: 0.7626 (mtm180) cc_final: 0.7059 (mtm180) REVERT: E 233 GLU cc_start: 0.8438 (pt0) cc_final: 0.8126 (pt0) REVERT: E 249 MET cc_start: 0.8346 (ppp) cc_final: 0.8119 (ppp) REVERT: E 253 LEU cc_start: 0.8784 (mt) cc_final: 0.8553 (mt) REVERT: E 256 MET cc_start: 0.7760 (ptm) cc_final: 0.7468 (ptm) REVERT: E 316 TYR cc_start: 0.8045 (t80) cc_final: 0.7594 (t80) REVERT: E 319 ASN cc_start: 0.8090 (t0) cc_final: 0.6845 (t0) REVERT: E 320 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7700 (mm-30) REVERT: E 334 PHE cc_start: 0.8463 (t80) cc_final: 0.8248 (t80) REVERT: E 344 LYS cc_start: 0.8418 (pptt) cc_final: 0.8161 (mttt) REVERT: E 356 MET cc_start: 0.7060 (ppp) cc_final: 0.6772 (ppp) REVERT: E 360 PHE cc_start: 0.8251 (p90) cc_final: 0.7973 (p90) REVERT: F 88 LYS cc_start: 0.8489 (mmmt) cc_final: 0.7986 (mmmt) REVERT: F 125 TYR cc_start: 0.8144 (m-80) cc_final: 0.7446 (m-80) REVERT: F 163 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7864 (mt-10) REVERT: F 175 LYS cc_start: 0.8690 (ptmt) cc_final: 0.8202 (ptmt) REVERT: F 219 MET cc_start: 0.7791 (mtp) cc_final: 0.7472 (mtp) REVERT: F 227 ARG cc_start: 0.7576 (mtm180) cc_final: 0.7059 (mtm180) REVERT: F 249 MET cc_start: 0.8362 (ppp) cc_final: 0.8112 (ppp) REVERT: F 253 LEU cc_start: 0.8752 (mt) cc_final: 0.8540 (mt) REVERT: F 256 MET cc_start: 0.7824 (ptm) cc_final: 0.7457 (ptm) REVERT: F 267 ASP cc_start: 0.7768 (p0) cc_final: 0.7200 (p0) REVERT: F 316 TYR cc_start: 0.8063 (t80) cc_final: 0.7548 (t80) REVERT: F 318 VAL cc_start: 0.8442 (p) cc_final: 0.8132 (m) REVERT: F 319 ASN cc_start: 0.8028 (t0) cc_final: 0.6807 (t0) REVERT: F 320 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7673 (mm-30) REVERT: F 324 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7542 (mmtt) REVERT: F 334 PHE cc_start: 0.8424 (t80) cc_final: 0.8211 (t80) REVERT: F 344 LYS cc_start: 0.8319 (tmmt) cc_final: 0.8106 (tmmt) outliers start: 1 outliers final: 0 residues processed: 658 average time/residue: 0.3163 time to fit residues: 284.7513 Evaluate side-chains 645 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 116 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 78 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 HIS C 200 GLN D 117 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN F 195 ASN ** 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 = 0.3903 r_free = 0.3903 target = 0.130189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.106521 restraints weight = 28564.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.110781 restraints weight = 15682.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.113801 restraints weight = 10058.787| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12876 Z= 0.201 Angle : 0.707 11.687 17364 Z= 0.371 Chirality : 0.046 0.175 1918 Planarity : 0.005 0.073 2216 Dihedral : 5.554 42.286 1740 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.21), residues: 1538 helix: 0.44 (0.16), residues: 898 sheet: -2.26 (0.53), residues: 76 loop : -1.02 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 368 HIS 0.013 0.001 HIS E 358 PHE 0.017 0.002 PHE E 360 TYR 0.026 0.002 TYR C 131 ARG 0.011 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 710) hydrogen bonds : angle 4.88216 ( 2070) covalent geometry : bond 0.00396 (12876) covalent geometry : angle 0.70708 (17364) *********************** 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 652 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 652 time to evaluate : 1.293 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: A 342 TRP cc_start: 0.8574 (m100) cc_final: 0.7983 (m100) REVERT: A 350 MET cc_start: 0.7498 (mtm) cc_final: 0.7099 (mtm) REVERT: A 367 LYS cc_start: 0.7607 (mmtt) cc_final: 0.6752 (mmtt) REVERT: A 387 PHE cc_start: 0.8158 (t80) cc_final: 0.7221 (t80) REVERT: A 391 ARG cc_start: 0.8391 (mmt90) cc_final: 0.7727 (mmm-85) REVERT: A 393 GLU cc_start: 0.8084 (tp30) cc_final: 0.7678 (tp30) REVERT: A 399 LYS cc_start: 0.8437 (mmtp) cc_final: 0.7926 (mmtp) REVERT: A 402 HIS cc_start: 0.7612 (t-90) cc_final: 0.7175 (t-90) REVERT: A 404 ASN cc_start: 0.7950 (m110) cc_final: 0.7500 (m110) REVERT: A 409 MET cc_start: 0.7333 (mtt) cc_final: 0.7106 (mtt) REVERT: A 412 MET cc_start: 0.6351 (ppp) cc_final: 0.5619 (ppp) REVERT: A 414 LYS cc_start: 0.8256 (tppt) cc_final: 0.7975 (tppt) REVERT: A 417 LEU cc_start: 0.8000 (pt) cc_final: 0.7795 (pt) REVERT: A 439 LYS cc_start: 0.8303 (mppt) cc_final: 0.7625 (mppt) REVERT: A 444 GLN cc_start: 0.7838 (mt0) cc_final: 0.7631 (mp10) REVERT: A 456 MET cc_start: 0.8304 (mmm) cc_final: 0.7572 (mmm) REVERT: A 457 ASP cc_start: 0.7942 (t0) cc_final: 0.7609 (t0) REVERT: A 458 TYR cc_start: 0.8527 (t80) cc_final: 0.8278 (t80) REVERT: A 460 HIS cc_start: 0.8531 (m170) cc_final: 0.7970 (m90) REVERT: A 463 ASN cc_start: 0.7271 (m-40) cc_final: 0.7046 (m-40) REVERT: A 466 HIS cc_start: 0.8480 (t-90) cc_final: 0.8034 (t-90) REVERT: A 470 LYS cc_start: 0.8274 (mtmt) cc_final: 0.7581 (mtmt) REVERT: A 484 ILE cc_start: 0.8038 (mt) cc_final: 0.7636 (mt) REVERT: A 512 MET cc_start: 0.6114 (ttm) cc_final: 0.5697 (ttm) REVERT: A 518 ARG cc_start: 0.8222 (ptp-110) cc_final: 0.7502 (ptp-110) REVERT: A 528 GLN cc_start: 0.7731 (mm-40) cc_final: 0.6967 (mm-40) REVERT: A 534 TYR cc_start: 0.8545 (t80) cc_final: 0.8067 (t80) REVERT: A 541 LEU cc_start: 0.8667 (mt) cc_final: 0.8268 (mt) REVERT: A 545 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7344 (mt-10) REVERT: A 559 PHE cc_start: 0.8605 (t80) cc_final: 0.7657 (t80) REVERT: A 560 MET cc_start: 0.8444 (mmp) cc_final: 0.7541 (mmp) REVERT: A 563 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.8042 (ttm-80) REVERT: A 572 LYS cc_start: 0.8271 (mmmm) cc_final: 0.7730 (mmmm) REVERT: A 574 TYR cc_start: 0.7793 (m-10) cc_final: 0.7427 (m-10) REVERT: A 581 MET cc_start: 0.7819 (mmm) cc_final: 0.7248 (mmm) REVERT: A 591 LYS cc_start: 0.8689 (ptpp) cc_final: 0.8471 (ptpp) REVERT: A 592 VAL cc_start: 0.7842 (t) cc_final: 0.7368 (m) REVERT: A 601 GLN cc_start: 0.8443 (tt0) cc_final: 0.8174 (tm-30) REVERT: A 622 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7027 (tm-30) REVERT: B 342 TRP cc_start: 0.8635 (m100) cc_final: 0.8218 (m100) REVERT: B 350 MET cc_start: 0.7530 (mtm) cc_final: 0.7050 (mtm) REVERT: B 362 THR cc_start: 0.7812 (m) cc_final: 0.7568 (m) REVERT: B 367 LYS cc_start: 0.7734 (mmtt) cc_final: 0.6825 (mmtt) REVERT: B 387 PHE cc_start: 0.8252 (t80) cc_final: 0.7947 (t80) REVERT: B 398 ARG cc_start: 0.8289 (ttm170) cc_final: 0.7846 (ttm170) REVERT: B 399 LYS cc_start: 0.8380 (mmtp) cc_final: 0.8005 (mmtp) REVERT: B 402 HIS cc_start: 0.7783 (t-90) cc_final: 0.7470 (t-90) REVERT: B 409 MET cc_start: 0.7477 (mtm) cc_final: 0.6978 (mtm) REVERT: B 412 MET cc_start: 0.5924 (ppp) cc_final: 0.5506 (ppp) REVERT: B 419 ILE cc_start: 0.7492 (mm) cc_final: 0.7074 (mm) REVERT: B 439 LYS cc_start: 0.8501 (mppt) cc_final: 0.7983 (mppt) REVERT: B 442 MET cc_start: 0.7513 (mpp) cc_final: 0.7088 (mpp) REVERT: B 456 MET cc_start: 0.8224 (mmm) cc_final: 0.7844 (mmm) REVERT: B 457 ASP cc_start: 0.7871 (t70) cc_final: 0.7616 (t70) REVERT: B 458 TYR cc_start: 0.8549 (t80) cc_final: 0.7594 (t80) REVERT: B 466 HIS cc_start: 0.8608 (t-90) cc_final: 0.8226 (t-90) REVERT: B 470 LYS cc_start: 0.8444 (mtpt) cc_final: 0.7800 (mtpt) REVERT: B 473 ASN cc_start: 0.7587 (m110) cc_final: 0.7179 (m110) REVERT: B 483 LYS cc_start: 0.8263 (mttp) cc_final: 0.7976 (mttp) REVERT: B 484 ILE cc_start: 0.8026 (mt) cc_final: 0.7677 (mt) REVERT: B 492 VAL cc_start: 0.7845 (t) cc_final: 0.7615 (m) REVERT: B 493 LYS cc_start: 0.7155 (mmtm) cc_final: 0.6831 (mmtm) REVERT: B 511 TRP cc_start: 0.7355 (m-90) cc_final: 0.6874 (m-90) REVERT: B 512 MET cc_start: 0.6190 (ttm) cc_final: 0.5715 (ttm) REVERT: B 517 ILE cc_start: 0.8582 (mt) cc_final: 0.8304 (mt) REVERT: B 528 GLN cc_start: 0.7596 (mm-40) cc_final: 0.6873 (mm-40) REVERT: B 534 TYR cc_start: 0.8457 (t80) cc_final: 0.8122 (t80) REVERT: B 542 MET cc_start: 0.7322 (mtp) cc_final: 0.6837 (mtp) REVERT: B 545 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7350 (mt-10) REVERT: B 551 ILE cc_start: 0.8714 (mp) cc_final: 0.8423 (mp) REVERT: B 554 ARG cc_start: 0.7674 (tmm-80) cc_final: 0.7389 (tmm-80) REVERT: B 563 ARG cc_start: 0.8426 (mmm-85) cc_final: 0.7633 (ttm-80) REVERT: B 583 ARG cc_start: 0.8674 (ptp-170) cc_final: 0.8115 (ptp-110) REVERT: B 591 LYS cc_start: 0.8681 (ptpp) cc_final: 0.8470 (ptpp) REVERT: B 601 GLN cc_start: 0.8585 (tt0) cc_final: 0.8289 (tt0) REVERT: B 618 ARG cc_start: 0.7611 (ptm160) cc_final: 0.7363 (ptm160) REVERT: C 25 MET cc_start: 0.7651 (pmm) cc_final: 0.7171 (pmm) REVERT: C 43 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8230 (mt-10) REVERT: C 51 TYR cc_start: 0.8437 (m-10) cc_final: 0.8203 (m-10) REVERT: C 52 LYS cc_start: 0.8679 (tptt) cc_final: 0.8390 (tptt) REVERT: C 69 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8372 (tm-30) REVERT: C 81 LYS cc_start: 0.8309 (ptpp) cc_final: 0.7989 (pptt) REVERT: C 84 MET cc_start: 0.7788 (ptp) cc_final: 0.7435 (ptp) REVERT: C 87 GLU cc_start: 0.8301 (pt0) cc_final: 0.8009 (pt0) REVERT: C 91 LYS cc_start: 0.8737 (tppt) cc_final: 0.7835 (tppt) REVERT: C 92 VAL cc_start: 0.9109 (m) cc_final: 0.8907 (m) REVERT: C 93 GLU cc_start: 0.8694 (tt0) cc_final: 0.8258 (tt0) REVERT: C 94 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8458 (ttpt) REVERT: C 95 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7762 (mt-10) REVERT: C 97 ARG cc_start: 0.8711 (mtm110) cc_final: 0.8337 (mtm110) REVERT: C 98 GLU cc_start: 0.7414 (tp30) cc_final: 0.6269 (tp30) REVERT: C 102 ASP cc_start: 0.8041 (m-30) cc_final: 0.7184 (m-30) REVERT: C 103 VAL cc_start: 0.8598 (t) cc_final: 0.8184 (t) REVERT: C 125 LEU cc_start: 0.8339 (mt) cc_final: 0.8080 (mt) REVERT: C 126 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8255 (ttpp) REVERT: C 130 ASP cc_start: 0.7767 (m-30) cc_final: 0.7452 (m-30) REVERT: C 132 TYR cc_start: 0.8496 (m-80) cc_final: 0.7927 (m-80) REVERT: C 134 TYR cc_start: 0.8300 (m-10) cc_final: 0.7699 (m-80) REVERT: C 149 GLU cc_start: 0.8408 (tp30) cc_final: 0.8112 (tp30) REVERT: C 153 LYS cc_start: 0.8696 (tppt) cc_final: 0.8032 (tppt) REVERT: C 155 TYR cc_start: 0.8039 (m-10) cc_final: 0.7376 (m-80) REVERT: C 170 HIS cc_start: 0.8188 (t-90) cc_final: 0.7779 (t70) REVERT: C 174 LEU cc_start: 0.8178 (mt) cc_final: 0.7869 (mt) REVERT: C 180 PHE cc_start: 0.8628 (m-80) cc_final: 0.7877 (m-80) REVERT: C 202 PHE cc_start: 0.9041 (t80) cc_final: 0.8824 (t80) REVERT: C 204 ASP cc_start: 0.8214 (t0) cc_final: 0.7950 (t0) REVERT: C 206 ILE cc_start: 0.8053 (mt) cc_final: 0.7839 (mt) REVERT: C 218 LYS cc_start: 0.7596 (mmpt) cc_final: 0.7345 (mmpt) REVERT: C 224 MET cc_start: 0.7381 (ptm) cc_final: 0.6503 (ptm) REVERT: C 225 GLN cc_start: 0.7452 (mm110) cc_final: 0.6652 (mm110) REVERT: D 7 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8179 (mm-30) REVERT: D 10 VAL cc_start: 0.8932 (t) cc_final: 0.8726 (t) REVERT: D 14 LYS cc_start: 0.8744 (mttt) cc_final: 0.8330 (mttm) REVERT: D 20 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7288 (tm-30) REVERT: D 25 MET cc_start: 0.7722 (pmm) cc_final: 0.7198 (pmm) REVERT: D 29 MET cc_start: 0.8980 (tpp) cc_final: 0.8429 (tpp) REVERT: D 34 GLU cc_start: 0.7980 (pp20) cc_final: 0.7557 (pp20) REVERT: D 43 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8362 (mt-10) REVERT: D 52 LYS cc_start: 0.8662 (tptm) cc_final: 0.8301 (tptm) REVERT: D 59 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.7969 (mtp180) REVERT: D 65 ILE cc_start: 0.8765 (pt) cc_final: 0.8518 (pt) REVERT: D 66 SER cc_start: 0.8071 (m) cc_final: 0.7660 (m) REVERT: D 84 MET cc_start: 0.7828 (ptp) cc_final: 0.7280 (ptp) REVERT: D 87 GLU cc_start: 0.8388 (pt0) cc_final: 0.8085 (pt0) REVERT: D 91 LYS cc_start: 0.8753 (tppt) cc_final: 0.7726 (tppt) REVERT: D 92 VAL cc_start: 0.9136 (m) cc_final: 0.8804 (m) REVERT: D 95 GLU cc_start: 0.8615 (mt-10) cc_final: 0.7769 (mt-10) REVERT: D 102 ASP cc_start: 0.7779 (m-30) cc_final: 0.7412 (m-30) REVERT: D 119 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7765 (tp30) REVERT: D 127 MET cc_start: 0.8377 (mmm) cc_final: 0.7741 (mmp) REVERT: D 128 LYS cc_start: 0.8121 (tttt) cc_final: 0.7713 (tttt) REVERT: D 133 ARG cc_start: 0.8546 (ttp-110) cc_final: 0.8276 (ttp-110) REVERT: D 153 LYS cc_start: 0.8449 (tppt) cc_final: 0.7720 (tppt) REVERT: D 155 TYR cc_start: 0.8015 (m-10) cc_final: 0.7373 (m-80) REVERT: D 170 HIS cc_start: 0.8384 (t-90) cc_final: 0.8028 (t-90) REVERT: D 172 ILE cc_start: 0.8665 (tt) cc_final: 0.8185 (tt) REVERT: D 174 LEU cc_start: 0.8194 (mt) cc_final: 0.7971 (mt) REVERT: D 192 ASP cc_start: 0.8212 (p0) cc_final: 0.7823 (p0) REVERT: D 193 LYS cc_start: 0.8354 (mttt) cc_final: 0.8003 (mttt) REVERT: D 195 CYS cc_start: 0.8415 (p) cc_final: 0.8104 (p) REVERT: D 220 SER cc_start: 0.7469 (m) cc_final: 0.7156 (m) REVERT: D 224 MET cc_start: 0.7581 (ptm) cc_final: 0.6677 (ptm) REVERT: D 225 GLN cc_start: 0.7594 (mm110) cc_final: 0.6869 (mm110) REVERT: E 121 CYS cc_start: 0.7571 (m) cc_final: 0.7216 (m) REVERT: E 125 TYR cc_start: 0.8052 (m-80) cc_final: 0.7184 (m-80) REVERT: E 144 GLU cc_start: 0.7313 (pt0) cc_final: 0.7047 (pt0) REVERT: E 160 ARG cc_start: 0.7205 (mpp80) cc_final: 0.6530 (mpt-90) REVERT: E 175 LYS cc_start: 0.8709 (ptmt) cc_final: 0.8186 (ptmt) REVERT: E 195 ASN cc_start: 0.7916 (t0) cc_final: 0.7703 (t0) REVERT: E 206 LEU cc_start: 0.6742 (tp) cc_final: 0.6376 (tp) REVERT: E 215 LEU cc_start: 0.5408 (tp) cc_final: 0.5133 (tt) REVERT: E 219 MET cc_start: 0.7859 (mtp) cc_final: 0.7496 (mtp) REVERT: E 227 ARG cc_start: 0.7639 (mtm180) cc_final: 0.7048 (mtm180) REVERT: E 233 GLU cc_start: 0.8415 (pt0) cc_final: 0.8131 (pt0) REVERT: E 235 LEU cc_start: 0.8662 (mt) cc_final: 0.8338 (mt) REVERT: E 249 MET cc_start: 0.8316 (ppp) cc_final: 0.8066 (ppp) REVERT: E 253 LEU cc_start: 0.8810 (mt) cc_final: 0.8562 (mt) REVERT: E 256 MET cc_start: 0.7745 (ptm) cc_final: 0.7460 (ptm) REVERT: E 316 TYR cc_start: 0.8021 (t80) cc_final: 0.7584 (t80) REVERT: E 319 ASN cc_start: 0.8058 (t0) cc_final: 0.6750 (t0) REVERT: E 320 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7670 (mm-30) REVERT: E 324 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7598 (mmtt) REVERT: E 334 PHE cc_start: 0.8465 (t80) cc_final: 0.8253 (t80) REVERT: E 356 MET cc_start: 0.7085 (ppp) cc_final: 0.6789 (ppp) REVERT: E 360 PHE cc_start: 0.8232 (p90) cc_final: 0.8005 (p90) REVERT: E 371 PHE cc_start: 0.7577 (m-10) cc_final: 0.7287 (m-10) REVERT: F 88 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8007 (mmmt) REVERT: F 125 TYR cc_start: 0.8158 (m-80) cc_final: 0.7463 (m-80) REVERT: F 160 ARG cc_start: 0.7015 (mpp80) cc_final: 0.5835 (mtm180) REVERT: F 163 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7748 (mt-10) REVERT: F 175 LYS cc_start: 0.8697 (ptmt) cc_final: 0.8222 (ptmt) REVERT: F 195 ASN cc_start: 0.8040 (m110) cc_final: 0.6971 (t0) REVERT: F 206 LEU cc_start: 0.6781 (tp) cc_final: 0.6469 (tp) REVERT: F 219 MET cc_start: 0.7788 (mtp) cc_final: 0.7476 (mtp) REVERT: F 227 ARG cc_start: 0.7603 (mtm180) cc_final: 0.7054 (mtm180) REVERT: F 249 MET cc_start: 0.8337 (ppp) cc_final: 0.8089 (ppp) REVERT: F 253 LEU cc_start: 0.8742 (mt) cc_final: 0.8522 (mt) REVERT: F 256 MET cc_start: 0.7874 (ptm) cc_final: 0.7456 (ptm) REVERT: F 267 ASP cc_start: 0.7752 (p0) cc_final: 0.7188 (p0) REVERT: F 316 TYR cc_start: 0.8063 (t80) cc_final: 0.7545 (t80) REVERT: F 318 VAL cc_start: 0.8422 (p) cc_final: 0.8118 (m) REVERT: F 319 ASN cc_start: 0.7998 (t0) cc_final: 0.6737 (t0) REVERT: F 320 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7693 (mm-30) REVERT: F 324 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7519 (mmtt) REVERT: F 334 PHE cc_start: 0.8453 (t80) cc_final: 0.8067 (t80) REVERT: F 344 LYS cc_start: 0.8315 (tmmt) cc_final: 0.8097 (tmmt) REVERT: F 360 PHE cc_start: 0.8507 (p90) cc_final: 0.8056 (p90) outliers start: 0 outliers final: 0 residues processed: 652 average time/residue: 0.3080 time to fit residues: 273.9529 Evaluate side-chains 645 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 62 optimal weight: 0.0970 chunk 72 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 141 optimal weight: 0.0010 chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN E 195 ASN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN F 110 GLN ** 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 = 0.3958 r_free = 0.3958 target = 0.136754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.111606 restraints weight = 27864.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.115985 restraints weight = 15288.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.119121 restraints weight = 9844.538| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12876 Z= 0.139 Angle : 0.690 16.541 17364 Z= 0.355 Chirality : 0.045 0.176 1918 Planarity : 0.004 0.055 2216 Dihedral : 5.380 37.948 1740 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1538 helix: 0.53 (0.17), residues: 896 sheet: -2.28 (0.52), residues: 76 loop : -0.90 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 368 HIS 0.012 0.001 HIS E 358 PHE 0.031 0.002 PHE C 180 TYR 0.034 0.002 TYR F 134 ARG 0.008 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 710) hydrogen bonds : angle 4.76131 ( 2070) covalent geometry : bond 0.00309 (12876) covalent geometry : angle 0.69001 (17364) *********************** 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 645 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 2.726 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: 0.7467 (mtm) cc_final: 0.7033 (mtm) REVERT: A 367 LYS cc_start: 0.7643 (mmtt) cc_final: 0.6714 (mmtt) REVERT: A 368 TRP cc_start: 0.8471 (t60) cc_final: 0.8209 (t60) REVERT: A 387 PHE cc_start: 0.8100 (t80) cc_final: 0.7163 (t80) REVERT: A 391 ARG cc_start: 0.8365 (mmt90) cc_final: 0.7734 (mmm-85) REVERT: A 393 GLU cc_start: 0.8068 (tp30) cc_final: 0.7635 (tp30) REVERT: A 399 LYS cc_start: 0.8406 (mmtp) cc_final: 0.7844 (mmtp) REVERT: A 402 HIS cc_start: 0.7561 (t-90) cc_final: 0.7155 (t-90) REVERT: A 404 ASN cc_start: 0.8005 (m110) cc_final: 0.7577 (m110) REVERT: A 407 LEU cc_start: 0.7327 (mp) cc_final: 0.6801 (mp) REVERT: A 408 PHE cc_start: 0.7302 (t80) cc_final: 0.7043 (t80) REVERT: A 411 TYR cc_start: 0.7333 (p90) cc_final: 0.7102 (p90) REVERT: A 412 MET cc_start: 0.6043 (ppp) cc_final: 0.5560 (ppp) REVERT: A 417 LEU cc_start: 0.7959 (pt) cc_final: 0.7744 (pt) REVERT: A 419 ILE cc_start: 0.7277 (mm) cc_final: 0.7055 (mm) REVERT: A 422 GLN cc_start: 0.8233 (tt0) cc_final: 0.6726 (pt0) REVERT: A 439 LYS cc_start: 0.8227 (mppt) cc_final: 0.7538 (mppt) REVERT: A 454 GLN cc_start: 0.8705 (mt0) cc_final: 0.8105 (mt0) REVERT: A 456 MET cc_start: 0.8436 (mmm) cc_final: 0.7060 (mmm) REVERT: A 458 TYR cc_start: 0.8552 (t80) cc_final: 0.8257 (t80) REVERT: A 460 HIS cc_start: 0.8176 (m170) cc_final: 0.7925 (m-70) REVERT: A 463 ASN cc_start: 0.7334 (m-40) cc_final: 0.7129 (m-40) REVERT: A 466 HIS cc_start: 0.8530 (t-90) cc_final: 0.8092 (t-90) REVERT: A 470 LYS cc_start: 0.8274 (mtmt) cc_final: 0.7518 (mtmt) REVERT: A 484 ILE cc_start: 0.8024 (mt) cc_final: 0.7751 (mt) REVERT: A 512 MET cc_start: 0.5912 (ttm) cc_final: 0.5578 (ttm) REVERT: A 518 ARG cc_start: 0.8188 (ptp-110) cc_final: 0.7555 (ptp-110) REVERT: A 528 GLN cc_start: 0.7509 (mm-40) cc_final: 0.6973 (mm-40) REVERT: A 534 TYR cc_start: 0.8433 (t80) cc_final: 0.7953 (t80) REVERT: A 541 LEU cc_start: 0.8669 (mt) cc_final: 0.8245 (mt) REVERT: A 545 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7363 (mt-10) REVERT: A 559 PHE cc_start: 0.8586 (t80) cc_final: 0.7622 (t80) REVERT: A 560 MET cc_start: 0.8383 (mmp) cc_final: 0.7581 (mmp) REVERT: A 563 ARG cc_start: 0.8702 (mmm-85) cc_final: 0.8235 (ttm-80) REVERT: A 572 LYS cc_start: 0.8240 (mmmm) cc_final: 0.7698 (mmmm) REVERT: A 574 TYR cc_start: 0.7882 (m-10) cc_final: 0.7179 (m-10) REVERT: A 581 MET cc_start: 0.7693 (mmm) cc_final: 0.7191 (mmm) REVERT: A 591 LYS cc_start: 0.8676 (ptpp) cc_final: 0.8450 (ptpp) REVERT: A 592 VAL cc_start: 0.7806 (t) cc_final: 0.7325 (m) REVERT: A 601 GLN cc_start: 0.8410 (tt0) cc_final: 0.8097 (tm-30) REVERT: A 622 GLU cc_start: 0.7596 (tm-30) cc_final: 0.6997 (tm-30) REVERT: B 342 TRP cc_start: 0.8627 (m100) cc_final: 0.8169 (m100) REVERT: B 350 MET cc_start: 0.7492 (mtm) cc_final: 0.7038 (mtm) REVERT: B 362 THR cc_start: 0.7797 (m) cc_final: 0.7530 (m) REVERT: B 367 LYS cc_start: 0.7785 (mmtt) cc_final: 0.6835 (mmtt) REVERT: B 369 HIS cc_start: 0.8235 (m-70) cc_final: 0.7989 (m-70) REVERT: B 387 PHE cc_start: 0.8241 (t80) cc_final: 0.7930 (t80) REVERT: B 398 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7689 (ttm170) REVERT: B 399 LYS cc_start: 0.8350 (mmtp) cc_final: 0.7817 (mmtp) REVERT: B 402 HIS cc_start: 0.7782 (t-90) cc_final: 0.7426 (t-90) REVERT: B 409 MET cc_start: 0.7465 (mtm) cc_final: 0.6929 (mtm) REVERT: B 412 MET cc_start: 0.5921 (ppp) cc_final: 0.5507 (ppp) REVERT: B 419 ILE cc_start: 0.7406 (mm) cc_final: 0.6979 (mm) REVERT: B 429 LEU cc_start: 0.8260 (tp) cc_final: 0.8057 (tp) REVERT: B 433 LEU cc_start: 0.8391 (mt) cc_final: 0.8172 (mt) REVERT: B 439 LYS cc_start: 0.8480 (mppt) cc_final: 0.7887 (mppt) REVERT: B 456 MET cc_start: 0.8209 (mmm) cc_final: 0.7756 (mmm) REVERT: B 457 ASP cc_start: 0.7945 (t70) cc_final: 0.7559 (t70) REVERT: B 458 TYR cc_start: 0.8532 (t80) cc_final: 0.7541 (t80) REVERT: B 466 HIS cc_start: 0.8596 (t-90) cc_final: 0.8273 (t70) REVERT: B 470 LYS cc_start: 0.8379 (mtpt) cc_final: 0.7685 (mtpt) REVERT: B 473 ASN cc_start: 0.7601 (m110) cc_final: 0.7233 (m110) REVERT: B 483 LYS cc_start: 0.8220 (mttp) cc_final: 0.7927 (mttp) REVERT: B 484 ILE cc_start: 0.7940 (mt) cc_final: 0.7588 (mt) REVERT: B 511 TRP cc_start: 0.7320 (m-90) cc_final: 0.6881 (m-90) REVERT: B 512 MET cc_start: 0.6140 (ttm) cc_final: 0.5857 (ttm) REVERT: B 516 VAL cc_start: 0.8597 (t) cc_final: 0.8157 (t) REVERT: B 528 GLN cc_start: 0.7517 (mm-40) cc_final: 0.6991 (mm-40) REVERT: B 534 TYR cc_start: 0.8450 (t80) cc_final: 0.7996 (t80) REVERT: B 541 LEU cc_start: 0.8721 (mt) cc_final: 0.8339 (mt) REVERT: B 545 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7294 (mt-10) REVERT: B 551 ILE cc_start: 0.8773 (mp) cc_final: 0.8411 (mp) REVERT: B 554 ARG cc_start: 0.7714 (tmm-80) cc_final: 0.7395 (tmm-80) REVERT: B 563 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.7709 (ttm-80) REVERT: B 567 SER cc_start: 0.8074 (t) cc_final: 0.7835 (t) REVERT: B 574 TYR cc_start: 0.7644 (m-80) cc_final: 0.7321 (m-10) REVERT: B 583 ARG cc_start: 0.8699 (ptp-170) cc_final: 0.8107 (ptp-110) REVERT: B 591 LYS cc_start: 0.8657 (ptpp) cc_final: 0.8452 (ptpp) REVERT: B 601 GLN cc_start: 0.8549 (tt0) cc_final: 0.8261 (tt0) REVERT: B 618 ARG cc_start: 0.7580 (ptm160) cc_final: 0.7341 (ptm160) REVERT: B 619 SER cc_start: 0.7968 (p) cc_final: 0.7763 (p) REVERT: C 25 MET cc_start: 0.7300 (pmm) cc_final: 0.6885 (pmm) REVERT: C 43 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8207 (mt-10) REVERT: C 51 TYR cc_start: 0.8398 (m-10) cc_final: 0.8158 (m-10) REVERT: C 52 LYS cc_start: 0.8647 (tptt) cc_final: 0.8387 (tptt) REVERT: C 69 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 81 LYS cc_start: 0.8260 (ptpp) cc_final: 0.7995 (pptt) REVERT: C 84 MET cc_start: 0.7657 (ptp) cc_final: 0.7299 (ptp) REVERT: C 87 GLU cc_start: 0.8237 (pt0) cc_final: 0.7954 (pt0) REVERT: C 91 LYS cc_start: 0.8696 (tppt) cc_final: 0.7798 (tppt) REVERT: C 93 GLU cc_start: 0.8598 (tt0) cc_final: 0.8075 (tt0) REVERT: C 94 LYS cc_start: 0.8759 (ttpt) cc_final: 0.8408 (ttpt) REVERT: C 95 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7720 (mt-10) REVERT: C 97 ARG cc_start: 0.8682 (mtm110) cc_final: 0.8320 (mtm110) REVERT: C 98 GLU cc_start: 0.7313 (tp30) cc_final: 0.6141 (tp30) REVERT: C 102 ASP cc_start: 0.7962 (m-30) cc_final: 0.7108 (m-30) REVERT: C 103 VAL cc_start: 0.8541 (t) cc_final: 0.8136 (t) REVERT: C 126 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8254 (ttpp) REVERT: C 128 LYS cc_start: 0.7995 (tttt) cc_final: 0.7730 (tttt) REVERT: C 132 TYR cc_start: 0.8331 (m-80) cc_final: 0.8009 (m-80) REVERT: C 153 LYS cc_start: 0.8668 (tppt) cc_final: 0.7995 (tppt) REVERT: C 155 TYR cc_start: 0.7851 (m-10) cc_final: 0.7532 (m-80) REVERT: C 170 HIS cc_start: 0.8122 (t-90) cc_final: 0.7817 (t-90) REVERT: C 174 LEU cc_start: 0.8044 (mt) cc_final: 0.7761 (mt) REVERT: C 197 LEU cc_start: 0.8455 (mm) cc_final: 0.8222 (mm) REVERT: C 204 ASP cc_start: 0.8171 (t0) cc_final: 0.7886 (t0) REVERT: C 218 LYS cc_start: 0.7608 (mmpt) cc_final: 0.7361 (mmpt) REVERT: C 224 MET cc_start: 0.7312 (ptm) cc_final: 0.6410 (ptm) REVERT: C 225 GLN cc_start: 0.7420 (mm110) cc_final: 0.6626 (mm110) REVERT: D 6 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8228 (ttpt) REVERT: D 7 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8152 (mm-30) REVERT: D 14 LYS cc_start: 0.8747 (mttt) cc_final: 0.8330 (mttm) REVERT: D 20 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7113 (tm-30) REVERT: D 25 MET cc_start: 0.7600 (pmm) cc_final: 0.7126 (pmm) REVERT: D 29 MET cc_start: 0.8782 (tpp) cc_final: 0.8439 (tpp) REVERT: D 34 GLU cc_start: 0.7960 (pp20) cc_final: 0.7558 (pp20) REVERT: D 52 LYS cc_start: 0.8623 (tptm) cc_final: 0.8271 (tptm) REVERT: D 59 ARG cc_start: 0.8270 (mtp-110) cc_final: 0.7923 (mtp180) REVERT: D 65 ILE cc_start: 0.8703 (pt) cc_final: 0.8425 (pt) REVERT: D 66 SER cc_start: 0.8000 (m) cc_final: 0.7578 (m) REVERT: D 84 MET cc_start: 0.7717 (ptp) cc_final: 0.7177 (ptp) REVERT: D 87 GLU cc_start: 0.8375 (pt0) cc_final: 0.8059 (pt0) REVERT: D 91 LYS cc_start: 0.8759 (tppt) cc_final: 0.8079 (tppt) REVERT: D 93 GLU cc_start: 0.8446 (tt0) cc_final: 0.8177 (tt0) REVERT: D 102 ASP cc_start: 0.7733 (m-30) cc_final: 0.7394 (m-30) REVERT: D 119 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7766 (tp30) REVERT: D 123 PHE cc_start: 0.7935 (t80) cc_final: 0.7696 (t80) REVERT: D 125 LEU cc_start: 0.8210 (mt) cc_final: 0.7984 (mt) REVERT: D 127 MET cc_start: 0.8320 (mmm) cc_final: 0.7655 (mmp) REVERT: D 130 ASP cc_start: 0.7697 (m-30) cc_final: 0.7317 (m-30) REVERT: D 133 ARG cc_start: 0.8602 (ttp-110) cc_final: 0.8360 (ttp-110) REVERT: D 153 LYS cc_start: 0.8327 (tppt) cc_final: 0.7584 (tppt) REVERT: D 155 TYR cc_start: 0.8033 (m-10) cc_final: 0.7421 (m-80) REVERT: D 172 ILE cc_start: 0.8665 (tt) cc_final: 0.8400 (tt) REVERT: D 174 LEU cc_start: 0.8152 (mt) cc_final: 0.7932 (mt) REVERT: D 192 ASP cc_start: 0.8278 (p0) cc_final: 0.7889 (p0) REVERT: D 193 LYS cc_start: 0.8392 (mttt) cc_final: 0.8048 (mttt) REVERT: D 195 CYS cc_start: 0.8407 (p) cc_final: 0.8172 (p) REVERT: D 220 SER cc_start: 0.7441 (m) cc_final: 0.7140 (m) REVERT: D 224 MET cc_start: 0.7602 (ptm) cc_final: 0.6518 (ptm) REVERT: D 225 GLN cc_start: 0.7566 (mm110) cc_final: 0.6781 (mm110) REVERT: E 121 CYS cc_start: 0.7546 (m) cc_final: 0.7188 (m) REVERT: E 125 TYR cc_start: 0.7963 (m-80) cc_final: 0.7060 (m-80) REVERT: E 144 GLU cc_start: 0.7206 (pt0) cc_final: 0.6820 (pt0) REVERT: E 160 ARG cc_start: 0.7131 (mpp80) cc_final: 0.6589 (mpp80) REVERT: E 175 LYS cc_start: 0.8654 (ptmt) cc_final: 0.8125 (ptmt) REVERT: E 206 LEU cc_start: 0.6810 (tp) cc_final: 0.6445 (tp) REVERT: E 215 LEU cc_start: 0.5382 (tp) cc_final: 0.5142 (tt) REVERT: E 219 MET cc_start: 0.7907 (mtp) cc_final: 0.7557 (mtp) REVERT: E 227 ARG cc_start: 0.7566 (mtm180) cc_final: 0.7036 (mtm180) REVERT: E 235 LEU cc_start: 0.8587 (mt) cc_final: 0.8280 (mt) REVERT: E 253 LEU cc_start: 0.8800 (mt) cc_final: 0.8576 (mt) REVERT: E 256 MET cc_start: 0.7680 (ptm) cc_final: 0.7302 (ptm) REVERT: E 316 TYR cc_start: 0.8025 (t80) cc_final: 0.7579 (t80) REVERT: E 318 VAL cc_start: 0.8561 (p) cc_final: 0.8344 (m) REVERT: E 324 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7525 (mmtt) REVERT: E 334 PHE cc_start: 0.8443 (t80) cc_final: 0.8220 (t80) REVERT: E 371 PHE cc_start: 0.7580 (m-10) cc_final: 0.7293 (m-10) REVERT: F 88 LYS cc_start: 0.8468 (mmmt) cc_final: 0.7949 (mmmt) REVERT: F 160 ARG cc_start: 0.6917 (mpp80) cc_final: 0.5710 (mtm180) REVERT: F 175 LYS cc_start: 0.8658 (ptmt) cc_final: 0.8151 (ptmt) REVERT: F 187 MET cc_start: 0.4392 (ttt) cc_final: 0.3602 (ttt) REVERT: F 195 ASN cc_start: 0.8058 (m110) cc_final: 0.7103 (t0) REVERT: F 206 LEU cc_start: 0.6841 (tp) cc_final: 0.6560 (tp) REVERT: F 219 MET cc_start: 0.7795 (mtp) cc_final: 0.7507 (mtp) REVERT: F 227 ARG cc_start: 0.7566 (mtm180) cc_final: 0.7022 (mtm180) REVERT: F 249 MET cc_start: 0.8320 (ppp) cc_final: 0.8001 (ppp) REVERT: F 256 MET cc_start: 0.7803 (ptm) cc_final: 0.7412 (ptm) REVERT: F 267 ASP cc_start: 0.7761 (p0) cc_final: 0.7204 (p0) REVERT: F 316 TYR cc_start: 0.8048 (t80) cc_final: 0.7544 (t80) REVERT: F 318 VAL cc_start: 0.8429 (p) cc_final: 0.8122 (m) REVERT: F 319 ASN cc_start: 0.7961 (t0) cc_final: 0.6709 (t0) REVERT: F 320 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7615 (mm-30) REVERT: F 324 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7473 (mmtt) REVERT: F 334 PHE cc_start: 0.8354 (t80) cc_final: 0.8122 (t80) REVERT: F 360 PHE cc_start: 0.8470 (p90) cc_final: 0.7819 (p90) outliers start: 0 outliers final: 0 residues processed: 645 average time/residue: 0.4194 time to fit residues: 373.3102 Evaluate side-chains 634 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 57 optimal weight: 0.6980 chunk 96 optimal weight: 8.9990 chunk 22 optimal weight: 0.0050 chunk 64 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.7576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN D 117 ASN D 200 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.125457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.102483 restraints weight = 28632.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.106869 restraints weight = 15432.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.109894 restraints weight = 9697.495| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 12876 Z= 0.149 Angle : 0.693 11.376 17364 Z= 0.362 Chirality : 0.046 0.246 1918 Planarity : 0.005 0.054 2216 Dihedral : 5.351 40.451 1740 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1538 helix: 0.49 (0.16), residues: 896 sheet: -2.53 (0.49), residues: 80 loop : -0.95 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP D 62 HIS 0.012 0.001 HIS E 358 PHE 0.025 0.002 PHE D 202 TYR 0.025 0.002 TYR C 131 ARG 0.017 0.001 ARG D 144 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 710) hydrogen bonds : angle 4.72479 ( 2070) covalent geometry : bond 0.00330 (12876) covalent geometry : angle 0.69255 (17364) *********************** 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 636 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 636 time to evaluate : 2.629 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 342 TRP cc_start: 0.8561 (m100) cc_final: 0.7912 (m100) REVERT: A 350 MET cc_start: 0.7427 (mtm) cc_final: 0.7038 (mtm) REVERT: A 367 LYS cc_start: 0.7637 (mmtt) cc_final: 0.6750 (mmtt) REVERT: A 387 PHE cc_start: 0.8111 (t80) cc_final: 0.7154 (t80) REVERT: A 391 ARG cc_start: 0.8410 (mmt90) cc_final: 0.7775 (mmm-85) REVERT: A 399 LYS cc_start: 0.8411 (mmtp) cc_final: 0.7860 (mmtp) REVERT: A 402 HIS cc_start: 0.7584 (t-90) cc_final: 0.7260 (t-90) REVERT: A 404 ASN cc_start: 0.7979 (m110) cc_final: 0.7447 (m110) REVERT: A 408 PHE cc_start: 0.7277 (t80) cc_final: 0.6971 (t80) REVERT: A 409 MET cc_start: 0.7252 (mtt) cc_final: 0.6761 (mtt) REVERT: A 412 MET cc_start: 0.6058 (ppp) cc_final: 0.5487 (ppp) REVERT: A 419 ILE cc_start: 0.7295 (mm) cc_final: 0.7037 (mm) REVERT: A 439 LYS cc_start: 0.8202 (mppt) cc_final: 0.7483 (mppt) REVERT: A 442 MET cc_start: 0.7406 (mpp) cc_final: 0.7086 (mpp) REVERT: A 454 GLN cc_start: 0.8708 (mt0) cc_final: 0.8149 (mt0) REVERT: A 456 MET cc_start: 0.8246 (mmm) cc_final: 0.7491 (mmm) REVERT: A 457 ASP cc_start: 0.7971 (t0) cc_final: 0.7561 (t0) REVERT: A 458 TYR cc_start: 0.8549 (t80) cc_final: 0.8227 (t80) REVERT: A 460 HIS cc_start: 0.8416 (m170) cc_final: 0.7843 (m90) REVERT: A 463 ASN cc_start: 0.7329 (m-40) cc_final: 0.7103 (m-40) REVERT: A 466 HIS cc_start: 0.8579 (t-90) cc_final: 0.8172 (t-90) REVERT: A 470 LYS cc_start: 0.8305 (mtmt) cc_final: 0.8050 (mtmt) REVERT: A 477 HIS cc_start: 0.6496 (t-90) cc_final: 0.6294 (t-90) REVERT: A 484 ILE cc_start: 0.8031 (mt) cc_final: 0.7581 (mt) REVERT: A 512 MET cc_start: 0.5931 (ttm) cc_final: 0.5720 (ttm) REVERT: A 516 VAL cc_start: 0.8549 (t) cc_final: 0.8315 (t) REVERT: A 518 ARG cc_start: 0.8155 (ptp-110) cc_final: 0.7730 (ptp-110) REVERT: A 528 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7094 (mm-40) REVERT: A 533 SER cc_start: 0.8606 (m) cc_final: 0.8305 (p) REVERT: A 534 TYR cc_start: 0.8523 (t80) cc_final: 0.7901 (t80) REVERT: A 536 ILE cc_start: 0.8568 (mm) cc_final: 0.8261 (mm) REVERT: A 541 LEU cc_start: 0.8652 (mt) cc_final: 0.8245 (mt) REVERT: A 559 PHE cc_start: 0.8594 (t80) cc_final: 0.7544 (t80) REVERT: A 560 MET cc_start: 0.8391 (mmp) cc_final: 0.7555 (mmp) REVERT: A 563 ARG cc_start: 0.8702 (mmm-85) cc_final: 0.8261 (ttm-80) REVERT: A 572 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7664 (mmmm) REVERT: A 574 TYR cc_start: 0.7570 (m-10) cc_final: 0.7264 (m-10) REVERT: A 581 MET cc_start: 0.7775 (mmm) cc_final: 0.7254 (mmm) REVERT: A 591 LYS cc_start: 0.8654 (ptpp) cc_final: 0.8443 (ptpp) REVERT: A 592 VAL cc_start: 0.7776 (t) cc_final: 0.7283 (m) REVERT: A 601 GLN cc_start: 0.8432 (tt0) cc_final: 0.8107 (tm-30) REVERT: B 342 TRP cc_start: 0.8630 (m100) cc_final: 0.8173 (m100) REVERT: B 350 MET cc_start: 0.7495 (mtm) cc_final: 0.7032 (mtm) REVERT: B 362 THR cc_start: 0.7776 (m) cc_final: 0.7507 (m) REVERT: B 367 LYS cc_start: 0.7811 (mmtt) cc_final: 0.6870 (mmtt) REVERT: B 369 HIS cc_start: 0.8217 (m-70) cc_final: 0.7965 (m-70) REVERT: B 387 PHE cc_start: 0.8260 (t80) cc_final: 0.7951 (t80) REVERT: B 398 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7815 (ttm170) REVERT: B 399 LYS cc_start: 0.8339 (mmtp) cc_final: 0.7972 (mmtp) REVERT: B 402 HIS cc_start: 0.7781 (t-90) cc_final: 0.7523 (t-90) REVERT: B 407 LEU cc_start: 0.7427 (mp) cc_final: 0.7057 (mp) REVERT: B 409 MET cc_start: 0.7420 (mtm) cc_final: 0.6924 (mtm) REVERT: B 412 MET cc_start: 0.5872 (ppp) cc_final: 0.5456 (ppp) REVERT: B 417 LEU cc_start: 0.8221 (pt) cc_final: 0.7974 (pt) REVERT: B 419 ILE cc_start: 0.7412 (mm) cc_final: 0.6801 (mm) REVERT: B 422 GLN cc_start: 0.8324 (tt0) cc_final: 0.7054 (pt0) REVERT: B 429 LEU cc_start: 0.8311 (tp) cc_final: 0.8086 (tp) REVERT: B 433 LEU cc_start: 0.8392 (mt) cc_final: 0.8163 (mt) REVERT: B 439 LYS cc_start: 0.8451 (mppt) cc_final: 0.7867 (mppt) REVERT: B 445 LEU cc_start: 0.8589 (tp) cc_final: 0.8277 (tp) REVERT: B 454 GLN cc_start: 0.8815 (mt0) cc_final: 0.8612 (mt0) REVERT: B 456 MET cc_start: 0.8057 (mmm) cc_final: 0.7065 (mmm) REVERT: B 457 ASP cc_start: 0.7889 (t70) cc_final: 0.7597 (t70) REVERT: B 458 TYR cc_start: 0.8539 (t80) cc_final: 0.7558 (t80) REVERT: B 466 HIS cc_start: 0.8574 (t-90) cc_final: 0.8153 (t70) REVERT: B 470 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7734 (mtpt) REVERT: B 471 SER cc_start: 0.7467 (p) cc_final: 0.7180 (p) REVERT: B 473 ASN cc_start: 0.7619 (m110) cc_final: 0.7189 (m110) REVERT: B 483 LYS cc_start: 0.8284 (mttp) cc_final: 0.7352 (mttp) REVERT: B 484 ILE cc_start: 0.7964 (mt) cc_final: 0.7171 (mt) REVERT: B 511 TRP cc_start: 0.7303 (m-90) cc_final: 0.6959 (m-90) REVERT: B 512 MET cc_start: 0.6215 (ttm) cc_final: 0.5893 (ttm) REVERT: B 516 VAL cc_start: 0.8618 (t) cc_final: 0.8264 (t) REVERT: B 517 ILE cc_start: 0.8500 (mt) cc_final: 0.8158 (mt) REVERT: B 534 TYR cc_start: 0.8440 (t80) cc_final: 0.7984 (t80) REVERT: B 541 LEU cc_start: 0.8681 (mt) cc_final: 0.8315 (mt) REVERT: B 545 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7276 (mt-10) REVERT: B 551 ILE cc_start: 0.8717 (mp) cc_final: 0.8434 (mp) REVERT: B 554 ARG cc_start: 0.7719 (tmm-80) cc_final: 0.7460 (tmm-80) REVERT: B 563 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.7719 (ttm-80) REVERT: B 567 SER cc_start: 0.8080 (t) cc_final: 0.7866 (t) REVERT: B 583 ARG cc_start: 0.8707 (ptp-170) cc_final: 0.8124 (ptp-110) REVERT: B 591 LYS cc_start: 0.8665 (ptpp) cc_final: 0.8449 (ptpp) REVERT: B 601 GLN cc_start: 0.8554 (tt0) cc_final: 0.8275 (tt0) REVERT: B 618 ARG cc_start: 0.7609 (ptm160) cc_final: 0.7359 (ptm160) REVERT: C 25 MET cc_start: 0.7203 (pmm) cc_final: 0.6790 (pmm) REVERT: C 43 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8179 (mt-10) REVERT: C 51 TYR cc_start: 0.8359 (m-10) cc_final: 0.8087 (m-10) REVERT: C 59 ARG cc_start: 0.8319 (mtp-110) cc_final: 0.8089 (mtp-110) REVERT: C 69 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8357 (tm-30) REVERT: C 84 MET cc_start: 0.7653 (ptp) cc_final: 0.7305 (ptp) REVERT: C 87 GLU cc_start: 0.8247 (pt0) cc_final: 0.7958 (pt0) REVERT: C 91 LYS cc_start: 0.8715 (tppt) cc_final: 0.7791 (tppt) REVERT: C 93 GLU cc_start: 0.8602 (tt0) cc_final: 0.8121 (tt0) REVERT: C 94 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8433 (ttpt) REVERT: C 95 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7754 (mt-10) REVERT: C 97 ARG cc_start: 0.8687 (mtm110) cc_final: 0.7712 (mtm110) REVERT: C 98 GLU cc_start: 0.7274 (tp30) cc_final: 0.6313 (tp30) REVERT: C 102 ASP cc_start: 0.7993 (m-30) cc_final: 0.7139 (m-30) REVERT: C 103 VAL cc_start: 0.8525 (t) cc_final: 0.8081 (t) REVERT: C 126 LYS cc_start: 0.8792 (ttpp) cc_final: 0.8544 (ttpp) REVERT: C 128 LYS cc_start: 0.8036 (tttt) cc_final: 0.7773 (tttt) REVERT: C 132 TYR cc_start: 0.8368 (m-80) cc_final: 0.8100 (m-80) REVERT: C 153 LYS cc_start: 0.8629 (tppt) cc_final: 0.7910 (tppt) REVERT: C 155 TYR cc_start: 0.8010 (m-10) cc_final: 0.7374 (m-80) REVERT: C 170 HIS cc_start: 0.8089 (t-90) cc_final: 0.7810 (t-90) REVERT: C 174 LEU cc_start: 0.8082 (mt) cc_final: 0.7796 (mt) REVERT: C 176 LEU cc_start: 0.8542 (tt) cc_final: 0.7829 (tt) REVERT: C 180 PHE cc_start: 0.8585 (m-80) cc_final: 0.7808 (m-80) REVERT: C 204 ASP cc_start: 0.8278 (t0) cc_final: 0.8033 (t0) REVERT: C 218 LYS cc_start: 0.7638 (mmpt) cc_final: 0.7407 (mmpt) REVERT: C 224 MET cc_start: 0.7583 (ptm) cc_final: 0.6439 (ptm) REVERT: C 225 GLN cc_start: 0.7436 (mm110) cc_final: 0.6623 (mm110) REVERT: D 14 LYS cc_start: 0.8747 (mttt) cc_final: 0.8335 (mttm) REVERT: D 20 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7140 (tm-30) REVERT: D 25 MET cc_start: 0.7540 (pmm) cc_final: 0.7101 (pmm) REVERT: D 29 MET cc_start: 0.8776 (tpp) cc_final: 0.8428 (tpp) REVERT: D 34 GLU cc_start: 0.7914 (pp20) cc_final: 0.7509 (pp20) REVERT: D 52 LYS cc_start: 0.8647 (tptm) cc_final: 0.8299 (tptm) REVERT: D 59 ARG cc_start: 0.8345 (mtp-110) cc_final: 0.8007 (mtp180) REVERT: D 65 ILE cc_start: 0.8758 (pt) cc_final: 0.8530 (pt) REVERT: D 66 SER cc_start: 0.8036 (m) cc_final: 0.7674 (m) REVERT: D 84 MET cc_start: 0.7678 (ptp) cc_final: 0.7118 (ptp) REVERT: D 87 GLU cc_start: 0.8360 (pt0) cc_final: 0.8048 (pt0) REVERT: D 91 LYS cc_start: 0.8779 (tppt) cc_final: 0.7710 (tppt) REVERT: D 92 VAL cc_start: 0.9124 (m) cc_final: 0.8787 (m) REVERT: D 95 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7819 (mt-10) REVERT: D 101 TYR cc_start: 0.8181 (m-10) cc_final: 0.7918 (m-80) REVERT: D 102 ASP cc_start: 0.7771 (m-30) cc_final: 0.7432 (m-30) REVERT: D 119 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7744 (tp30) REVERT: D 123 PHE cc_start: 0.7938 (t80) cc_final: 0.7708 (t80) REVERT: D 125 LEU cc_start: 0.8220 (mt) cc_final: 0.7991 (mt) REVERT: D 127 MET cc_start: 0.8335 (mmm) cc_final: 0.7675 (mmp) REVERT: D 130 ASP cc_start: 0.7713 (m-30) cc_final: 0.7302 (m-30) REVERT: D 133 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8315 (ttp-110) REVERT: D 153 LYS cc_start: 0.8362 (tppt) cc_final: 0.7606 (tppt) REVERT: D 155 TYR cc_start: 0.7970 (m-10) cc_final: 0.7426 (m-80) REVERT: D 167 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7957 (tp-100) REVERT: D 172 ILE cc_start: 0.8670 (tt) cc_final: 0.8404 (tt) REVERT: D 174 LEU cc_start: 0.8161 (mt) cc_final: 0.7940 (mt) REVERT: D 192 ASP cc_start: 0.8243 (p0) cc_final: 0.7819 (p0) REVERT: D 193 LYS cc_start: 0.8381 (mttt) cc_final: 0.8024 (mttt) REVERT: D 195 CYS cc_start: 0.8393 (p) cc_final: 0.8162 (p) REVERT: D 220 SER cc_start: 0.7410 (m) cc_final: 0.7097 (m) REVERT: D 224 MET cc_start: 0.7647 (ptm) cc_final: 0.7414 (ptm) REVERT: E 121 CYS cc_start: 0.7425 (m) cc_final: 0.7076 (m) REVERT: E 125 TYR cc_start: 0.7930 (m-80) cc_final: 0.7019 (m-80) REVERT: E 160 ARG cc_start: 0.7159 (mpp80) cc_final: 0.6869 (mpp80) REVERT: E 175 LYS cc_start: 0.8671 (ptmt) cc_final: 0.8144 (ptmt) REVERT: E 215 LEU cc_start: 0.5403 (tp) cc_final: 0.5141 (tt) REVERT: E 219 MET cc_start: 0.7897 (mtp) cc_final: 0.7528 (mtp) REVERT: E 227 ARG cc_start: 0.7554 (mtm180) cc_final: 0.6974 (mtm180) REVERT: E 235 LEU cc_start: 0.8622 (mt) cc_final: 0.8172 (mt) REVERT: E 249 MET cc_start: 0.8262 (ppp) cc_final: 0.8035 (ppp) REVERT: E 253 LEU cc_start: 0.8840 (mt) cc_final: 0.8590 (mt) REVERT: E 256 MET cc_start: 0.7711 (ptm) cc_final: 0.7311 (ptm) REVERT: E 316 TYR cc_start: 0.8015 (t80) cc_final: 0.7548 (t80) REVERT: E 319 ASN cc_start: 0.8051 (t0) cc_final: 0.6808 (t0) REVERT: E 320 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7623 (mm-30) REVERT: E 324 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7579 (mmtt) REVERT: E 340 LYS cc_start: 0.8781 (mttp) cc_final: 0.8180 (tptp) REVERT: E 356 MET cc_start: 0.6989 (ppp) cc_final: 0.6652 (ppp) REVERT: E 371 PHE cc_start: 0.7589 (m-10) cc_final: 0.7363 (m-10) REVERT: F 88 LYS cc_start: 0.8483 (mmmt) cc_final: 0.7952 (mmmt) REVERT: F 160 ARG cc_start: 0.6911 (mpp80) cc_final: 0.5860 (mtm180) REVERT: F 187 MET cc_start: 0.4048 (ttt) cc_final: 0.3420 (ttt) REVERT: F 195 ASN cc_start: 0.8085 (m110) cc_final: 0.7137 (t0) REVERT: F 206 LEU cc_start: 0.6845 (tp) cc_final: 0.6530 (tp) REVERT: F 219 MET cc_start: 0.7791 (mtp) cc_final: 0.7489 (mtp) REVERT: F 227 ARG cc_start: 0.7575 (mtm180) cc_final: 0.7007 (mtm180) REVERT: F 249 MET cc_start: 0.8354 (ppp) cc_final: 0.8028 (ppp) REVERT: F 253 LEU cc_start: 0.8727 (mt) cc_final: 0.8483 (mt) REVERT: F 256 MET cc_start: 0.7793 (ptm) cc_final: 0.7406 (ptm) REVERT: F 267 ASP cc_start: 0.7754 (p0) cc_final: 0.7175 (p0) REVERT: F 316 TYR cc_start: 0.8033 (t80) cc_final: 0.7506 (t80) REVERT: F 318 VAL cc_start: 0.8425 (p) cc_final: 0.8121 (m) REVERT: F 319 ASN cc_start: 0.7928 (t0) cc_final: 0.6651 (t0) REVERT: F 320 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7620 (mm-30) REVERT: F 324 LYS cc_start: 0.7911 (mmtt) cc_final: 0.7498 (mmtt) REVERT: F 334 PHE cc_start: 0.8346 (t80) cc_final: 0.8126 (t80) REVERT: F 344 LYS cc_start: 0.8148 (pptt) cc_final: 0.7947 (pptt) REVERT: F 360 PHE cc_start: 0.8475 (p90) cc_final: 0.8050 (p90) REVERT: F 371 PHE cc_start: 0.7456 (m-80) cc_final: 0.7005 (m-80) outliers start: 0 outliers final: 0 residues processed: 636 average time/residue: 0.3316 time to fit residues: 287.2221 Evaluate side-chains 627 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 627 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 124 optimal weight: 0.0670 chunk 28 optimal weight: 0.5980 chunk 148 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS A 444 GLN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.125320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.102371 restraints weight = 28708.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.106732 restraints weight = 15554.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.109826 restraints weight = 9803.599| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12876 Z= 0.149 Angle : 0.717 16.483 17364 Z= 0.370 Chirality : 0.047 0.286 1918 Planarity : 0.005 0.086 2216 Dihedral : 5.357 41.656 1740 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.21), residues: 1538 helix: 0.45 (0.17), residues: 896 sheet: -2.81 (0.43), residues: 100 loop : -0.95 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP D 62 HIS 0.015 0.001 HIS E 358 PHE 0.020 0.002 PHE F 371 TYR 0.058 0.002 TYR C 101 ARG 0.011 0.001 ARG E 234 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 710) hydrogen bonds : angle 4.74728 ( 2070) covalent geometry : bond 0.00326 (12876) covalent geometry : angle 0.71708 (17364) ********************** 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 618 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 618 time to evaluate : 1.466 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 342 TRP cc_start: 0.8574 (m100) cc_final: 0.7989 (m100) REVERT: A 350 MET cc_start: 0.7464 (mtm) cc_final: 0.7062 (mtm) REVERT: A 387 PHE cc_start: 0.8085 (t80) cc_final: 0.7142 (t80) REVERT: A 391 ARG cc_start: 0.8416 (mmt90) cc_final: 0.7749 (mmm-85) REVERT: A 399 LYS cc_start: 0.8403 (mmtp) cc_final: 0.7866 (mmtp) REVERT: A 402 HIS cc_start: 0.7605 (t-90) cc_final: 0.7304 (t-90) REVERT: A 404 ASN cc_start: 0.7994 (m110) cc_final: 0.7389 (m110) REVERT: A 408 PHE cc_start: 0.7272 (t80) cc_final: 0.6930 (t80) REVERT: A 409 MET cc_start: 0.7261 (mtt) cc_final: 0.6659 (mtt) REVERT: A 411 TYR cc_start: 0.7377 (p90) cc_final: 0.7172 (p90) REVERT: A 412 MET cc_start: 0.5976 (ppp) cc_final: 0.5486 (ppp) REVERT: A 417 LEU cc_start: 0.7983 (pt) cc_final: 0.7728 (pt) REVERT: A 419 ILE cc_start: 0.7290 (mm) cc_final: 0.7011 (mm) REVERT: A 422 GLN cc_start: 0.8297 (tt0) cc_final: 0.7439 (pt0) REVERT: A 439 LYS cc_start: 0.8224 (mppt) cc_final: 0.7520 (mppt) REVERT: A 442 MET cc_start: 0.7397 (mpp) cc_final: 0.7056 (mpp) REVERT: A 444 GLN cc_start: 0.7988 (pt0) cc_final: 0.7574 (pt0) REVERT: A 457 ASP cc_start: 0.8042 (t0) cc_final: 0.7523 (t0) REVERT: A 458 TYR cc_start: 0.8544 (t80) cc_final: 0.8282 (t80) REVERT: A 463 ASN cc_start: 0.7323 (m-40) cc_final: 0.7120 (m-40) REVERT: A 466 HIS cc_start: 0.8576 (t-90) cc_final: 0.8151 (t70) REVERT: A 470 LYS cc_start: 0.8378 (mtmt) cc_final: 0.7633 (mtmt) REVERT: A 477 HIS cc_start: 0.6588 (t-90) cc_final: 0.6366 (t-90) REVERT: A 516 VAL cc_start: 0.8543 (t) cc_final: 0.8329 (t) REVERT: A 518 ARG cc_start: 0.8211 (ptp-110) cc_final: 0.7695 (ptp-110) REVERT: A 534 TYR cc_start: 0.8444 (t80) cc_final: 0.7919 (t80) REVERT: A 541 LEU cc_start: 0.8609 (mt) cc_final: 0.8255 (mt) REVERT: A 559 PHE cc_start: 0.8536 (t80) cc_final: 0.7455 (t80) REVERT: A 560 MET cc_start: 0.8356 (mmp) cc_final: 0.7520 (mmp) REVERT: A 563 ARG cc_start: 0.8698 (mmm-85) cc_final: 0.8240 (ttm-80) REVERT: A 572 LYS cc_start: 0.8243 (mmmm) cc_final: 0.7682 (mmmm) REVERT: A 574 TYR cc_start: 0.7648 (m-10) cc_final: 0.7358 (m-10) REVERT: A 576 ASN cc_start: 0.7468 (t0) cc_final: 0.7032 (t0) REVERT: A 581 MET cc_start: 0.7796 (mmm) cc_final: 0.7181 (mmm) REVERT: A 591 LYS cc_start: 0.8636 (ptpp) cc_final: 0.8414 (ptpp) REVERT: A 592 VAL cc_start: 0.7820 (t) cc_final: 0.7308 (m) REVERT: A 601 GLN cc_start: 0.8479 (tt0) cc_final: 0.8174 (tm-30) REVERT: B 342 TRP cc_start: 0.8610 (m100) cc_final: 0.8185 (m100) REVERT: B 350 MET cc_start: 0.7463 (mtm) cc_final: 0.7055 (mtm) REVERT: B 362 THR cc_start: 0.7781 (m) cc_final: 0.7510 (m) REVERT: B 367 LYS cc_start: 0.7830 (mmtt) cc_final: 0.6882 (mmtt) REVERT: B 375 LYS cc_start: 0.7832 (tmmt) cc_final: 0.7316 (tmmt) REVERT: B 387 PHE cc_start: 0.8240 (t80) cc_final: 0.7937 (t80) REVERT: B 398 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7794 (ttm170) REVERT: B 399 LYS cc_start: 0.8348 (mmtp) cc_final: 0.7966 (mmtp) REVERT: B 402 HIS cc_start: 0.7775 (t-90) cc_final: 0.7485 (t-90) REVERT: B 407 LEU cc_start: 0.7412 (mp) cc_final: 0.7075 (mp) REVERT: B 409 MET cc_start: 0.7433 (mtm) cc_final: 0.6994 (mtm) REVERT: B 412 MET cc_start: 0.5926 (ppp) cc_final: 0.5475 (ppp) REVERT: B 417 LEU cc_start: 0.8279 (pt) cc_final: 0.8057 (pt) REVERT: B 419 ILE cc_start: 0.7433 (mm) cc_final: 0.6788 (mm) REVERT: B 422 GLN cc_start: 0.8311 (tt0) cc_final: 0.6933 (pt0) REVERT: B 429 LEU cc_start: 0.8315 (tp) cc_final: 0.8074 (tp) REVERT: B 439 LYS cc_start: 0.8455 (mppt) cc_final: 0.7895 (mppt) REVERT: B 442 MET cc_start: 0.7785 (mpp) cc_final: 0.7454 (mpp) REVERT: B 456 MET cc_start: 0.7944 (mmm) cc_final: 0.6918 (mmm) REVERT: B 458 TYR cc_start: 0.8551 (t80) cc_final: 0.7535 (t80) REVERT: B 466 HIS cc_start: 0.8549 (t-90) cc_final: 0.8139 (t70) REVERT: B 470 LYS cc_start: 0.8394 (mtpt) cc_final: 0.7756 (mtpt) REVERT: B 473 ASN cc_start: 0.7673 (m110) cc_final: 0.7241 (m110) REVERT: B 477 HIS cc_start: 0.6866 (t-90) cc_final: 0.6625 (t-90) REVERT: B 483 LYS cc_start: 0.8282 (mttp) cc_final: 0.7002 (mttp) REVERT: B 484 ILE cc_start: 0.7955 (mt) cc_final: 0.7112 (mt) REVERT: B 504 GLN cc_start: 0.8019 (mm110) cc_final: 0.7780 (mm-40) REVERT: B 511 TRP cc_start: 0.7364 (m-90) cc_final: 0.6940 (m-90) REVERT: B 512 MET cc_start: 0.6153 (ttm) cc_final: 0.5835 (ttm) REVERT: B 516 VAL cc_start: 0.8537 (t) cc_final: 0.8167 (t) REVERT: B 518 ARG cc_start: 0.8023 (ptp-110) cc_final: 0.7615 (ptp-110) REVERT: B 534 TYR cc_start: 0.8475 (t80) cc_final: 0.8004 (t80) REVERT: B 545 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7171 (mt-10) REVERT: B 551 ILE cc_start: 0.8776 (mp) cc_final: 0.8415 (mp) REVERT: B 554 ARG cc_start: 0.7762 (tmm-80) cc_final: 0.7538 (tmm-80) REVERT: B 563 ARG cc_start: 0.8355 (mmm-85) cc_final: 0.7719 (ttm-80) REVERT: B 567 SER cc_start: 0.8104 (t) cc_final: 0.7848 (t) REVERT: B 581 MET cc_start: 0.8123 (tpp) cc_final: 0.7802 (tpp) REVERT: B 583 ARG cc_start: 0.8716 (ptp-170) cc_final: 0.8116 (ptp-110) REVERT: B 591 LYS cc_start: 0.8642 (ptpp) cc_final: 0.8430 (ptpp) REVERT: B 601 GLN cc_start: 0.8535 (tt0) cc_final: 0.8284 (tt0) REVERT: B 618 ARG cc_start: 0.7634 (ptm160) cc_final: 0.7355 (ptm160) REVERT: C 6 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8385 (ttpt) REVERT: C 25 MET cc_start: 0.7253 (pmm) cc_final: 0.6868 (pmm) REVERT: C 43 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8243 (mt-10) REVERT: C 51 TYR cc_start: 0.8323 (m-10) cc_final: 0.8047 (m-10) REVERT: C 52 LYS cc_start: 0.8837 (tptt) cc_final: 0.8455 (tptt) REVERT: C 59 ARG cc_start: 0.8307 (mtp-110) cc_final: 0.8075 (mtp-110) REVERT: C 69 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8313 (tm-30) REVERT: C 84 MET cc_start: 0.7590 (ptp) cc_final: 0.7214 (ptp) REVERT: C 87 GLU cc_start: 0.8241 (pt0) cc_final: 0.7961 (pt0) REVERT: C 91 LYS cc_start: 0.8706 (tppt) cc_final: 0.7772 (tppt) REVERT: C 93 GLU cc_start: 0.8602 (tt0) cc_final: 0.8127 (tt0) REVERT: C 94 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8408 (ttpt) REVERT: C 95 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7702 (mt-10) REVERT: C 97 ARG cc_start: 0.8642 (mtm110) cc_final: 0.7943 (mtm110) REVERT: C 98 GLU cc_start: 0.7338 (tp30) cc_final: 0.6662 (tp30) REVERT: C 101 TYR cc_start: 0.7985 (m-80) cc_final: 0.7625 (m-80) REVERT: C 103 VAL cc_start: 0.8534 (t) cc_final: 0.8094 (t) REVERT: C 126 LYS cc_start: 0.8774 (ttpp) cc_final: 0.8540 (ttpp) REVERT: C 128 LYS cc_start: 0.8048 (tttt) cc_final: 0.7782 (tttt) REVERT: C 132 TYR cc_start: 0.8344 (m-80) cc_final: 0.8130 (m-80) REVERT: C 153 LYS cc_start: 0.8628 (tppt) cc_final: 0.7903 (tppt) REVERT: C 155 TYR cc_start: 0.8054 (m-10) cc_final: 0.7644 (m-80) REVERT: C 170 HIS cc_start: 0.8063 (t-90) cc_final: 0.7829 (t-90) REVERT: C 174 LEU cc_start: 0.8096 (mt) cc_final: 0.7823 (mt) REVERT: C 197 LEU cc_start: 0.8413 (mm) cc_final: 0.8181 (mm) REVERT: C 218 LYS cc_start: 0.7657 (mmpt) cc_final: 0.7369 (mmpt) REVERT: C 224 MET cc_start: 0.7483 (ptm) cc_final: 0.6406 (ptm) REVERT: C 225 GLN cc_start: 0.7420 (mm110) cc_final: 0.6612 (mm110) REVERT: D 14 LYS cc_start: 0.8750 (mttt) cc_final: 0.8346 (mttm) REVERT: D 20 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7102 (tm-30) REVERT: D 25 MET cc_start: 0.7542 (pmm) cc_final: 0.7065 (pmm) REVERT: D 29 MET cc_start: 0.8780 (tpp) cc_final: 0.8432 (tpp) REVERT: D 32 VAL cc_start: 0.8236 (t) cc_final: 0.8032 (t) REVERT: D 34 GLU cc_start: 0.7888 (pp20) cc_final: 0.7484 (pp20) REVERT: D 52 LYS cc_start: 0.8633 (tptm) cc_final: 0.8285 (tptm) REVERT: D 59 ARG cc_start: 0.8335 (mtp-110) cc_final: 0.7992 (mtp180) REVERT: D 65 ILE cc_start: 0.8780 (pt) cc_final: 0.8553 (pt) REVERT: D 66 SER cc_start: 0.8043 (m) cc_final: 0.7687 (m) REVERT: D 84 MET cc_start: 0.7636 (ptp) cc_final: 0.7068 (ptp) REVERT: D 87 GLU cc_start: 0.8344 (pt0) cc_final: 0.8014 (pt0) REVERT: D 91 LYS cc_start: 0.8784 (tppt) cc_final: 0.7709 (tppt) REVERT: D 92 VAL cc_start: 0.9121 (m) cc_final: 0.8797 (m) REVERT: D 95 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7809 (mt-10) REVERT: D 101 TYR cc_start: 0.8173 (m-10) cc_final: 0.7906 (m-80) REVERT: D 102 ASP cc_start: 0.7776 (m-30) cc_final: 0.7422 (m-30) REVERT: D 119 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7760 (tp30) REVERT: D 123 PHE cc_start: 0.7902 (t80) cc_final: 0.7678 (t80) REVERT: D 125 LEU cc_start: 0.8223 (mt) cc_final: 0.8003 (mt) REVERT: D 127 MET cc_start: 0.8339 (mmm) cc_final: 0.7682 (mmp) REVERT: D 130 ASP cc_start: 0.7735 (m-30) cc_final: 0.7291 (m-30) REVERT: D 133 ARG cc_start: 0.8637 (ttp-110) cc_final: 0.8314 (ttp-110) REVERT: D 153 LYS cc_start: 0.8335 (tppt) cc_final: 0.7601 (tppt) REVERT: D 155 TYR cc_start: 0.7683 (m-10) cc_final: 0.7337 (m-80) REVERT: D 172 ILE cc_start: 0.8631 (tt) cc_final: 0.8400 (tt) REVERT: D 174 LEU cc_start: 0.8098 (mt) cc_final: 0.7874 (mt) REVERT: D 192 ASP cc_start: 0.8220 (p0) cc_final: 0.7563 (p0) REVERT: D 193 LYS cc_start: 0.8380 (mttt) cc_final: 0.7854 (mptt) REVERT: D 195 CYS cc_start: 0.8401 (p) cc_final: 0.8169 (p) REVERT: D 220 SER cc_start: 0.7470 (m) cc_final: 0.7179 (m) REVERT: E 121 CYS cc_start: 0.7418 (m) cc_final: 0.7085 (m) REVERT: E 125 TYR cc_start: 0.7916 (m-80) cc_final: 0.7021 (m-80) REVERT: E 144 GLU cc_start: 0.7350 (pp20) cc_final: 0.6534 (pp20) REVERT: E 160 ARG cc_start: 0.7186 (mpp80) cc_final: 0.6661 (mpp80) REVERT: E 175 LYS cc_start: 0.8671 (ptmt) cc_final: 0.8148 (ptmt) REVERT: E 187 MET cc_start: 0.4210 (ttt) cc_final: 0.3307 (ttt) REVERT: E 206 LEU cc_start: 0.7041 (tp) cc_final: 0.6683 (tp) REVERT: E 219 MET cc_start: 0.7862 (mtp) cc_final: 0.7580 (mtp) REVERT: E 227 ARG cc_start: 0.7522 (mtm180) cc_final: 0.6958 (mtm180) REVERT: E 234 ARG cc_start: 0.7802 (ttm-80) cc_final: 0.7572 (ttm-80) REVERT: E 235 LEU cc_start: 0.8683 (mt) cc_final: 0.8051 (mt) REVERT: E 249 MET cc_start: 0.8294 (ppp) cc_final: 0.8040 (ppp) REVERT: E 253 LEU cc_start: 0.8856 (mt) cc_final: 0.8580 (mt) REVERT: E 256 MET cc_start: 0.7699 (ptm) cc_final: 0.7292 (ptm) REVERT: E 316 TYR cc_start: 0.8016 (t80) cc_final: 0.7565 (t80) REVERT: E 319 ASN cc_start: 0.8002 (t0) cc_final: 0.6824 (t0) REVERT: E 320 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7656 (mm-30) REVERT: E 324 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7524 (mmtt) REVERT: E 340 LYS cc_start: 0.8770 (mttp) cc_final: 0.8195 (tptp) REVERT: E 344 LYS cc_start: 0.8566 (tmmt) cc_final: 0.8245 (mttt) REVERT: E 356 MET cc_start: 0.6923 (ppp) cc_final: 0.6558 (ppp) REVERT: F 88 LYS cc_start: 0.8470 (mmmt) cc_final: 0.7944 (mmmt) REVERT: F 110 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8067 (mp10) REVERT: F 160 ARG cc_start: 0.6945 (mpp80) cc_final: 0.5917 (mtm180) REVERT: F 187 MET cc_start: 0.4100 (ttt) cc_final: 0.3806 (ttt) REVERT: F 195 ASN cc_start: 0.8104 (m110) cc_final: 0.7142 (t0) REVERT: F 206 LEU cc_start: 0.6783 (tp) cc_final: 0.6481 (tp) REVERT: F 219 MET cc_start: 0.7810 (mtp) cc_final: 0.7506 (mtp) REVERT: F 227 ARG cc_start: 0.7563 (mtm180) cc_final: 0.6977 (mtm180) REVERT: F 249 MET cc_start: 0.8338 (ppp) cc_final: 0.8021 (ppp) REVERT: F 253 LEU cc_start: 0.8737 (mt) cc_final: 0.8495 (mt) REVERT: F 256 MET cc_start: 0.7773 (ptm) cc_final: 0.7365 (ptm) REVERT: F 316 TYR cc_start: 0.8018 (t80) cc_final: 0.7517 (t80) REVERT: F 318 VAL cc_start: 0.8407 (p) cc_final: 0.8103 (m) REVERT: F 319 ASN cc_start: 0.7928 (t0) cc_final: 0.6666 (t0) REVERT: F 320 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7619 (mm-30) REVERT: F 324 LYS cc_start: 0.7895 (mmtt) cc_final: 0.7469 (mmtt) REVERT: F 371 PHE cc_start: 0.7456 (m-80) cc_final: 0.7044 (m-80) outliers start: 0 outliers final: 0 residues processed: 618 average time/residue: 0.3193 time to fit residues: 271.3889 Evaluate side-chains 612 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 612 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.2980 chunk 91 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 125 optimal weight: 0.0770 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 113 optimal weight: 0.3980 chunk 132 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS B 444 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 200 GLN D 225 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.127689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.105018 restraints weight = 28527.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.109419 restraints weight = 15467.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.112527 restraints weight = 9730.201| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 12876 Z= 0.138 Angle : 0.700 11.639 17364 Z= 0.364 Chirality : 0.046 0.205 1918 Planarity : 0.005 0.062 2216 Dihedral : 5.324 43.577 1740 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1538 helix: 0.45 (0.17), residues: 896 sheet: -2.82 (0.43), residues: 100 loop : -0.92 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 368 HIS 0.013 0.001 HIS E 358 PHE 0.029 0.002 PHE F 360 TYR 0.054 0.002 TYR C 101 ARG 0.008 0.000 ARG E 234 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 710) hydrogen bonds : angle 4.67289 ( 2070) covalent geometry : bond 0.00311 (12876) covalent geometry : angle 0.70015 (17364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6345.67 seconds wall clock time: 117 minutes 9.13 seconds (7029.13 seconds total)