Starting phenix.real_space_refine on Sun Nov 17 01:51:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chf_16660/11_2024/8chf_16660.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chf_16660/11_2024/8chf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chf_16660/11_2024/8chf_16660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chf_16660/11_2024/8chf_16660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chf_16660/11_2024/8chf_16660.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chf_16660/11_2024/8chf_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-5513/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: 7.85, per 1000 atoms: 0.62 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: 3.72 Conformation dependent library (CDL) restraints added in 1.7 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: 1.30 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: 3.95 Time building geometry restraints manager: 3.99 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 30.820 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- 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= 0.364 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 *********************** 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 : 1.501 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: 0.2899 time to fit residues: 266.5750 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 : 1.445 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 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= 0.223 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 *********************** 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 : 1.459 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 351 LEU cc_start: 0.8380 (mt) cc_final: 0.8166 (mt) REVERT: A 359 SER cc_start: 0.8161 (m) cc_final: 0.7662 (p) REVERT: A 387 PHE cc_start: 0.7875 (t80) cc_final: 0.7319 (t80) REVERT: A 391 ARG cc_start: 0.8013 (mmt90) cc_final: 0.7675 (mmm-85) REVERT: A 392 ASN cc_start: 0.8045 (m-40) cc_final: 0.7725 (m-40) REVERT: A 399 LYS cc_start: 0.8246 (mmtp) cc_final: 0.7798 (mmtp) REVERT: A 412 MET cc_start: 0.6599 (ppp) cc_final: 0.5897 (ppp) REVERT: A 416 ASN cc_start: 0.7471 (p0) cc_final: 0.6987 (p0) REVERT: A 422 GLN cc_start: 0.7842 (tt0) cc_final: 0.7514 (pt0) REVERT: A 423 TRP cc_start: 0.7759 (t-100) cc_final: 0.7450 (t60) REVERT: A 425 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6345 (mm-30) REVERT: A 431 LYS cc_start: 0.8175 (mppt) cc_final: 0.7878 (mppt) REVERT: A 439 LYS cc_start: 0.8141 (mppt) cc_final: 0.7606 (mppt) REVERT: A 445 LEU cc_start: 0.8222 (tp) cc_final: 0.7947 (tp) REVERT: A 450 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7593 (ttp-170) REVERT: A 451 GLN cc_start: 0.7932 (mt0) cc_final: 0.6658 (tt0) REVERT: A 516 VAL cc_start: 0.8520 (t) cc_final: 0.7793 (t) REVERT: A 518 ARG cc_start: 0.7928 (ptp-110) cc_final: 0.7102 (ptp-110) REVERT: A 528 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7507 (mm110) REVERT: A 534 TYR cc_start: 0.7965 (t80) cc_final: 0.7757 (t80) REVERT: A 541 LEU cc_start: 0.8255 (mt) cc_final: 0.7892 (mt) REVERT: A 542 MET cc_start: 0.6449 (mtp) cc_final: 0.6037 (mtp) REVERT: A 560 MET cc_start: 0.7956 (mmp) cc_final: 0.7699 (mmt) REVERT: A 590 LYS cc_start: 0.7692 (mmtm) cc_final: 0.7232 (mmtm) REVERT: A 592 VAL cc_start: 0.8262 (t) cc_final: 0.7833 (m) REVERT: A 601 GLN cc_start: 0.8049 (tt0) cc_final: 0.7780 (tm-30) REVERT: A 609 LEU cc_start: 0.8173 (tp) cc_final: 0.7478 (tt) REVERT: A 622 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7306 (tm-30) REVERT: B 367 LYS cc_start: 0.7534 (mmtt) cc_final: 0.6554 (mmtt) REVERT: B 383 THR cc_start: 0.8434 (p) cc_final: 0.8146 (p) REVERT: B 393 GLU cc_start: 0.6938 (tp30) cc_final: 0.6493 (tp30) REVERT: B 399 LYS cc_start: 0.8295 (mmtp) cc_final: 0.7812 (mmtp) REVERT: B 412 MET cc_start: 0.6611 (ppp) cc_final: 0.6027 (ppp) REVERT: B 416 ASN cc_start: 0.7760 (p0) cc_final: 0.7315 (p0) REVERT: B 422 GLN cc_start: 0.7832 (tt0) cc_final: 0.7571 (pm20) REVERT: B 432 HIS cc_start: 0.6999 (m90) cc_final: 0.6259 (m90) REVERT: B 439 LYS cc_start: 0.8343 (mppt) cc_final: 0.7901 (mppt) REVERT: B 442 MET cc_start: 0.7021 (mpp) cc_final: 0.6799 (mpp) REVERT: B 450 ARG cc_start: 0.7952 (ttp-170) cc_final: 0.7658 (ttp-170) REVERT: B 458 TYR cc_start: 0.8025 (t80) cc_final: 0.7379 (t80) REVERT: B 460 HIS cc_start: 0.7562 (m170) cc_final: 0.7345 (m-70) REVERT: B 484 ILE cc_start: 0.7876 (mt) cc_final: 0.7628 (mt) REVERT: B 516 VAL cc_start: 0.8628 (t) cc_final: 0.8127 (t) REVERT: B 528 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7486 (mm110) REVERT: B 534 TYR cc_start: 0.7919 (t80) cc_final: 0.7698 (t80) REVERT: B 541 LEU cc_start: 0.8262 (mt) cc_final: 0.8001 (mt) REVERT: B 542 MET cc_start: 0.6489 (mtp) cc_final: 0.6279 (mtp) REVERT: B 545 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7232 (mt-10) REVERT: B 551 ILE cc_start: 0.8658 (mp) cc_final: 0.8430 (mp) REVERT: B 556 GLN cc_start: 0.8099 (tt0) cc_final: 0.7640 (tp40) REVERT: B 563 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7442 (ttm-80) REVERT: B 583 ARG cc_start: 0.8197 (ptp-170) cc_final: 0.7835 (ptp-110) REVERT: B 592 VAL cc_start: 0.8122 (t) cc_final: 0.7668 (m) REVERT: B 615 LYS cc_start: 0.7785 (mttm) cc_final: 0.7433 (mttm) REVERT: B 622 GLU cc_start: 0.7459 (tm-30) cc_final: 0.6892 (tm-30) REVERT: C 20 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6791 (tm-30) REVERT: C 25 MET cc_start: 0.7558 (pmm) cc_final: 0.7138 (pmm) REVERT: C 29 MET cc_start: 0.8826 (tpp) cc_final: 0.8474 (mmm) REVERT: C 43 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8341 (mt-10) REVERT: C 49 VAL cc_start: 0.7966 (t) cc_final: 0.7536 (m) REVERT: C 52 LYS cc_start: 0.8416 (tptm) cc_final: 0.8054 (tptm) REVERT: C 53 ASN cc_start: 0.8025 (m-40) cc_final: 0.7738 (m-40) REVERT: C 59 ARG cc_start: 0.8103 (mtp-110) cc_final: 0.7890 (mtp-110) REVERT: C 69 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7857 (tm-30) REVERT: C 87 GLU cc_start: 0.8090 (pt0) cc_final: 0.7823 (pt0) REVERT: C 91 LYS cc_start: 0.8493 (tppt) cc_final: 0.7551 (tppt) REVERT: C 93 GLU cc_start: 0.7977 (tt0) cc_final: 0.7707 (tt0) REVERT: C 94 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8196 (ttpt) REVERT: C 95 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7349 (mt-10) REVERT: C 98 GLU cc_start: 0.6830 (tp30) cc_final: 0.5625 (tp30) REVERT: C 102 ASP cc_start: 0.7645 (m-30) cc_final: 0.6713 (m-30) REVERT: C 119 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7773 (tp30) REVERT: C 127 MET cc_start: 0.7806 (mmm) cc_final: 0.7309 (mmm) REVERT: C 132 TYR cc_start: 0.8092 (m-80) cc_final: 0.7292 (m-80) REVERT: C 133 ARG cc_start: 0.8461 (ttp-110) cc_final: 0.7883 (ttp-110) REVERT: C 149 GLU cc_start: 0.8136 (tp30) cc_final: 0.7725 (tp30) REVERT: C 150 ASP cc_start: 0.8017 (m-30) cc_final: 0.7806 (m-30) REVERT: C 155 TYR cc_start: 0.7209 (m-10) cc_final: 0.6942 (m-80) REVERT: C 159 PHE cc_start: 0.8020 (t80) cc_final: 0.7804 (t80) REVERT: C 196 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7847 (pp30) REVERT: C 200 GLN cc_start: 0.8681 (pt0) cc_final: 0.8403 (pt0) REVERT: C 224 MET cc_start: 0.7189 (ptm) cc_final: 0.6288 (ptm) REVERT: C 225 GLN cc_start: 0.7523 (mm110) cc_final: 0.6788 (mm110) REVERT: C 227 LEU cc_start: 0.8554 (mt) cc_final: 0.8350 (mt) REVERT: D 14 LYS cc_start: 0.8778 (mttt) cc_final: 0.8519 (mttt) REVERT: D 20 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7096 (tm-30) REVERT: D 25 MET cc_start: 0.7639 (pmm) cc_final: 0.7332 (pmm) REVERT: D 29 MET cc_start: 0.8634 (tpp) cc_final: 0.8307 (mmm) REVERT: D 34 GLU cc_start: 0.7793 (pp20) cc_final: 0.7431 (pp20) REVERT: D 43 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8481 (mt-10) REVERT: D 59 ARG cc_start: 0.8121 (mtp-110) cc_final: 0.7531 (mtp85) REVERT: D 65 ILE cc_start: 0.8704 (pt) cc_final: 0.8401 (pt) REVERT: D 66 SER cc_start: 0.8068 (m) cc_final: 0.7339 (m) REVERT: D 87 GLU cc_start: 0.8096 (pt0) cc_final: 0.7860 (pt0) REVERT: D 91 LYS cc_start: 0.8609 (tppt) cc_final: 0.7887 (tppt) REVERT: D 93 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7977 (mt-10) REVERT: D 97 ARG cc_start: 0.8819 (mtm110) cc_final: 0.8432 (mtm110) REVERT: D 119 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7716 (tp30) REVERT: D 125 LEU cc_start: 0.8001 (mt) cc_final: 0.7720 (mt) REVERT: D 127 MET cc_start: 0.7923 (mmm) cc_final: 0.7386 (mmp) REVERT: D 130 ASP cc_start: 0.7431 (m-30) cc_final: 0.6345 (m-30) REVERT: D 132 TYR cc_start: 0.8165 (m-80) cc_final: 0.6824 (m-80) REVERT: D 133 ARG cc_start: 0.8466 (ttp-110) cc_final: 0.7586 (ttp80) REVERT: D 153 LYS cc_start: 0.8521 (tppt) cc_final: 0.7668 (tppt) REVERT: D 155 TYR cc_start: 0.6984 (m-10) cc_final: 0.6679 (m-80) REVERT: D 180 PHE cc_start: 0.8237 (m-80) cc_final: 0.7489 (m-80) REVERT: D 192 ASP cc_start: 0.8229 (p0) cc_final: 0.7571 (p0) REVERT: D 193 LYS cc_start: 0.8037 (mttt) cc_final: 0.7661 (mptt) REVERT: D 206 ILE cc_start: 0.7767 (mt) cc_final: 0.7550 (mt) REVERT: D 220 SER cc_start: 0.7162 (m) cc_final: 0.6356 (p) REVERT: D 224 MET cc_start: 0.7210 (ptm) cc_final: 0.6297 (ptm) REVERT: D 225 GLN cc_start: 0.7469 (mm110) cc_final: 0.6746 (mm110) REVERT: E 88 LYS cc_start: 0.8412 (mmmt) cc_final: 0.7968 (mmmt) REVERT: E 121 CYS cc_start: 0.7722 (m) cc_final: 0.7499 (m) REVERT: E 160 ARG cc_start: 0.7649 (mpp80) cc_final: 0.6190 (mtt180) REVERT: E 175 LYS cc_start: 0.8547 (ptmt) cc_final: 0.7986 (ptmt) REVERT: E 187 MET cc_start: 0.6661 (mtt) cc_final: 0.5940 (mtm) REVERT: E 206 LEU cc_start: 0.6761 (tp) cc_final: 0.6351 (tp) REVERT: E 227 ARG cc_start: 0.7203 (mtm180) cc_final: 0.6951 (mtm180) REVERT: E 249 MET cc_start: 0.8171 (ppp) cc_final: 0.7930 (ppp) REVERT: E 253 LEU cc_start: 0.8792 (mt) cc_final: 0.8524 (mt) REVERT: E 256 MET cc_start: 0.7677 (ptm) cc_final: 0.7289 (ptm) REVERT: E 267 ASP cc_start: 0.7575 (p0) cc_final: 0.7105 (p0) REVERT: E 310 ILE cc_start: 0.8728 (mp) cc_final: 0.8516 (mt) REVERT: E 311 PHE cc_start: 0.6993 (t80) cc_final: 0.6328 (t80) REVERT: E 312 GLU cc_start: 0.7667 (pp20) cc_final: 0.7268 (pp20) REVERT: E 313 LEU cc_start: 0.8202 (mt) cc_final: 0.7954 (mt) REVERT: E 316 TYR cc_start: 0.7748 (t80) cc_final: 0.7348 (t80) REVERT: E 319 ASN cc_start: 0.7723 (t0) cc_final: 0.6495 (t0) REVERT: E 320 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7593 (mm-30) REVERT: E 333 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8336 (mt-10) REVERT: E 344 LYS cc_start: 0.8407 (tttt) cc_final: 0.8012 (mttt) REVERT: F 88 LYS cc_start: 0.8503 (mmmt) cc_final: 0.7980 (mmmt) REVERT: F 96 ARG cc_start: 0.7592 (ptm160) cc_final: 0.6946 (ptm160) REVERT: F 125 TYR cc_start: 0.8064 (m-80) cc_final: 0.7152 (m-80) REVERT: F 168 LYS cc_start: 0.8470 (ttmm) cc_final: 0.7916 (ttmm) REVERT: F 175 LYS cc_start: 0.8582 (ptmt) cc_final: 0.8085 (ptmt) REVERT: F 187 MET cc_start: 0.6322 (mtm) cc_final: 0.5803 (mtm) REVERT: F 195 ASN cc_start: 0.7323 (t0) cc_final: 0.7096 (t0) REVERT: F 206 LEU cc_start: 0.6695 (tp) cc_final: 0.6259 (tp) REVERT: F 219 MET cc_start: 0.7512 (mtp) cc_final: 0.7218 (mtp) REVERT: F 249 MET cc_start: 0.8141 (ppp) cc_final: 0.7895 (ppp) REVERT: F 256 MET cc_start: 0.7678 (ptm) cc_final: 0.7408 (ptm) REVERT: F 267 ASP cc_start: 0.7211 (p0) cc_final: 0.6443 (p0) REVERT: F 270 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7577 (mt-10) REVERT: F 316 TYR cc_start: 0.7770 (t80) cc_final: 0.7257 (t80) REVERT: F 318 VAL cc_start: 0.8476 (p) cc_final: 0.8221 (m) REVERT: F 319 ASN cc_start: 0.7634 (t0) cc_final: 0.6313 (t0) REVERT: F 320 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7534 (mm-30) REVERT: F 333 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8239 (mt-10) REVERT: F 344 LYS cc_start: 0.8282 (tmmt) cc_final: 0.8077 (tmmt) REVERT: F 356 MET cc_start: 0.6705 (ppp) cc_final: 0.6430 (ppp) outliers start: 1 outliers final: 0 residues processed: 673 average time/residue: 0.2966 time to fit residues: 270.1887 Evaluate side-chains 669 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 668 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ** 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 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12876 Z= 0.224 Angle : 0.656 11.457 17364 Z= 0.348 Chirality : 0.045 0.206 1918 Planarity : 0.005 0.062 2216 Dihedral : 6.030 92.955 1740 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % 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: -0.40 (0.21), residues: 1538 helix: 0.55 (0.16), residues: 894 sheet: -2.70 (0.45), residues: 96 loop : -1.04 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 368 HIS 0.006 0.001 HIS E 358 PHE 0.014 0.002 PHE A 599 TYR 0.028 0.002 TYR C 101 ARG 0.008 0.001 ARG E 160 *********************** 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 672 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 672 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 LYS cc_start: 0.7392 (mmtt) cc_final: 0.6472 (mmtt) REVERT: A 387 PHE cc_start: 0.7868 (t80) cc_final: 0.7174 (t80) REVERT: A 391 ARG cc_start: 0.8038 (mmt90) cc_final: 0.7664 (mmm-85) REVERT: A 392 ASN cc_start: 0.8098 (m-40) cc_final: 0.7778 (m-40) REVERT: A 399 LYS cc_start: 0.8281 (mmtp) cc_final: 0.7860 (mmtp) REVERT: A 411 TYR cc_start: 0.6971 (p90) cc_final: 0.6617 (p90) REVERT: A 412 MET cc_start: 0.6244 (ppp) cc_final: 0.5614 (ppp) REVERT: A 413 THR cc_start: 0.7822 (p) cc_final: 0.7590 (p) REVERT: A 414 LYS cc_start: 0.8235 (tppt) cc_final: 0.7818 (tppt) REVERT: A 416 ASN cc_start: 0.7401 (p0) cc_final: 0.7045 (p0) REVERT: A 439 LYS cc_start: 0.8199 (mppt) cc_final: 0.7576 (mppt) REVERT: A 445 LEU cc_start: 0.8245 (tp) cc_final: 0.7945 (tp) REVERT: A 460 HIS cc_start: 0.7830 (m170) cc_final: 0.7614 (m-70) REVERT: A 463 ASN cc_start: 0.6734 (m-40) cc_final: 0.6456 (m-40) REVERT: A 518 ARG cc_start: 0.7998 (ptp-110) cc_final: 0.7435 (ptp-110) REVERT: A 528 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7610 (mm110) REVERT: A 534 TYR cc_start: 0.8092 (t80) cc_final: 0.7774 (t80) REVERT: A 541 LEU cc_start: 0.8261 (mt) cc_final: 0.7854 (mt) REVERT: A 576 ASN cc_start: 0.7366 (t0) cc_final: 0.7013 (t0) REVERT: A 590 LYS cc_start: 0.7672 (mmtm) cc_final: 0.7176 (mmtm) REVERT: A 592 VAL cc_start: 0.8230 (t) cc_final: 0.7728 (m) REVERT: A 601 GLN cc_start: 0.8059 (tt0) cc_final: 0.7812 (tm-30) REVERT: A 606 ILE cc_start: 0.8678 (mm) cc_final: 0.8436 (tp) REVERT: A 622 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7251 (tm-30) REVERT: B 367 LYS cc_start: 0.7479 (mmtt) cc_final: 0.6534 (mmtt) REVERT: B 393 GLU cc_start: 0.7020 (tp30) cc_final: 0.6534 (tp30) REVERT: B 398 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7117 (ptm160) REVERT: B 399 LYS cc_start: 0.8338 (mmtp) cc_final: 0.7944 (mmtp) REVERT: B 412 MET cc_start: 0.6289 (ppp) cc_final: 0.5677 (ppp) REVERT: B 414 LYS cc_start: 0.8258 (tppt) cc_final: 0.8017 (mmmt) REVERT: B 416 ASN cc_start: 0.7666 (p0) cc_final: 0.7327 (p0) REVERT: B 417 LEU cc_start: 0.7737 (pt) cc_final: 0.7527 (pt) REVERT: B 419 ILE cc_start: 0.7046 (mm) cc_final: 0.6744 (mm) REVERT: B 422 GLN cc_start: 0.7726 (tt0) cc_final: 0.7437 (pt0) REVERT: B 425 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6825 (mm-30) REVERT: B 429 LEU cc_start: 0.8199 (tp) cc_final: 0.7923 (tp) REVERT: B 432 HIS cc_start: 0.7095 (m90) cc_final: 0.6406 (m90) REVERT: B 439 LYS cc_start: 0.8407 (mppt) cc_final: 0.7927 (mppt) REVERT: B 442 MET cc_start: 0.7014 (mpp) cc_final: 0.6645 (mpp) REVERT: B 450 ARG cc_start: 0.7931 (ttp-170) cc_final: 0.7542 (ttp-170) REVERT: B 463 ASN cc_start: 0.7018 (m-40) cc_final: 0.6745 (m-40) REVERT: B 470 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7967 (mtpt) REVERT: B 471 SER cc_start: 0.7301 (p) cc_final: 0.6943 (p) REVERT: B 483 LYS cc_start: 0.8090 (mttm) cc_final: 0.6947 (mttm) REVERT: B 511 TRP cc_start: 0.7179 (m-90) cc_final: 0.6948 (m-90) REVERT: B 528 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7293 (mm-40) REVERT: B 534 TYR cc_start: 0.7840 (t80) cc_final: 0.7613 (t80) REVERT: B 542 MET cc_start: 0.6533 (mtp) cc_final: 0.6276 (mtp) REVERT: B 545 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7262 (mt-10) REVERT: B 554 ARG cc_start: 0.7547 (tmm-80) cc_final: 0.7257 (tmm-80) REVERT: B 556 GLN cc_start: 0.8136 (tt0) cc_final: 0.7694 (tp40) REVERT: B 560 MET cc_start: 0.7831 (tpp) cc_final: 0.7590 (tpp) REVERT: B 563 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7561 (ttm-80) REVERT: B 583 ARG cc_start: 0.8220 (ptp-170) cc_final: 0.7884 (ptp-110) REVERT: B 592 VAL cc_start: 0.8118 (t) cc_final: 0.7583 (m) REVERT: B 622 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6933 (tm-30) REVERT: C 25 MET cc_start: 0.7567 (pmm) cc_final: 0.7196 (pmm) REVERT: C 29 MET cc_start: 0.8876 (tpp) cc_final: 0.8379 (mmm) REVERT: C 34 GLU cc_start: 0.7568 (pp20) cc_final: 0.7065 (pp20) REVERT: C 43 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8387 (mt-10) REVERT: C 49 VAL cc_start: 0.7997 (t) cc_final: 0.7620 (m) REVERT: C 52 LYS cc_start: 0.8367 (tptm) cc_final: 0.8054 (tptm) REVERT: C 53 ASN cc_start: 0.8051 (m-40) cc_final: 0.7797 (m-40) REVERT: C 87 GLU cc_start: 0.8074 (pt0) cc_final: 0.7810 (pt0) REVERT: C 91 LYS cc_start: 0.8555 (tppt) cc_final: 0.7574 (tppt) REVERT: C 93 GLU cc_start: 0.8189 (tt0) cc_final: 0.7858 (tt0) REVERT: C 94 LYS cc_start: 0.8596 (ttpt) cc_final: 0.8281 (ttpt) REVERT: C 95 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7433 (mt-10) REVERT: C 98 GLU cc_start: 0.6849 (tp30) cc_final: 0.5559 (tp30) REVERT: C 102 ASP cc_start: 0.7719 (m-30) cc_final: 0.6706 (m-30) REVERT: C 119 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7794 (tp30) REVERT: C 126 LYS cc_start: 0.8597 (ttpp) cc_final: 0.8346 (ttpp) REVERT: C 130 ASP cc_start: 0.7168 (m-30) cc_final: 0.6627 (m-30) REVERT: C 132 TYR cc_start: 0.8182 (m-80) cc_final: 0.7426 (m-80) REVERT: C 133 ARG cc_start: 0.8464 (ttp-110) cc_final: 0.8024 (ttp-110) REVERT: C 149 GLU cc_start: 0.8160 (tp30) cc_final: 0.7766 (tp30) REVERT: C 150 ASP cc_start: 0.8050 (m-30) cc_final: 0.7820 (m-30) REVERT: C 153 LYS cc_start: 0.8776 (tppt) cc_final: 0.7961 (tppt) REVERT: C 155 TYR cc_start: 0.7317 (m-10) cc_final: 0.7064 (m-80) REVERT: C 174 LEU cc_start: 0.8054 (mt) cc_final: 0.7635 (mt) REVERT: C 224 MET cc_start: 0.7253 (ptm) cc_final: 0.6227 (ptm) REVERT: C 225 GLN cc_start: 0.7521 (mm110) cc_final: 0.6649 (mm110) REVERT: D 14 LYS cc_start: 0.8806 (mttt) cc_final: 0.8500 (mttt) REVERT: D 20 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7054 (tm-30) REVERT: D 25 MET cc_start: 0.7530 (pmm) cc_final: 0.7301 (pmm) REVERT: D 29 MET cc_start: 0.8595 (tpp) cc_final: 0.8305 (mmm) REVERT: D 30 LYS cc_start: 0.7998 (mtmm) cc_final: 0.7674 (mttm) REVERT: D 34 GLU cc_start: 0.7771 (pp20) cc_final: 0.7442 (pp20) REVERT: D 43 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8426 (mt-10) REVERT: D 52 LYS cc_start: 0.8430 (tptm) cc_final: 0.7901 (tptm) REVERT: D 59 ARG cc_start: 0.8017 (mtp-110) cc_final: 0.7726 (mtp180) REVERT: D 65 ILE cc_start: 0.8704 (pt) cc_final: 0.8390 (pt) REVERT: D 66 SER cc_start: 0.8067 (m) cc_final: 0.7360 (m) REVERT: D 87 GLU cc_start: 0.8124 (pt0) cc_final: 0.7833 (pt0) REVERT: D 91 LYS cc_start: 0.8637 (tppt) cc_final: 0.7938 (tppt) REVERT: D 93 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7995 (mt-10) REVERT: D 97 ARG cc_start: 0.8821 (mtm110) cc_final: 0.8390 (mtm110) REVERT: D 119 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7616 (tp30) REVERT: D 125 LEU cc_start: 0.8038 (mt) cc_final: 0.7823 (mt) REVERT: D 127 MET cc_start: 0.7880 (mmm) cc_final: 0.7473 (mmp) REVERT: D 130 ASP cc_start: 0.7175 (m-30) cc_final: 0.6678 (m-30) REVERT: D 133 ARG cc_start: 0.8407 (ttp-110) cc_final: 0.8027 (ttp-110) REVERT: D 153 LYS cc_start: 0.8546 (tppt) cc_final: 0.7638 (tppt) REVERT: D 174 LEU cc_start: 0.8085 (mt) cc_final: 0.7800 (mt) REVERT: D 192 ASP cc_start: 0.8238 (p0) cc_final: 0.7584 (p0) REVERT: D 193 LYS cc_start: 0.8071 (mttt) cc_final: 0.7616 (mptt) REVERT: D 195 CYS cc_start: 0.7637 (m) cc_final: 0.7433 (m) REVERT: D 206 ILE cc_start: 0.7809 (mt) cc_final: 0.7576 (mt) REVERT: D 220 SER cc_start: 0.7180 (m) cc_final: 0.6853 (m) REVERT: D 224 MET cc_start: 0.7356 (ptm) cc_final: 0.6376 (ptm) REVERT: D 225 GLN cc_start: 0.7553 (mm110) cc_final: 0.6690 (mm110) REVERT: E 88 LYS cc_start: 0.8413 (mmmt) cc_final: 0.7962 (mmmt) REVERT: E 121 CYS cc_start: 0.7591 (m) cc_final: 0.7339 (m) REVERT: E 125 TYR cc_start: 0.7940 (m-80) cc_final: 0.6999 (m-80) REVERT: E 146 MET cc_start: 0.6728 (tpp) cc_final: 0.6221 (tpp) REVERT: E 168 LYS cc_start: 0.8313 (ttmm) cc_final: 0.7797 (ttmm) REVERT: E 175 LYS cc_start: 0.8606 (ptmt) cc_final: 0.8098 (ptmt) REVERT: E 187 MET cc_start: 0.6154 (mtt) cc_final: 0.5773 (mtm) REVERT: E 206 LEU cc_start: 0.6632 (tp) cc_final: 0.6357 (tp) REVERT: E 215 LEU cc_start: 0.5142 (tp) cc_final: 0.4857 (tt) REVERT: E 219 MET cc_start: 0.7640 (mtp) cc_final: 0.7261 (mtp) REVERT: E 233 GLU cc_start: 0.8278 (pt0) cc_final: 0.8067 (pt0) REVERT: E 236 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7451 (tm-30) REVERT: E 249 MET cc_start: 0.8138 (ppp) cc_final: 0.7922 (ppp) REVERT: E 253 LEU cc_start: 0.8782 (mt) cc_final: 0.8535 (mt) REVERT: E 256 MET cc_start: 0.7679 (ptm) cc_final: 0.7289 (ptm) REVERT: E 267 ASP cc_start: 0.7774 (p0) cc_final: 0.7262 (p0) REVERT: E 312 GLU cc_start: 0.7700 (pp20) cc_final: 0.7197 (pp20) REVERT: E 313 LEU cc_start: 0.8188 (mt) cc_final: 0.7960 (mt) REVERT: E 316 TYR cc_start: 0.7726 (t80) cc_final: 0.7367 (t80) REVERT: E 319 ASN cc_start: 0.7896 (t0) cc_final: 0.6654 (t0) REVERT: E 320 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7643 (mm-30) REVERT: E 333 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8366 (mt-10) REVERT: E 344 LYS cc_start: 0.8476 (tttt) cc_final: 0.8111 (mttt) REVERT: E 353 LYS cc_start: 0.7888 (mptt) cc_final: 0.7678 (mptt) REVERT: E 356 MET cc_start: 0.6787 (ppp) cc_final: 0.6443 (ppp) REVERT: F 88 LYS cc_start: 0.8525 (mmmt) cc_final: 0.8000 (mmmt) REVERT: F 96 ARG cc_start: 0.7595 (ptm160) cc_final: 0.6966 (ptm160) REVERT: F 125 TYR cc_start: 0.8030 (m-80) cc_final: 0.7195 (m-80) REVERT: F 146 MET cc_start: 0.6713 (tpp) cc_final: 0.6251 (tpp) REVERT: F 175 LYS cc_start: 0.8603 (ptmt) cc_final: 0.8070 (ptmt) REVERT: F 195 ASN cc_start: 0.7514 (t0) cc_final: 0.7198 (t0) REVERT: F 206 LEU cc_start: 0.6616 (tp) cc_final: 0.6205 (tp) REVERT: F 219 MET cc_start: 0.7455 (mtp) cc_final: 0.7168 (mtp) REVERT: F 227 ARG cc_start: 0.7209 (mtm180) cc_final: 0.6946 (mtm180) REVERT: F 256 MET cc_start: 0.7777 (ptm) cc_final: 0.7397 (ptm) REVERT: F 267 ASP cc_start: 0.7424 (p0) cc_final: 0.6727 (p0) REVERT: F 316 TYR cc_start: 0.7735 (t80) cc_final: 0.7281 (t80) REVERT: F 318 VAL cc_start: 0.8454 (p) cc_final: 0.8218 (m) REVERT: F 319 ASN cc_start: 0.7721 (t0) cc_final: 0.6382 (t0) REVERT: F 320 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7456 (mm-30) REVERT: F 344 LYS cc_start: 0.8278 (tmmt) cc_final: 0.8063 (tmmt) REVERT: F 356 MET cc_start: 0.6853 (ppp) cc_final: 0.6613 (ppp) outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 0.3166 time to fit residues: 289.9491 Evaluate side-chains 667 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 667 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12876 Z= 0.216 Angle : 0.654 11.539 17364 Z= 0.348 Chirality : 0.045 0.179 1918 Planarity : 0.005 0.074 2216 Dihedral : 5.770 76.176 1740 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.07 % Allowed : 3.67 % Favored : 96.25 % 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 (0.16), residues: 896 sheet: -2.96 (0.47), residues: 88 loop : -1.03 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 368 HIS 0.014 0.002 HIS B 460 PHE 0.023 0.002 PHE B 599 TYR 0.025 0.002 TYR D 155 ARG 0.010 0.001 ARG E 227 *********************** 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 668 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 667 time to evaluate : 1.403 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 345 GLU cc_start: 0.6363 (mp0) cc_final: 0.5990 (mp0) REVERT: A 367 LYS cc_start: 0.7394 (mmtt) cc_final: 0.6473 (mmtt) REVERT: A 387 PHE cc_start: 0.7870 (t80) cc_final: 0.7158 (t80) REVERT: A 391 ARG cc_start: 0.8063 (mmt90) cc_final: 0.7656 (mmm-85) REVERT: A 399 LYS cc_start: 0.8281 (mmtp) cc_final: 0.8032 (mmtp) REVERT: A 411 TYR cc_start: 0.7134 (p90) cc_final: 0.6712 (p90) REVERT: A 412 MET cc_start: 0.6268 (ppp) cc_final: 0.5615 (ppp) REVERT: A 414 LYS cc_start: 0.8242 (tppt) cc_final: 0.7961 (tppt) REVERT: A 416 ASN cc_start: 0.7411 (p0) cc_final: 0.7058 (p0) REVERT: A 439 LYS cc_start: 0.8206 (mppt) cc_final: 0.7606 (mppt) REVERT: A 444 GLN cc_start: 0.7965 (mp10) cc_final: 0.7278 (mp10) REVERT: A 458 TYR cc_start: 0.7976 (t80) cc_final: 0.7760 (t80) REVERT: A 460 HIS cc_start: 0.7707 (m170) cc_final: 0.7361 (m-70) REVERT: A 463 ASN cc_start: 0.6747 (m-40) cc_final: 0.6439 (m-40) REVERT: A 518 ARG cc_start: 0.7959 (ptp-110) cc_final: 0.7350 (ptp-110) REVERT: A 528 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7053 (mm110) REVERT: A 534 TYR cc_start: 0.8148 (t80) cc_final: 0.7808 (t80) REVERT: A 536 ILE cc_start: 0.8083 (mm) cc_final: 0.7683 (mm) REVERT: A 541 LEU cc_start: 0.8291 (mt) cc_final: 0.7839 (mt) REVERT: A 559 PHE cc_start: 0.8066 (t80) cc_final: 0.7847 (t80) REVERT: A 560 MET cc_start: 0.7774 (tpp) cc_final: 0.7039 (tpp) REVERT: A 563 ARG cc_start: 0.8625 (mmm-85) cc_final: 0.7829 (ttm-80) REVERT: A 574 TYR cc_start: 0.7369 (m-10) cc_final: 0.7166 (m-10) REVERT: A 576 ASN cc_start: 0.7433 (t0) cc_final: 0.7055 (t0) REVERT: A 592 VAL cc_start: 0.8192 (t) cc_final: 0.7719 (m) REVERT: A 601 GLN cc_start: 0.8070 (tt0) cc_final: 0.7804 (tm-30) REVERT: A 622 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7229 (tm-30) REVERT: B 342 TRP cc_start: 0.8536 (m100) cc_final: 0.8137 (m100) REVERT: B 348 GLU cc_start: 0.7068 (pt0) cc_final: 0.6765 (pt0) REVERT: B 367 LYS cc_start: 0.7521 (mmtt) cc_final: 0.6581 (mmtt) REVERT: B 398 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7632 (ptm160) REVERT: B 399 LYS cc_start: 0.8303 (mmtp) cc_final: 0.7913 (mmtp) REVERT: B 409 MET cc_start: 0.6278 (mtm) cc_final: 0.5926 (mtm) REVERT: B 412 MET cc_start: 0.6308 (ppp) cc_final: 0.5715 (ppp) REVERT: B 413 THR cc_start: 0.7750 (p) cc_final: 0.7547 (p) REVERT: B 414 LYS cc_start: 0.8269 (tppt) cc_final: 0.8026 (mmmt) REVERT: B 416 ASN cc_start: 0.7633 (p0) cc_final: 0.7291 (p0) REVERT: B 417 LEU cc_start: 0.7779 (pt) cc_final: 0.7572 (pt) REVERT: B 419 ILE cc_start: 0.7017 (mm) cc_final: 0.6685 (mm) REVERT: B 429 LEU cc_start: 0.8195 (tp) cc_final: 0.7926 (tp) REVERT: B 432 HIS cc_start: 0.7157 (m90) cc_final: 0.6595 (m90) REVERT: B 439 LYS cc_start: 0.8415 (mppt) cc_final: 0.7990 (mppt) REVERT: B 441 GLN cc_start: 0.7348 (mt0) cc_final: 0.7062 (mp10) REVERT: B 442 MET cc_start: 0.6753 (mpp) cc_final: 0.6494 (mpp) REVERT: B 450 ARG cc_start: 0.8014 (ttp-170) cc_final: 0.7709 (ttp-170) REVERT: B 458 TYR cc_start: 0.8195 (t80) cc_final: 0.7691 (t80) REVERT: B 463 ASN cc_start: 0.7016 (m-40) cc_final: 0.6812 (m-40) REVERT: B 470 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7816 (mtpt) REVERT: B 471 SER cc_start: 0.7442 (p) cc_final: 0.7110 (p) REVERT: B 484 ILE cc_start: 0.7819 (mt) cc_final: 0.7591 (mt) REVERT: B 511 TRP cc_start: 0.7251 (m-90) cc_final: 0.6842 (m-90) REVERT: B 512 MET cc_start: 0.5769 (ttt) cc_final: 0.5508 (ttt) REVERT: B 528 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7099 (mm-40) REVERT: B 542 MET cc_start: 0.6499 (mtp) cc_final: 0.6243 (mtp) REVERT: B 545 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7341 (mt-10) REVERT: B 549 SER cc_start: 0.8172 (t) cc_final: 0.7940 (t) REVERT: B 554 ARG cc_start: 0.7489 (tmm-80) cc_final: 0.7102 (tmm-80) REVERT: B 560 MET cc_start: 0.7973 (tpp) cc_final: 0.7626 (tpp) REVERT: B 563 ARG cc_start: 0.8294 (mmm-85) cc_final: 0.7603 (ttm-80) REVERT: B 583 ARG cc_start: 0.8297 (ptp-170) cc_final: 0.7926 (ptp-110) REVERT: B 603 LEU cc_start: 0.8296 (tp) cc_final: 0.8090 (tp) REVERT: B 610 GLN cc_start: 0.8064 (mm110) cc_final: 0.7515 (mm110) REVERT: C 25 MET cc_start: 0.7457 (pmm) cc_final: 0.7149 (pmm) REVERT: C 29 MET cc_start: 0.8845 (tpp) cc_final: 0.8394 (mmm) REVERT: C 43 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8393 (mp0) REVERT: C 52 LYS cc_start: 0.8364 (tptm) cc_final: 0.8122 (tptm) REVERT: C 87 GLU cc_start: 0.8076 (pt0) cc_final: 0.7791 (pt0) REVERT: C 91 LYS cc_start: 0.8549 (tppt) cc_final: 0.7578 (tppt) REVERT: C 93 GLU cc_start: 0.8412 (tt0) cc_final: 0.7937 (tt0) REVERT: C 94 LYS cc_start: 0.8595 (ttpt) cc_final: 0.8261 (ttpt) REVERT: C 95 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7488 (mt-10) REVERT: C 97 ARG cc_start: 0.8588 (mtm110) cc_final: 0.8172 (mtm110) REVERT: C 98 GLU cc_start: 0.6874 (tp30) cc_final: 0.5549 (tp30) REVERT: C 102 ASP cc_start: 0.7739 (m-30) cc_final: 0.6688 (m-30) REVERT: C 119 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7753 (tp30) REVERT: C 126 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8132 (ttpp) REVERT: C 127 MET cc_start: 0.7761 (mmm) cc_final: 0.7111 (mmm) REVERT: C 130 ASP cc_start: 0.7113 (m-30) cc_final: 0.6604 (m-30) REVERT: C 132 TYR cc_start: 0.8236 (m-80) cc_final: 0.7483 (m-80) REVERT: C 133 ARG cc_start: 0.8507 (ttp-110) cc_final: 0.8081 (ttp-110) REVERT: C 149 GLU cc_start: 0.8173 (tp30) cc_final: 0.7825 (tp30) REVERT: C 153 LYS cc_start: 0.8698 (tppt) cc_final: 0.7890 (tppt) REVERT: C 155 TYR cc_start: 0.7339 (m-10) cc_final: 0.7011 (m-80) REVERT: C 174 LEU cc_start: 0.8144 (mt) cc_final: 0.7781 (mt) REVERT: C 202 PHE cc_start: 0.8612 (t80) cc_final: 0.8337 (t80) REVERT: C 204 ASP cc_start: 0.7964 (t0) cc_final: 0.7676 (t0) REVERT: C 206 ILE cc_start: 0.8061 (mt) cc_final: 0.7817 (mt) REVERT: C 218 LYS cc_start: 0.7637 (mmpt) cc_final: 0.7382 (mmpt) REVERT: C 224 MET cc_start: 0.7317 (ptm) cc_final: 0.6243 (ptm) REVERT: C 225 GLN cc_start: 0.7541 (mm110) cc_final: 0.6649 (mm110) REVERT: D 14 LYS cc_start: 0.8794 (mttt) cc_final: 0.8459 (mttm) REVERT: D 20 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6915 (tm-30) REVERT: D 25 MET cc_start: 0.7647 (pmm) cc_final: 0.7390 (pmm) REVERT: D 29 MET cc_start: 0.8625 (tpp) cc_final: 0.8264 (mmm) REVERT: D 30 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7696 (mttm) REVERT: D 34 GLU cc_start: 0.7776 (pp20) cc_final: 0.7432 (pp20) REVERT: D 43 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8350 (mt-10) REVERT: D 52 LYS cc_start: 0.8416 (tptm) cc_final: 0.7951 (tptm) REVERT: D 59 ARG cc_start: 0.7930 (mtp-110) cc_final: 0.7649 (mtp180) REVERT: D 65 ILE cc_start: 0.8691 (pt) cc_final: 0.8361 (pt) REVERT: D 66 SER cc_start: 0.8085 (m) cc_final: 0.7359 (m) REVERT: D 87 GLU cc_start: 0.8134 (pt0) cc_final: 0.7818 (pt0) REVERT: D 91 LYS cc_start: 0.8666 (tppt) cc_final: 0.7914 (tppt) REVERT: D 93 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8043 (mt-10) REVERT: D 102 ASP cc_start: 0.7397 (m-30) cc_final: 0.7057 (m-30) REVERT: D 119 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7603 (tp30) REVERT: D 125 LEU cc_start: 0.7981 (mt) cc_final: 0.7753 (mt) REVERT: D 127 MET cc_start: 0.7737 (mmm) cc_final: 0.7315 (mmp) REVERT: D 130 ASP cc_start: 0.7196 (m-30) cc_final: 0.6757 (m-30) REVERT: D 133 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.8018 (ttp-110) REVERT: D 149 GLU cc_start: 0.7813 (tp30) cc_final: 0.7557 (tp30) REVERT: D 151 SER cc_start: 0.8292 (p) cc_final: 0.7459 (p) REVERT: D 153 LYS cc_start: 0.8485 (tppt) cc_final: 0.7578 (tppt) REVERT: D 155 TYR cc_start: 0.6882 (m-80) cc_final: 0.6615 (m-80) REVERT: D 174 LEU cc_start: 0.8159 (mt) cc_final: 0.7898 (mt) REVERT: D 176 LEU cc_start: 0.8683 (tt) cc_final: 0.7622 (tt) REVERT: D 180 PHE cc_start: 0.8211 (m-80) cc_final: 0.7673 (m-80) REVERT: D 192 ASP cc_start: 0.8238 (p0) cc_final: 0.7575 (p0) REVERT: D 193 LYS cc_start: 0.8095 (mttt) cc_final: 0.7669 (mptt) REVERT: D 195 CYS cc_start: 0.7740 (m) cc_final: 0.7511 (m) REVERT: D 220 SER cc_start: 0.7178 (m) cc_final: 0.6949 (m) REVERT: D 224 MET cc_start: 0.7366 (ptm) cc_final: 0.6273 (ptm) REVERT: D 225 GLN cc_start: 0.7560 (mm110) cc_final: 0.6737 (mm110) REVERT: E 88 LYS cc_start: 0.8411 (mmmt) cc_final: 0.7968 (mmmt) REVERT: E 121 CYS cc_start: 0.7697 (m) cc_final: 0.7413 (m) REVERT: E 125 TYR cc_start: 0.7971 (m-80) cc_final: 0.7069 (m-80) REVERT: E 144 GLU cc_start: 0.7199 (pt0) cc_final: 0.6989 (pt0) REVERT: E 146 MET cc_start: 0.6660 (tpp) cc_final: 0.6396 (tpp) REVERT: E 160 ARG cc_start: 0.7457 (mpp80) cc_final: 0.6666 (mpt-90) REVERT: E 168 LYS cc_start: 0.8334 (ttmm) cc_final: 0.7808 (ttmm) REVERT: E 175 LYS cc_start: 0.8673 (ptmt) cc_final: 0.8125 (ptmt) REVERT: E 189 ARG cc_start: 0.7825 (tpp-160) cc_final: 0.7122 (tpp-160) REVERT: E 206 LEU cc_start: 0.6732 (tp) cc_final: 0.6236 (tp) REVERT: E 219 MET cc_start: 0.7560 (mtp) cc_final: 0.7325 (mtp) REVERT: E 233 GLU cc_start: 0.8314 (pt0) cc_final: 0.8034 (pt0) REVERT: E 236 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7504 (tm-30) REVERT: E 253 LEU cc_start: 0.8783 (mt) cc_final: 0.8522 (mt) REVERT: E 255 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7312 (tm-30) REVERT: E 256 MET cc_start: 0.7639 (ptm) cc_final: 0.6856 (ptm) REVERT: E 267 ASP cc_start: 0.7891 (p0) cc_final: 0.7368 (p0) REVERT: E 316 TYR cc_start: 0.7717 (t80) cc_final: 0.7319 (t80) REVERT: E 319 ASN cc_start: 0.7889 (t0) cc_final: 0.6645 (t0) REVERT: E 334 PHE cc_start: 0.8433 (t80) cc_final: 0.8191 (t80) REVERT: E 344 LYS cc_start: 0.8491 (tttt) cc_final: 0.8122 (mttt) REVERT: F 88 LYS cc_start: 0.8507 (mmmt) cc_final: 0.8001 (mmmt) REVERT: F 96 ARG cc_start: 0.7549 (ptm160) cc_final: 0.7001 (ptm160) REVERT: F 125 TYR cc_start: 0.8003 (m-80) cc_final: 0.7186 (m-80) REVERT: F 175 LYS cc_start: 0.8633 (ptmt) cc_final: 0.8116 (ptmt) REVERT: F 195 ASN cc_start: 0.7588 (t0) cc_final: 0.7259 (t0) REVERT: F 206 LEU cc_start: 0.6564 (tp) cc_final: 0.6141 (tp) REVERT: F 219 MET cc_start: 0.7494 (mtp) cc_final: 0.7164 (mtp) REVERT: F 227 ARG cc_start: 0.7274 (mtm180) cc_final: 0.6947 (mtm180) REVERT: F 249 MET cc_start: 0.8216 (ppp) cc_final: 0.7955 (ppp) REVERT: F 253 LEU cc_start: 0.8751 (mt) cc_final: 0.8550 (mt) REVERT: F 256 MET cc_start: 0.7789 (ptm) cc_final: 0.7423 (ptm) REVERT: F 267 ASP cc_start: 0.7576 (p0) cc_final: 0.6927 (p0) REVERT: F 316 TYR cc_start: 0.7731 (t80) cc_final: 0.7268 (t80) REVERT: F 318 VAL cc_start: 0.8398 (p) cc_final: 0.8154 (m) REVERT: F 319 ASN cc_start: 0.7795 (t0) cc_final: 0.6452 (t0) REVERT: F 320 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7560 (mm-30) REVERT: F 324 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7682 (mmtt) REVERT: F 333 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8297 (mt-10) REVERT: F 344 LYS cc_start: 0.8273 (tmmt) cc_final: 0.8060 (tmmt) REVERT: F 356 MET cc_start: 0.6875 (ppp) cc_final: 0.6626 (ppp) outliers start: 1 outliers final: 0 residues processed: 667 average time/residue: 0.3008 time to fit residues: 272.1648 Evaluate side-chains 663 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 663 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.0770 chunk 133 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS B 369 HIS C 200 GLN D 11 GLN D 117 ASN D 200 GLN E 109 ASN ** E 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12876 Z= 0.204 Angle : 0.662 15.172 17364 Z= 0.342 Chirality : 0.045 0.183 1918 Planarity : 0.005 0.052 2216 Dihedral : 5.565 63.325 1740 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: -0.39 (0.21), residues: 1538 helix: 0.57 (0.16), residues: 894 sheet: -2.82 (0.45), residues: 98 loop : -1.01 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 368 HIS 0.011 0.001 HIS E 358 PHE 0.026 0.002 PHE C 180 TYR 0.021 0.002 TYR B 534 ARG 0.009 0.001 ARG E 96 *********************** 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 660 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 1.409 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 367 LYS cc_start: 0.7375 (mmtt) cc_final: 0.6474 (mmtt) REVERT: A 387 PHE cc_start: 0.7853 (t80) cc_final: 0.7065 (t80) REVERT: A 391 ARG cc_start: 0.8048 (mmt90) cc_final: 0.7623 (mmm-85) REVERT: A 399 LYS cc_start: 0.8253 (mmtp) cc_final: 0.8014 (mmtp) REVERT: A 411 TYR cc_start: 0.7116 (p90) cc_final: 0.6771 (p90) REVERT: A 412 MET cc_start: 0.6448 (ppp) cc_final: 0.5790 (ppp) REVERT: A 413 THR cc_start: 0.7799 (p) cc_final: 0.7587 (p) REVERT: A 414 LYS cc_start: 0.8234 (tppt) cc_final: 0.7926 (tppt) REVERT: A 416 ASN cc_start: 0.7378 (p0) cc_final: 0.7178 (p0) REVERT: A 429 LEU cc_start: 0.8011 (tp) cc_final: 0.7706 (tp) REVERT: A 439 LYS cc_start: 0.8207 (mppt) cc_final: 0.7567 (mppt) REVERT: A 444 GLN cc_start: 0.7942 (mp10) cc_final: 0.7397 (mp10) REVERT: A 454 GLN cc_start: 0.8275 (mt0) cc_final: 0.7857 (mt0) REVERT: A 456 MET cc_start: 0.7025 (tpt) cc_final: 0.6703 (tpt) REVERT: A 458 TYR cc_start: 0.8099 (t80) cc_final: 0.7844 (t80) REVERT: A 518 ARG cc_start: 0.7963 (ptp-110) cc_final: 0.7425 (ptp-110) REVERT: A 528 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7318 (mm-40) REVERT: A 534 TYR cc_start: 0.8024 (t80) cc_final: 0.7582 (t80) REVERT: A 536 ILE cc_start: 0.8075 (mm) cc_final: 0.7758 (mm) REVERT: A 541 LEU cc_start: 0.8320 (mt) cc_final: 0.7884 (mt) REVERT: A 542 MET cc_start: 0.6477 (mtp) cc_final: 0.6137 (mtp) REVERT: A 560 MET cc_start: 0.7754 (tpp) cc_final: 0.7065 (tpp) REVERT: A 563 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.7970 (ttm-80) REVERT: A 567 SER cc_start: 0.7932 (t) cc_final: 0.7330 (t) REVERT: A 572 LYS cc_start: 0.7843 (mmmm) cc_final: 0.7458 (mmmm) REVERT: A 574 TYR cc_start: 0.7488 (m-10) cc_final: 0.7201 (m-10) REVERT: A 592 VAL cc_start: 0.8198 (t) cc_final: 0.7669 (m) REVERT: A 601 GLN cc_start: 0.8089 (tt0) cc_final: 0.7777 (tm-30) REVERT: B 342 TRP cc_start: 0.8500 (m100) cc_final: 0.8068 (m100) REVERT: B 348 GLU cc_start: 0.7077 (pt0) cc_final: 0.6649 (pt0) REVERT: B 362 THR cc_start: 0.7546 (m) cc_final: 0.7292 (m) REVERT: B 367 LYS cc_start: 0.7533 (mmtt) cc_final: 0.6651 (mmtt) REVERT: B 398 ARG cc_start: 0.7853 (mtp180) cc_final: 0.7563 (ptm160) REVERT: B 399 LYS cc_start: 0.8302 (mmtp) cc_final: 0.7899 (mmtp) REVERT: B 409 MET cc_start: 0.6221 (mtm) cc_final: 0.5943 (mtm) REVERT: B 412 MET cc_start: 0.6406 (ppp) cc_final: 0.5797 (ppp) REVERT: B 416 ASN cc_start: 0.7610 (p0) cc_final: 0.7241 (p0) REVERT: B 417 LEU cc_start: 0.7848 (pt) cc_final: 0.7645 (pt) REVERT: B 419 ILE cc_start: 0.6997 (mm) cc_final: 0.6618 (mm) REVERT: B 429 LEU cc_start: 0.8187 (tp) cc_final: 0.7954 (tp) REVERT: B 432 HIS cc_start: 0.7131 (m90) cc_final: 0.6590 (m90) REVERT: B 439 LYS cc_start: 0.8417 (mppt) cc_final: 0.7961 (mppt) REVERT: B 441 GLN cc_start: 0.7319 (mt0) cc_final: 0.7052 (mp10) REVERT: B 442 MET cc_start: 0.6886 (mpp) cc_final: 0.6429 (mpp) REVERT: B 450 ARG cc_start: 0.8004 (ttp-170) cc_final: 0.7748 (ttp-170) REVERT: B 458 TYR cc_start: 0.8208 (t80) cc_final: 0.7741 (t80) REVERT: B 470 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7800 (mtpt) REVERT: B 471 SER cc_start: 0.7464 (p) cc_final: 0.7034 (p) REVERT: B 483 LYS cc_start: 0.8158 (mttp) cc_final: 0.7886 (mttp) REVERT: B 484 ILE cc_start: 0.7804 (mt) cc_final: 0.7536 (mt) REVERT: B 492 VAL cc_start: 0.7655 (t) cc_final: 0.7362 (m) REVERT: B 511 TRP cc_start: 0.7277 (m-90) cc_final: 0.6834 (m-90) REVERT: B 518 ARG cc_start: 0.7635 (mtm-85) cc_final: 0.7148 (mtm-85) REVERT: B 528 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7109 (mm-40) REVERT: B 541 LEU cc_start: 0.8569 (mt) cc_final: 0.8320 (mt) REVERT: B 542 MET cc_start: 0.6544 (mtp) cc_final: 0.6221 (mtp) REVERT: B 545 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7338 (mt-10) REVERT: B 551 ILE cc_start: 0.8629 (mp) cc_final: 0.8409 (mp) REVERT: B 554 ARG cc_start: 0.7479 (tmm-80) cc_final: 0.7097 (tmm-80) REVERT: B 560 MET cc_start: 0.7937 (tpp) cc_final: 0.7517 (tpp) REVERT: B 563 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.7596 (ttm-80) REVERT: B 567 SER cc_start: 0.7983 (t) cc_final: 0.7567 (t) REVERT: B 583 ARG cc_start: 0.8287 (ptp-170) cc_final: 0.7981 (ptp-110) REVERT: B 610 GLN cc_start: 0.8002 (mm110) cc_final: 0.7250 (mm110) REVERT: C 25 MET cc_start: 0.7451 (pmm) cc_final: 0.7150 (pmm) REVERT: C 29 MET cc_start: 0.8858 (tpp) cc_final: 0.8437 (mmm) REVERT: C 43 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8268 (mt-10) REVERT: C 52 LYS cc_start: 0.8372 (tptm) cc_final: 0.8152 (tptm) REVERT: C 87 GLU cc_start: 0.8100 (pt0) cc_final: 0.7795 (pt0) REVERT: C 91 LYS cc_start: 0.8583 (tppt) cc_final: 0.7688 (tppt) REVERT: C 93 GLU cc_start: 0.8408 (tt0) cc_final: 0.7967 (tt0) REVERT: C 94 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8247 (ttpt) REVERT: C 95 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7541 (mt-10) REVERT: C 97 ARG cc_start: 0.8579 (mtm110) cc_final: 0.8164 (mtm110) REVERT: C 98 GLU cc_start: 0.6908 (tp30) cc_final: 0.5502 (tp30) REVERT: C 102 ASP cc_start: 0.7695 (m-30) cc_final: 0.6651 (m-30) REVERT: C 126 LYS cc_start: 0.8514 (ttpp) cc_final: 0.8215 (ttpp) REVERT: C 130 ASP cc_start: 0.7096 (m-30) cc_final: 0.6551 (m-30) REVERT: C 133 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8068 (ttp-110) REVERT: C 153 LYS cc_start: 0.8694 (tppt) cc_final: 0.7848 (tppt) REVERT: C 155 TYR cc_start: 0.7301 (m-10) cc_final: 0.7016 (m-80) REVERT: C 174 LEU cc_start: 0.8075 (mt) cc_final: 0.7680 (mt) REVERT: C 202 PHE cc_start: 0.8594 (t80) cc_final: 0.8370 (t80) REVERT: C 204 ASP cc_start: 0.7951 (t0) cc_final: 0.7668 (t0) REVERT: C 218 LYS cc_start: 0.7652 (mmpt) cc_final: 0.7376 (mmpt) REVERT: C 224 MET cc_start: 0.7355 (ptm) cc_final: 0.6305 (ptm) REVERT: C 225 GLN cc_start: 0.7551 (mm110) cc_final: 0.6649 (mm110) REVERT: D 10 VAL cc_start: 0.8866 (t) cc_final: 0.8658 (t) REVERT: D 14 LYS cc_start: 0.8812 (mttt) cc_final: 0.8503 (mttm) REVERT: D 20 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6929 (tm-30) REVERT: D 29 MET cc_start: 0.8605 (tpp) cc_final: 0.8251 (mmm) REVERT: D 30 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7727 (mttm) REVERT: D 34 GLU cc_start: 0.7805 (pp20) cc_final: 0.7441 (pp20) REVERT: D 43 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8355 (mt-10) REVERT: D 52 LYS cc_start: 0.8423 (tptm) cc_final: 0.7960 (tptm) REVERT: D 59 ARG cc_start: 0.7940 (mtp-110) cc_final: 0.7674 (mtp180) REVERT: D 65 ILE cc_start: 0.8675 (pt) cc_final: 0.8328 (pt) REVERT: D 66 SER cc_start: 0.8074 (m) cc_final: 0.7400 (m) REVERT: D 84 MET cc_start: 0.7593 (ptp) cc_final: 0.7112 (ptp) REVERT: D 87 GLU cc_start: 0.8144 (pt0) cc_final: 0.7805 (pt0) REVERT: D 91 LYS cc_start: 0.8665 (tppt) cc_final: 0.7946 (tppt) REVERT: D 93 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8058 (mt-10) REVERT: D 94 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8440 (ttpt) REVERT: D 102 ASP cc_start: 0.7379 (m-30) cc_final: 0.7036 (m-30) REVERT: D 119 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7589 (tp30) REVERT: D 125 LEU cc_start: 0.7985 (mt) cc_final: 0.7751 (mt) REVERT: D 127 MET cc_start: 0.7745 (mmm) cc_final: 0.7327 (mmp) REVERT: D 130 ASP cc_start: 0.7107 (m-30) cc_final: 0.6730 (m-30) REVERT: D 133 ARG cc_start: 0.8219 (ttp-110) cc_final: 0.7959 (ttp-110) REVERT: D 149 GLU cc_start: 0.7787 (tp30) cc_final: 0.7575 (tp30) REVERT: D 153 LYS cc_start: 0.8483 (tppt) cc_final: 0.7580 (tppt) REVERT: D 155 TYR cc_start: 0.6954 (m-80) cc_final: 0.6748 (m-80) REVERT: D 174 LEU cc_start: 0.8141 (mt) cc_final: 0.7873 (mt) REVERT: D 176 LEU cc_start: 0.8639 (tt) cc_final: 0.7529 (tt) REVERT: D 180 PHE cc_start: 0.8220 (m-80) cc_final: 0.7728 (m-80) REVERT: D 192 ASP cc_start: 0.8276 (p0) cc_final: 0.8002 (p0) REVERT: D 193 LYS cc_start: 0.8088 (mttt) cc_final: 0.7847 (mttt) REVERT: D 195 CYS cc_start: 0.7784 (m) cc_final: 0.7534 (m) REVERT: D 220 SER cc_start: 0.7173 (m) cc_final: 0.6893 (m) REVERT: D 224 MET cc_start: 0.7431 (ptm) cc_final: 0.6349 (ptm) REVERT: D 225 GLN cc_start: 0.7602 (mm110) cc_final: 0.6801 (mm110) REVERT: E 121 CYS cc_start: 0.7521 (m) cc_final: 0.7212 (m) REVERT: E 125 TYR cc_start: 0.7929 (m-80) cc_final: 0.7047 (m-80) REVERT: E 144 GLU cc_start: 0.7224 (pt0) cc_final: 0.7022 (pt0) REVERT: E 146 MET cc_start: 0.6725 (tpp) cc_final: 0.6506 (tpp) REVERT: E 160 ARG cc_start: 0.7400 (mpp80) cc_final: 0.6850 (mpp80) REVERT: E 168 LYS cc_start: 0.8274 (ttmm) cc_final: 0.7690 (ttmm) REVERT: E 175 LYS cc_start: 0.8657 (ptmt) cc_final: 0.8133 (ptmt) REVERT: E 206 LEU cc_start: 0.6699 (tp) cc_final: 0.6201 (tp) REVERT: E 219 MET cc_start: 0.7572 (mtp) cc_final: 0.7305 (mtp) REVERT: E 236 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7485 (tm-30) REVERT: E 249 MET cc_start: 0.8171 (ppp) cc_final: 0.7957 (ppp) REVERT: E 253 LEU cc_start: 0.8743 (mt) cc_final: 0.8468 (mt) REVERT: E 256 MET cc_start: 0.7651 (ptm) cc_final: 0.7218 (ptm) REVERT: E 267 ASP cc_start: 0.7969 (p0) cc_final: 0.7427 (p0) REVERT: E 274 MET cc_start: 0.6164 (ppp) cc_final: 0.5926 (ppp) REVERT: E 316 TYR cc_start: 0.7688 (t80) cc_final: 0.7312 (t80) REVERT: E 319 ASN cc_start: 0.7942 (t0) cc_final: 0.6677 (t0) REVERT: E 334 PHE cc_start: 0.8434 (t80) cc_final: 0.8198 (t80) REVERT: E 344 LYS cc_start: 0.8508 (tttt) cc_final: 0.8134 (mttt) REVERT: E 356 MET cc_start: 0.6913 (ppp) cc_final: 0.6493 (ppp) REVERT: E 360 PHE cc_start: 0.8381 (p90) cc_final: 0.8054 (p90) REVERT: E 362 LYS cc_start: 0.8890 (mppt) cc_final: 0.8645 (mmtt) REVERT: E 363 ARG cc_start: 0.8606 (mmp80) cc_final: 0.8294 (mmp80) REVERT: F 88 LYS cc_start: 0.8476 (mmmt) cc_final: 0.7989 (mmmt) REVERT: F 96 ARG cc_start: 0.7563 (ptm160) cc_final: 0.7020 (ptm160) REVERT: F 125 TYR cc_start: 0.8004 (m-80) cc_final: 0.7212 (m-80) REVERT: F 163 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7759 (mt-10) REVERT: F 175 LYS cc_start: 0.8662 (ptmt) cc_final: 0.8159 (ptmt) REVERT: F 195 ASN cc_start: 0.7700 (t0) cc_final: 0.7343 (t0) REVERT: F 206 LEU cc_start: 0.6590 (tp) cc_final: 0.6192 (tp) REVERT: F 219 MET cc_start: 0.7503 (mtp) cc_final: 0.7186 (mtp) REVERT: F 227 ARG cc_start: 0.7253 (mtm180) cc_final: 0.6912 (mtm180) REVERT: F 249 MET cc_start: 0.8186 (ppp) cc_final: 0.7931 (ppp) REVERT: F 253 LEU cc_start: 0.8751 (mt) cc_final: 0.8540 (mt) REVERT: F 256 MET cc_start: 0.7802 (ptm) cc_final: 0.7414 (ptm) REVERT: F 267 ASP cc_start: 0.7708 (p0) cc_final: 0.7183 (p0) REVERT: F 316 TYR cc_start: 0.7718 (t80) cc_final: 0.7272 (t80) REVERT: F 318 VAL cc_start: 0.8412 (p) cc_final: 0.8119 (m) REVERT: F 319 ASN cc_start: 0.7784 (t0) cc_final: 0.6460 (t0) REVERT: F 320 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7585 (mm-30) REVERT: F 324 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7674 (mmtt) REVERT: F 333 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8321 (mt-10) REVERT: F 344 LYS cc_start: 0.8236 (tmmt) cc_final: 0.8032 (tmmt) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.3041 time to fit residues: 270.9617 Evaluate side-chains 647 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 647 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 B 369 HIS ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 200 GLN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12876 Z= 0.203 Angle : 0.664 10.947 17364 Z= 0.344 Chirality : 0.045 0.182 1918 Planarity : 0.004 0.050 2216 Dihedral : 5.457 51.608 1740 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: 0.55 (0.16), residues: 894 sheet: -2.45 (0.52), residues: 78 loop : -0.99 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 368 HIS 0.013 0.001 HIS E 358 PHE 0.028 0.002 PHE E 371 TYR 0.026 0.002 TYR B 532 ARG 0.006 0.001 ARG E 181 *********************** 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 656 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 656 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: A 367 LYS cc_start: 0.7407 (mmtt) cc_final: 0.6502 (mmtt) REVERT: A 387 PHE cc_start: 0.7871 (t80) cc_final: 0.7002 (t80) REVERT: A 391 ARG cc_start: 0.8032 (mmt90) cc_final: 0.7607 (mmm-85) REVERT: A 399 LYS cc_start: 0.8219 (mmtp) cc_final: 0.7984 (mmtp) REVERT: A 412 MET cc_start: 0.6512 (ppp) cc_final: 0.5822 (ppp) REVERT: A 414 LYS cc_start: 0.8210 (tppt) cc_final: 0.7912 (tppt) REVERT: A 431 LYS cc_start: 0.8126 (mppt) cc_final: 0.7855 (mppt) REVERT: A 439 LYS cc_start: 0.8216 (mppt) cc_final: 0.7552 (mppt) REVERT: A 442 MET cc_start: 0.6842 (mpp) cc_final: 0.6389 (mpp) REVERT: A 445 LEU cc_start: 0.8201 (tp) cc_final: 0.7941 (tp) REVERT: A 457 ASP cc_start: 0.6828 (t0) cc_final: 0.6602 (t0) REVERT: A 458 TYR cc_start: 0.8157 (t80) cc_final: 0.7832 (t80) REVERT: A 466 HIS cc_start: 0.8154 (t-90) cc_final: 0.7942 (t-90) REVERT: A 477 HIS cc_start: 0.6376 (t-90) cc_final: 0.6148 (t-90) REVERT: A 518 ARG cc_start: 0.7926 (ptp-110) cc_final: 0.7449 (ptp-110) REVERT: A 528 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7310 (mm110) REVERT: A 534 TYR cc_start: 0.8170 (t80) cc_final: 0.7734 (t80) REVERT: A 536 ILE cc_start: 0.8062 (mm) cc_final: 0.7800 (mm) REVERT: A 541 LEU cc_start: 0.8305 (mt) cc_final: 0.7853 (mt) REVERT: A 542 MET cc_start: 0.6512 (mtp) cc_final: 0.6190 (mtp) REVERT: A 560 MET cc_start: 0.7756 (tpp) cc_final: 0.7120 (tpp) REVERT: A 563 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.7953 (ttm-80) REVERT: A 572 LYS cc_start: 0.7967 (mmmm) cc_final: 0.7515 (mmmm) REVERT: A 574 TYR cc_start: 0.7522 (m-10) cc_final: 0.6945 (m-10) REVERT: A 592 VAL cc_start: 0.8142 (t) cc_final: 0.7623 (m) REVERT: A 601 GLN cc_start: 0.8093 (tt0) cc_final: 0.7781 (tm-30) REVERT: B 342 TRP cc_start: 0.8483 (m100) cc_final: 0.8131 (m100) REVERT: B 348 GLU cc_start: 0.7090 (pt0) cc_final: 0.6733 (pt0) REVERT: B 362 THR cc_start: 0.7557 (m) cc_final: 0.7288 (m) REVERT: B 367 LYS cc_start: 0.7574 (mmtt) cc_final: 0.6630 (mmtt) REVERT: B 383 THR cc_start: 0.8443 (p) cc_final: 0.7935 (p) REVERT: B 398 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7503 (ptm160) REVERT: B 399 LYS cc_start: 0.8262 (mmtp) cc_final: 0.7863 (mmtp) REVERT: B 409 MET cc_start: 0.6264 (mtm) cc_final: 0.5902 (mtm) REVERT: B 412 MET cc_start: 0.6499 (ppp) cc_final: 0.5873 (ppp) REVERT: B 419 ILE cc_start: 0.6946 (mm) cc_final: 0.6584 (mm) REVERT: B 422 GLN cc_start: 0.7847 (tt0) cc_final: 0.7469 (pt0) REVERT: B 429 LEU cc_start: 0.8192 (tp) cc_final: 0.7952 (tp) REVERT: B 431 LYS cc_start: 0.8151 (mptt) cc_final: 0.7734 (mptt) REVERT: B 432 HIS cc_start: 0.7131 (m90) cc_final: 0.6670 (m90) REVERT: B 439 LYS cc_start: 0.8386 (mppt) cc_final: 0.7909 (mppt) REVERT: B 441 GLN cc_start: 0.7298 (mt0) cc_final: 0.7000 (mp10) REVERT: B 442 MET cc_start: 0.6729 (mpp) cc_final: 0.6383 (mpp) REVERT: B 458 TYR cc_start: 0.8204 (t80) cc_final: 0.7746 (t80) REVERT: B 470 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7616 (mtpt) REVERT: B 471 SER cc_start: 0.7504 (p) cc_final: 0.7188 (p) REVERT: B 511 TRP cc_start: 0.7160 (m-90) cc_final: 0.6757 (m-90) REVERT: B 512 MET cc_start: 0.5433 (ttt) cc_final: 0.5165 (ttt) REVERT: B 528 GLN cc_start: 0.7575 (mm-40) cc_final: 0.6835 (mm-40) REVERT: B 541 LEU cc_start: 0.8510 (mt) cc_final: 0.8285 (mt) REVERT: B 542 MET cc_start: 0.6680 (mtp) cc_final: 0.6309 (mtp) REVERT: B 545 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7338 (mt-10) REVERT: B 549 SER cc_start: 0.8163 (t) cc_final: 0.7957 (t) REVERT: B 551 ILE cc_start: 0.8656 (mp) cc_final: 0.8427 (mp) REVERT: B 554 ARG cc_start: 0.7603 (tmm-80) cc_final: 0.7226 (tmm-80) REVERT: B 560 MET cc_start: 0.7974 (tpp) cc_final: 0.7445 (tpp) REVERT: B 563 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7652 (ttm-80) REVERT: B 567 SER cc_start: 0.8069 (t) cc_final: 0.7641 (t) REVERT: B 583 ARG cc_start: 0.8307 (ptp-170) cc_final: 0.7937 (ptp-110) REVERT: C 12 ARG cc_start: 0.8544 (ttt180) cc_final: 0.8288 (ttt180) REVERT: C 25 MET cc_start: 0.7371 (pmm) cc_final: 0.7045 (pmm) REVERT: C 29 MET cc_start: 0.8870 (tpp) cc_final: 0.8439 (mmm) REVERT: C 43 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8266 (mt-10) REVERT: C 52 LYS cc_start: 0.8416 (tptm) cc_final: 0.8207 (tptm) REVERT: C 69 GLU cc_start: 0.8046 (pp20) cc_final: 0.7744 (pp20) REVERT: C 84 MET cc_start: 0.7304 (ptp) cc_final: 0.7042 (ptp) REVERT: C 87 GLU cc_start: 0.8113 (pt0) cc_final: 0.7806 (pt0) REVERT: C 91 LYS cc_start: 0.8563 (tppt) cc_final: 0.7638 (tppt) REVERT: C 93 GLU cc_start: 0.8406 (tt0) cc_final: 0.7910 (tt0) REVERT: C 94 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8235 (ttpt) REVERT: C 95 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7504 (mt-10) REVERT: C 97 ARG cc_start: 0.8578 (mtm110) cc_final: 0.8156 (mtm110) REVERT: C 98 GLU cc_start: 0.7007 (tp30) cc_final: 0.5644 (tp30) REVERT: C 102 ASP cc_start: 0.7688 (m-30) cc_final: 0.6720 (m-30) REVERT: C 126 LYS cc_start: 0.8519 (ttpp) cc_final: 0.7995 (ttpp) REVERT: C 127 MET cc_start: 0.7711 (mmm) cc_final: 0.7055 (mmm) REVERT: C 130 ASP cc_start: 0.7023 (m-30) cc_final: 0.6540 (m-30) REVERT: C 132 TYR cc_start: 0.8124 (m-80) cc_final: 0.7482 (m-80) REVERT: C 133 ARG cc_start: 0.8538 (ttp-110) cc_final: 0.8024 (ttp-110) REVERT: C 153 LYS cc_start: 0.8629 (tppt) cc_final: 0.7807 (tppt) REVERT: C 155 TYR cc_start: 0.7416 (m-10) cc_final: 0.6756 (m-80) REVERT: C 174 LEU cc_start: 0.8146 (mt) cc_final: 0.7772 (mt) REVERT: C 180 PHE cc_start: 0.8196 (m-80) cc_final: 0.7416 (m-80) REVERT: C 200 GLN cc_start: 0.8696 (pt0) cc_final: 0.8429 (pt0) REVERT: C 202 PHE cc_start: 0.8604 (t80) cc_final: 0.8356 (t80) REVERT: C 204 ASP cc_start: 0.7933 (t0) cc_final: 0.7653 (t0) REVERT: C 218 LYS cc_start: 0.7663 (mmpt) cc_final: 0.7380 (mmpt) REVERT: C 224 MET cc_start: 0.7287 (ptm) cc_final: 0.6229 (ptm) REVERT: C 225 GLN cc_start: 0.7517 (mm110) cc_final: 0.6633 (mm110) REVERT: D 14 LYS cc_start: 0.8797 (mttt) cc_final: 0.8445 (mttm) REVERT: D 20 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6756 (tm-30) REVERT: D 25 MET cc_start: 0.7563 (pmm) cc_final: 0.7291 (pmm) REVERT: D 29 MET cc_start: 0.8615 (tpp) cc_final: 0.8235 (mmm) REVERT: D 30 LYS cc_start: 0.7998 (mtmm) cc_final: 0.7472 (mttt) REVERT: D 34 GLU cc_start: 0.7755 (pp20) cc_final: 0.7309 (pp20) REVERT: D 43 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8330 (mt-10) REVERT: D 52 LYS cc_start: 0.8443 (tptm) cc_final: 0.8015 (tptm) REVERT: D 59 ARG cc_start: 0.7954 (mtp-110) cc_final: 0.7686 (mtp180) REVERT: D 65 ILE cc_start: 0.8673 (pt) cc_final: 0.8327 (pt) REVERT: D 66 SER cc_start: 0.8080 (m) cc_final: 0.7458 (m) REVERT: D 84 MET cc_start: 0.7551 (ptp) cc_final: 0.7027 (ptp) REVERT: D 87 GLU cc_start: 0.8139 (pt0) cc_final: 0.7815 (pt0) REVERT: D 91 LYS cc_start: 0.8664 (tppt) cc_final: 0.7540 (tppt) REVERT: D 93 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8078 (mt-10) REVERT: D 94 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8405 (ttpt) REVERT: D 95 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7595 (mt-10) REVERT: D 102 ASP cc_start: 0.7413 (m-30) cc_final: 0.7082 (m-30) REVERT: D 119 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7581 (tp30) REVERT: D 125 LEU cc_start: 0.7986 (mt) cc_final: 0.7751 (mt) REVERT: D 127 MET cc_start: 0.7744 (mmm) cc_final: 0.7320 (mmp) REVERT: D 130 ASP cc_start: 0.7088 (m-30) cc_final: 0.6711 (m-30) REVERT: D 133 ARG cc_start: 0.8246 (ttp-110) cc_final: 0.7956 (ttp-110) REVERT: D 153 LYS cc_start: 0.8456 (tppt) cc_final: 0.7517 (tppt) REVERT: D 155 TYR cc_start: 0.7008 (m-80) cc_final: 0.6780 (m-80) REVERT: D 174 LEU cc_start: 0.8127 (mt) cc_final: 0.7905 (mt) REVERT: D 176 LEU cc_start: 0.8642 (tt) cc_final: 0.7523 (tt) REVERT: D 180 PHE cc_start: 0.8226 (m-80) cc_final: 0.7773 (m-80) REVERT: D 192 ASP cc_start: 0.8146 (p0) cc_final: 0.7653 (p0) REVERT: D 193 LYS cc_start: 0.8090 (mttt) cc_final: 0.7759 (mttt) REVERT: D 195 CYS cc_start: 0.7794 (m) cc_final: 0.7514 (m) REVERT: D 220 SER cc_start: 0.7211 (m) cc_final: 0.6964 (m) REVERT: D 224 MET cc_start: 0.7473 (ptm) cc_final: 0.6311 (ptm) REVERT: D 225 GLN cc_start: 0.7574 (mm110) cc_final: 0.6817 (mm110) REVERT: E 121 CYS cc_start: 0.7370 (m) cc_final: 0.7031 (m) REVERT: E 125 TYR cc_start: 0.7901 (m-80) cc_final: 0.6997 (m-80) REVERT: E 160 ARG cc_start: 0.7408 (mpp80) cc_final: 0.6620 (mpt-90) REVERT: E 168 LYS cc_start: 0.8378 (ttmm) cc_final: 0.7979 (ttmm) REVERT: E 175 LYS cc_start: 0.8687 (ptmt) cc_final: 0.8142 (ptmt) REVERT: E 206 LEU cc_start: 0.6694 (tp) cc_final: 0.6173 (tp) REVERT: E 219 MET cc_start: 0.7582 (mtp) cc_final: 0.7319 (mtp) REVERT: E 236 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7505 (tm-30) REVERT: E 249 MET cc_start: 0.8142 (ppp) cc_final: 0.7929 (ppp) REVERT: E 253 LEU cc_start: 0.8786 (mt) cc_final: 0.8497 (mt) REVERT: E 255 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7343 (tm-30) REVERT: E 256 MET cc_start: 0.7624 (ptm) cc_final: 0.6890 (ptm) REVERT: E 316 TYR cc_start: 0.7678 (t80) cc_final: 0.7318 (t80) REVERT: E 319 ASN cc_start: 0.7955 (t0) cc_final: 0.6753 (t0) REVERT: E 324 LYS cc_start: 0.8049 (mmtt) cc_final: 0.7609 (mmtt) REVERT: E 334 PHE cc_start: 0.8397 (t80) cc_final: 0.8174 (t80) REVERT: E 344 LYS cc_start: 0.8541 (tttt) cc_final: 0.8165 (mttt) REVERT: E 356 MET cc_start: 0.6917 (ppp) cc_final: 0.6500 (ppp) REVERT: E 360 PHE cc_start: 0.8422 (p90) cc_final: 0.8117 (p90) REVERT: E 362 LYS cc_start: 0.8915 (mppt) cc_final: 0.8590 (mmtt) REVERT: E 363 ARG cc_start: 0.8611 (mmp80) cc_final: 0.8359 (mmp80) REVERT: E 371 PHE cc_start: 0.7556 (m-80) cc_final: 0.7183 (m-80) REVERT: F 88 LYS cc_start: 0.8477 (mmmt) cc_final: 0.7977 (mmmt) REVERT: F 110 GLN cc_start: 0.8233 (mm-40) cc_final: 0.8015 (mp10) REVERT: F 125 TYR cc_start: 0.8033 (m-80) cc_final: 0.7302 (m-80) REVERT: F 163 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7671 (mt-10) REVERT: F 175 LYS cc_start: 0.8665 (ptmt) cc_final: 0.8170 (ptmt) REVERT: F 189 ARG cc_start: 0.7714 (tpp-160) cc_final: 0.7235 (tpp-160) REVERT: F 195 ASN cc_start: 0.7723 (t0) cc_final: 0.7394 (t0) REVERT: F 206 LEU cc_start: 0.6620 (tp) cc_final: 0.6183 (tp) REVERT: F 219 MET cc_start: 0.7493 (mtp) cc_final: 0.7157 (mtp) REVERT: F 227 ARG cc_start: 0.7252 (mtm180) cc_final: 0.6885 (mtm180) REVERT: F 249 MET cc_start: 0.8130 (ppp) cc_final: 0.7917 (ppp) REVERT: F 253 LEU cc_start: 0.8731 (mt) cc_final: 0.8515 (mt) REVERT: F 256 MET cc_start: 0.7836 (ptm) cc_final: 0.7421 (ptm) REVERT: F 267 ASP cc_start: 0.7720 (p0) cc_final: 0.7193 (p0) REVERT: F 316 TYR cc_start: 0.7709 (t80) cc_final: 0.7281 (t80) REVERT: F 318 VAL cc_start: 0.8352 (p) cc_final: 0.8079 (m) REVERT: F 319 ASN cc_start: 0.7789 (t0) cc_final: 0.6477 (t0) REVERT: F 320 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7606 (mm-30) REVERT: F 324 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7568 (mmtt) REVERT: F 333 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8331 (mt-10) outliers start: 0 outliers final: 0 residues processed: 656 average time/residue: 0.3096 time to fit residues: 273.9895 Evaluate side-chains 641 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.6980 chunk 16 optimal weight: 0.0670 chunk 84 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 125 optimal weight: 0.0670 chunk 83 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 0.4856 ------------------------------------------------------------------------------- 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 441 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS B 504 GLN C 200 GLN D 11 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12876 Z= 0.189 Angle : 0.675 14.596 17364 Z= 0.348 Chirality : 0.045 0.177 1918 Planarity : 0.005 0.067 2216 Dihedral : 5.398 43.290 1740 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: 0.56 (0.16), residues: 894 sheet: -2.45 (0.52), residues: 78 loop : -0.90 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 368 HIS 0.013 0.001 HIS E 358 PHE 0.044 0.002 PHE D 180 TYR 0.057 0.002 TYR D 101 ARG 0.011 0.001 ARG F 234 *********************** 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 646 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 646 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 LYS cc_start: 0.7400 (mmtt) cc_final: 0.6398 (mmtt) REVERT: A 387 PHE cc_start: 0.7815 (t80) cc_final: 0.6992 (t80) REVERT: A 391 ARG cc_start: 0.8036 (mmt90) cc_final: 0.7620 (mmm-85) REVERT: A 399 LYS cc_start: 0.8238 (mmtp) cc_final: 0.7953 (mmtp) REVERT: A 411 TYR cc_start: 0.7056 (p90) cc_final: 0.6704 (p90) REVERT: A 412 MET cc_start: 0.6257 (ppp) cc_final: 0.5649 (ppp) REVERT: A 416 ASN cc_start: 0.7401 (p0) cc_final: 0.7075 (p0) REVERT: A 431 LYS cc_start: 0.8032 (mppt) cc_final: 0.7748 (mppt) REVERT: A 439 LYS cc_start: 0.8155 (mppt) cc_final: 0.7496 (mppt) REVERT: A 444 GLN cc_start: 0.7761 (mp10) cc_final: 0.7460 (mp10) REVERT: A 445 LEU cc_start: 0.8139 (tp) cc_final: 0.7842 (tp) REVERT: A 458 TYR cc_start: 0.8102 (t80) cc_final: 0.7774 (t80) REVERT: A 460 HIS cc_start: 0.7720 (m90) cc_final: 0.7033 (m90) REVERT: A 511 TRP cc_start: 0.6853 (m-90) cc_final: 0.6646 (m-90) REVERT: A 518 ARG cc_start: 0.7912 (ptp-110) cc_final: 0.7495 (ptp-110) REVERT: A 528 GLN cc_start: 0.7492 (mm-40) cc_final: 0.7192 (mm-40) REVERT: A 534 TYR cc_start: 0.8080 (t80) cc_final: 0.7682 (t80) REVERT: A 536 ILE cc_start: 0.8092 (mm) cc_final: 0.7768 (mm) REVERT: A 541 LEU cc_start: 0.8287 (mt) cc_final: 0.7792 (mt) REVERT: A 542 MET cc_start: 0.6614 (mtp) cc_final: 0.6177 (mtp) REVERT: A 560 MET cc_start: 0.7661 (tpp) cc_final: 0.7017 (tpp) REVERT: A 563 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.7963 (ttm-80) REVERT: A 572 LYS cc_start: 0.7966 (mmmm) cc_final: 0.7472 (mmmm) REVERT: A 591 LYS cc_start: 0.8361 (ptpp) cc_final: 0.8159 (ptpp) REVERT: A 592 VAL cc_start: 0.8116 (t) cc_final: 0.7538 (m) REVERT: A 601 GLN cc_start: 0.8074 (tt0) cc_final: 0.7703 (tm-30) REVERT: B 342 TRP cc_start: 0.8436 (m100) cc_final: 0.8101 (m100) REVERT: B 348 GLU cc_start: 0.7041 (pt0) cc_final: 0.6671 (pt0) REVERT: B 362 THR cc_start: 0.7573 (m) cc_final: 0.7248 (m) REVERT: B 367 LYS cc_start: 0.7590 (mmtt) cc_final: 0.6629 (mmtt) REVERT: B 376 ILE cc_start: 0.7057 (tp) cc_final: 0.6713 (tp) REVERT: B 383 THR cc_start: 0.8423 (p) cc_final: 0.7965 (p) REVERT: B 398 ARG cc_start: 0.7831 (mtp180) cc_final: 0.7514 (ptm160) REVERT: B 399 LYS cc_start: 0.8231 (mmtp) cc_final: 0.7854 (mmtp) REVERT: B 409 MET cc_start: 0.6052 (mtm) cc_final: 0.5634 (mtm) REVERT: B 412 MET cc_start: 0.6229 (ppp) cc_final: 0.5716 (ppp) REVERT: B 417 LEU cc_start: 0.7779 (pt) cc_final: 0.7551 (pt) REVERT: B 419 ILE cc_start: 0.6826 (mm) cc_final: 0.6440 (mm) REVERT: B 422 GLN cc_start: 0.7821 (tt0) cc_final: 0.7313 (pt0) REVERT: B 429 LEU cc_start: 0.8204 (tp) cc_final: 0.7842 (tp) REVERT: B 431 LYS cc_start: 0.8165 (mptt) cc_final: 0.7725 (mptt) REVERT: B 432 HIS cc_start: 0.7127 (m90) cc_final: 0.6635 (m90) REVERT: B 439 LYS cc_start: 0.8297 (mppt) cc_final: 0.7796 (mppt) REVERT: B 458 TYR cc_start: 0.8176 (t80) cc_final: 0.7825 (t80) REVERT: B 463 ASN cc_start: 0.7019 (m-40) cc_final: 0.6808 (m-40) REVERT: B 470 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7783 (mtpt) REVERT: B 471 SER cc_start: 0.7311 (p) cc_final: 0.6915 (p) REVERT: B 473 ASN cc_start: 0.7574 (m110) cc_final: 0.7328 (m110) REVERT: B 483 LYS cc_start: 0.8118 (mttp) cc_final: 0.6966 (mttp) REVERT: B 511 TRP cc_start: 0.7086 (m-90) cc_final: 0.6711 (m-90) REVERT: B 528 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7227 (mm-40) REVERT: B 542 MET cc_start: 0.6493 (mtp) cc_final: 0.6235 (mtp) REVERT: B 545 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7260 (mt-10) REVERT: B 554 ARG cc_start: 0.7627 (tmm-80) cc_final: 0.7247 (tmm-80) REVERT: B 560 MET cc_start: 0.7881 (tpp) cc_final: 0.7340 (tpp) REVERT: B 563 ARG cc_start: 0.8207 (mmm-85) cc_final: 0.7607 (ttm-80) REVERT: B 567 SER cc_start: 0.8000 (t) cc_final: 0.7610 (t) REVERT: B 583 ARG cc_start: 0.8290 (ptp-170) cc_final: 0.7928 (ptp-110) REVERT: C 25 MET cc_start: 0.7451 (pmm) cc_final: 0.7122 (pmm) REVERT: C 29 MET cc_start: 0.8779 (mmt) cc_final: 0.8496 (mmm) REVERT: C 43 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8179 (mt-10) REVERT: C 52 LYS cc_start: 0.8374 (tptm) cc_final: 0.8166 (tptm) REVERT: C 82 GLN cc_start: 0.8328 (pp30) cc_final: 0.7910 (pp30) REVERT: C 84 MET cc_start: 0.7139 (ptp) cc_final: 0.6748 (ptp) REVERT: C 87 GLU cc_start: 0.8097 (pt0) cc_final: 0.7747 (pt0) REVERT: C 91 LYS cc_start: 0.8584 (tppt) cc_final: 0.7583 (tppt) REVERT: C 93 GLU cc_start: 0.8403 (tt0) cc_final: 0.7917 (tt0) REVERT: C 94 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8197 (ttpt) REVERT: C 95 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7462 (mt-10) REVERT: C 97 ARG cc_start: 0.8569 (mtm110) cc_final: 0.8165 (mtm110) REVERT: C 98 GLU cc_start: 0.6924 (tp30) cc_final: 0.5563 (tp30) REVERT: C 102 ASP cc_start: 0.7661 (m-30) cc_final: 0.6642 (m-30) REVERT: C 103 VAL cc_start: 0.8345 (t) cc_final: 0.7997 (t) REVERT: C 126 LYS cc_start: 0.8500 (ttpp) cc_final: 0.7964 (ttpp) REVERT: C 127 MET cc_start: 0.7687 (mmm) cc_final: 0.7054 (mmm) REVERT: C 130 ASP cc_start: 0.7015 (m-30) cc_final: 0.6508 (m-30) REVERT: C 132 TYR cc_start: 0.8088 (m-80) cc_final: 0.7484 (m-80) REVERT: C 133 ARG cc_start: 0.8506 (ttp-110) cc_final: 0.7972 (ttp-110) REVERT: C 153 LYS cc_start: 0.8603 (tppt) cc_final: 0.7789 (tppt) REVERT: C 155 TYR cc_start: 0.7344 (m-10) cc_final: 0.6756 (m-80) REVERT: C 174 LEU cc_start: 0.8062 (mt) cc_final: 0.7740 (mt) REVERT: C 180 PHE cc_start: 0.8133 (m-80) cc_final: 0.7380 (m-80) REVERT: C 204 ASP cc_start: 0.7920 (t0) cc_final: 0.7653 (t0) REVERT: C 218 LYS cc_start: 0.7673 (mmpt) cc_final: 0.7367 (mmpt) REVERT: C 224 MET cc_start: 0.7277 (ptm) cc_final: 0.6188 (ptm) REVERT: C 225 GLN cc_start: 0.7489 (mm110) cc_final: 0.6626 (mm110) REVERT: D 10 VAL cc_start: 0.8858 (t) cc_final: 0.8634 (t) REVERT: D 14 LYS cc_start: 0.8795 (mttt) cc_final: 0.8426 (mttm) REVERT: D 20 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6716 (tm-30) REVERT: D 25 MET cc_start: 0.7429 (pmm) cc_final: 0.7185 (pmm) REVERT: D 29 MET cc_start: 0.8549 (tpp) cc_final: 0.8135 (tpp) REVERT: D 30 LYS cc_start: 0.8041 (mtmm) cc_final: 0.7505 (mttm) REVERT: D 32 VAL cc_start: 0.8241 (t) cc_final: 0.8027 (t) REVERT: D 34 GLU cc_start: 0.7716 (pp20) cc_final: 0.7309 (pp20) REVERT: D 43 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8260 (mt-10) REVERT: D 52 LYS cc_start: 0.8421 (tptm) cc_final: 0.7980 (tptm) REVERT: D 59 ARG cc_start: 0.7978 (mtp-110) cc_final: 0.7689 (mtp180) REVERT: D 65 ILE cc_start: 0.8654 (pt) cc_final: 0.8324 (pt) REVERT: D 66 SER cc_start: 0.8037 (m) cc_final: 0.7414 (m) REVERT: D 84 MET cc_start: 0.7449 (ptp) cc_final: 0.6925 (ptp) REVERT: D 87 GLU cc_start: 0.8135 (pt0) cc_final: 0.7787 (pt0) REVERT: D 91 LYS cc_start: 0.8674 (tppt) cc_final: 0.7900 (tppt) REVERT: D 93 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8057 (mt-10) REVERT: D 97 ARG cc_start: 0.8654 (mtm110) cc_final: 0.7936 (mtm110) REVERT: D 101 TYR cc_start: 0.7776 (m-80) cc_final: 0.7424 (m-80) REVERT: D 102 ASP cc_start: 0.7485 (m-30) cc_final: 0.7162 (m-30) REVERT: D 119 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7603 (tp30) REVERT: D 125 LEU cc_start: 0.7930 (mt) cc_final: 0.7723 (mt) REVERT: D 127 MET cc_start: 0.7679 (mmm) cc_final: 0.7296 (mmp) REVERT: D 130 ASP cc_start: 0.7132 (m-30) cc_final: 0.6673 (m-30) REVERT: D 133 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.7998 (ttp-110) REVERT: D 153 LYS cc_start: 0.8365 (tppt) cc_final: 0.7441 (tppt) REVERT: D 167 GLN cc_start: 0.8157 (tp-100) cc_final: 0.7943 (tp-100) REVERT: D 174 LEU cc_start: 0.8074 (mt) cc_final: 0.7835 (mt) REVERT: D 192 ASP cc_start: 0.8244 (p0) cc_final: 0.7809 (p0) REVERT: D 193 LYS cc_start: 0.8129 (mttt) cc_final: 0.7916 (mttt) REVERT: D 195 CYS cc_start: 0.7860 (m) cc_final: 0.7601 (m) REVERT: D 220 SER cc_start: 0.7205 (m) cc_final: 0.6958 (m) REVERT: D 224 MET cc_start: 0.7413 (ptm) cc_final: 0.6228 (ptm) REVERT: D 225 GLN cc_start: 0.7556 (mm110) cc_final: 0.6776 (mm110) REVERT: E 121 CYS cc_start: 0.7612 (m) cc_final: 0.7359 (m) REVERT: E 125 TYR cc_start: 0.7912 (m-80) cc_final: 0.6991 (m-80) REVERT: E 144 GLU cc_start: 0.7071 (pt0) cc_final: 0.6257 (pt0) REVERT: E 160 ARG cc_start: 0.6929 (mpp80) cc_final: 0.6649 (mpp80) REVERT: E 168 LYS cc_start: 0.8349 (ttmm) cc_final: 0.7904 (ttmm) REVERT: E 175 LYS cc_start: 0.8635 (ptmt) cc_final: 0.8095 (ptmt) REVERT: E 187 MET cc_start: 0.4608 (ttm) cc_final: 0.3424 (ttm) REVERT: E 206 LEU cc_start: 0.6631 (tp) cc_final: 0.6114 (tp) REVERT: E 219 MET cc_start: 0.7624 (mtp) cc_final: 0.7344 (mtp) REVERT: E 234 ARG cc_start: 0.7365 (ttm-80) cc_final: 0.6986 (ttm-80) REVERT: E 236 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7472 (tm-30) REVERT: E 249 MET cc_start: 0.8162 (ppp) cc_final: 0.7885 (ppp) REVERT: E 253 LEU cc_start: 0.8743 (mt) cc_final: 0.8465 (mt) REVERT: E 256 MET cc_start: 0.7595 (ptm) cc_final: 0.7208 (ptm) REVERT: E 316 TYR cc_start: 0.7654 (t80) cc_final: 0.7301 (t80) REVERT: E 324 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7579 (mmtt) REVERT: E 334 PHE cc_start: 0.8368 (t80) cc_final: 0.8151 (t80) REVERT: E 356 MET cc_start: 0.6919 (ppp) cc_final: 0.6453 (ppp) REVERT: E 360 PHE cc_start: 0.8420 (p90) cc_final: 0.8082 (p90) REVERT: E 371 PHE cc_start: 0.7554 (m-80) cc_final: 0.7191 (m-80) REVERT: F 88 LYS cc_start: 0.8483 (mmmt) cc_final: 0.7984 (mmmt) REVERT: F 110 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7951 (mp10) REVERT: F 125 TYR cc_start: 0.7981 (m-80) cc_final: 0.7293 (m-80) REVERT: F 163 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7687 (mt-10) REVERT: F 175 LYS cc_start: 0.8644 (ptmt) cc_final: 0.8151 (ptmt) REVERT: F 187 MET cc_start: 0.3736 (ttt) cc_final: 0.2321 (ttt) REVERT: F 195 ASN cc_start: 0.7723 (t0) cc_final: 0.7419 (t0) REVERT: F 206 LEU cc_start: 0.6596 (tp) cc_final: 0.6153 (tp) REVERT: F 219 MET cc_start: 0.7510 (mtp) cc_final: 0.7219 (mtp) REVERT: F 227 ARG cc_start: 0.7204 (mtm180) cc_final: 0.6847 (mtm180) REVERT: F 249 MET cc_start: 0.8205 (ppp) cc_final: 0.7939 (ppp) REVERT: F 256 MET cc_start: 0.7757 (ptm) cc_final: 0.7388 (ptm) REVERT: F 267 ASP cc_start: 0.7719 (p0) cc_final: 0.7199 (p0) REVERT: F 316 TYR cc_start: 0.7685 (t80) cc_final: 0.7268 (t80) REVERT: F 318 VAL cc_start: 0.8371 (p) cc_final: 0.8099 (m) REVERT: F 319 ASN cc_start: 0.7731 (t0) cc_final: 0.6404 (t0) REVERT: F 320 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7510 (mm-30) REVERT: F 324 LYS cc_start: 0.7978 (mmtt) cc_final: 0.7525 (mmtt) outliers start: 0 outliers final: 0 residues processed: 646 average time/residue: 0.3252 time to fit residues: 287.2710 Evaluate side-chains 639 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 44 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 73 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 116 optimal weight: 0.0970 chunk 135 optimal weight: 2.9990 overall best weight: 0.7736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS A 388 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS B 477 HIS ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 12876 Z= 0.202 Angle : 0.675 11.822 17364 Z= 0.350 Chirality : 0.045 0.186 1918 Planarity : 0.005 0.055 2216 Dihedral : 5.353 38.278 1740 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: -0.39 (0.21), residues: 1538 helix: 0.46 (0.16), residues: 894 sheet: -2.59 (0.50), residues: 80 loop : -0.94 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP D 62 HIS 0.011 0.001 HIS E 358 PHE 0.026 0.002 PHE F 371 TYR 0.046 0.002 TYR D 101 ARG 0.008 0.001 ARG E 160 *********************** 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 632 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 632 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 TRP cc_start: 0.8343 (m100) cc_final: 0.8026 (m100) REVERT: A 362 THR cc_start: 0.7758 (m) cc_final: 0.7509 (m) REVERT: A 367 LYS cc_start: 0.7397 (mmtt) cc_final: 0.6460 (mmtt) REVERT: A 387 PHE cc_start: 0.7826 (t80) cc_final: 0.6988 (t80) REVERT: A 391 ARG cc_start: 0.8086 (mmt90) cc_final: 0.7697 (mmm-85) REVERT: A 399 LYS cc_start: 0.8226 (mmtp) cc_final: 0.7990 (mmtp) REVERT: A 402 HIS cc_start: 0.7501 (t-90) cc_final: 0.7031 (t-90) REVERT: A 411 TYR cc_start: 0.7145 (p90) cc_final: 0.6776 (p90) REVERT: A 412 MET cc_start: 0.6101 (ppp) cc_final: 0.5557 (ppp) REVERT: A 417 LEU cc_start: 0.7690 (pt) cc_final: 0.7480 (pt) REVERT: A 431 LYS cc_start: 0.8054 (mppt) cc_final: 0.7839 (mppt) REVERT: A 439 LYS cc_start: 0.8096 (mppt) cc_final: 0.7501 (mppt) REVERT: A 442 MET cc_start: 0.6845 (mpp) cc_final: 0.6572 (mpp) REVERT: A 445 LEU cc_start: 0.8080 (tp) cc_final: 0.7456 (tp) REVERT: A 456 MET cc_start: 0.7160 (tpt) cc_final: 0.6956 (tpt) REVERT: A 458 TYR cc_start: 0.8096 (t80) cc_final: 0.7867 (t80) REVERT: A 460 HIS cc_start: 0.7882 (m90) cc_final: 0.7529 (m-70) REVERT: A 470 LYS cc_start: 0.8389 (mtpt) cc_final: 0.8082 (mtpt) REVERT: A 511 TRP cc_start: 0.6789 (m-90) cc_final: 0.6534 (m-90) REVERT: A 518 ARG cc_start: 0.7949 (ptp-110) cc_final: 0.7549 (ptp-110) REVERT: A 528 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7271 (mm-40) REVERT: A 534 TYR cc_start: 0.8104 (t80) cc_final: 0.7683 (t80) REVERT: A 536 ILE cc_start: 0.7954 (mm) cc_final: 0.7707 (mm) REVERT: A 541 LEU cc_start: 0.8263 (mt) cc_final: 0.7897 (mt) REVERT: A 560 MET cc_start: 0.7640 (tpp) cc_final: 0.7039 (tpp) REVERT: A 563 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.7973 (ttm-80) REVERT: A 572 LYS cc_start: 0.7957 (mmmm) cc_final: 0.7475 (mmmm) REVERT: A 592 VAL cc_start: 0.8051 (t) cc_final: 0.7566 (m) REVERT: A 601 GLN cc_start: 0.8069 (tt0) cc_final: 0.7722 (tm-30) REVERT: B 342 TRP cc_start: 0.8461 (m100) cc_final: 0.8110 (m100) REVERT: B 348 GLU cc_start: 0.7041 (pt0) cc_final: 0.6686 (pt0) REVERT: B 362 THR cc_start: 0.7594 (m) cc_final: 0.7265 (m) REVERT: B 367 LYS cc_start: 0.7613 (mmtt) cc_final: 0.6685 (mmtt) REVERT: B 369 HIS cc_start: 0.7912 (m90) cc_final: 0.7687 (m-70) REVERT: B 398 ARG cc_start: 0.7843 (mtp180) cc_final: 0.7602 (ptm160) REVERT: B 399 LYS cc_start: 0.8228 (mmtp) cc_final: 0.7975 (mmtp) REVERT: B 409 MET cc_start: 0.6029 (mtm) cc_final: 0.5691 (mtm) REVERT: B 412 MET cc_start: 0.6205 (ppp) cc_final: 0.5691 (ppp) REVERT: B 417 LEU cc_start: 0.7636 (pt) cc_final: 0.7337 (pt) REVERT: B 419 ILE cc_start: 0.6876 (mm) cc_final: 0.6493 (mm) REVERT: B 422 GLN cc_start: 0.7795 (tt0) cc_final: 0.7204 (pt0) REVERT: B 429 LEU cc_start: 0.8205 (tp) cc_final: 0.7955 (tp) REVERT: B 431 LYS cc_start: 0.8126 (mptt) cc_final: 0.7685 (mptt) REVERT: B 439 LYS cc_start: 0.8317 (mppt) cc_final: 0.7781 (mppt) REVERT: B 458 TYR cc_start: 0.8191 (t80) cc_final: 0.7782 (t80) REVERT: B 470 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7780 (mtpt) REVERT: B 471 SER cc_start: 0.7373 (p) cc_final: 0.6932 (p) REVERT: B 483 LYS cc_start: 0.8083 (mttp) cc_final: 0.6956 (mttp) REVERT: B 484 ILE cc_start: 0.7784 (mt) cc_final: 0.7514 (mt) REVERT: B 511 TRP cc_start: 0.6916 (m-90) cc_final: 0.6486 (m-90) REVERT: B 512 MET cc_start: 0.4213 (tmm) cc_final: 0.3823 (tmm) REVERT: B 541 LEU cc_start: 0.8482 (mt) cc_final: 0.8243 (mt) REVERT: B 542 MET cc_start: 0.6709 (mtp) cc_final: 0.6267 (mtp) REVERT: B 545 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7262 (mt-10) REVERT: B 554 ARG cc_start: 0.7668 (tmm-80) cc_final: 0.7357 (tmm-80) REVERT: B 560 MET cc_start: 0.7935 (tpp) cc_final: 0.7356 (tpp) REVERT: B 563 ARG cc_start: 0.8238 (mmm-85) cc_final: 0.7650 (ttm-80) REVERT: B 567 SER cc_start: 0.8017 (t) cc_final: 0.7609 (t) REVERT: B 583 ARG cc_start: 0.8312 (ptp-170) cc_final: 0.7918 (ptp-110) REVERT: C 25 MET cc_start: 0.7444 (pmm) cc_final: 0.7131 (pmm) REVERT: C 29 MET cc_start: 0.8769 (mmt) cc_final: 0.8502 (mmm) REVERT: C 43 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8099 (mt-10) REVERT: C 52 LYS cc_start: 0.8393 (tptm) cc_final: 0.8172 (tptm) REVERT: C 82 GLN cc_start: 0.8360 (pp30) cc_final: 0.7927 (pp30) REVERT: C 84 MET cc_start: 0.7137 (ptp) cc_final: 0.6721 (ptp) REVERT: C 87 GLU cc_start: 0.8045 (pt0) cc_final: 0.7695 (pt0) REVERT: C 91 LYS cc_start: 0.8560 (tppt) cc_final: 0.7607 (tppt) REVERT: C 93 GLU cc_start: 0.8406 (tt0) cc_final: 0.7908 (tt0) REVERT: C 94 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8184 (ttpt) REVERT: C 95 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7487 (mt-10) REVERT: C 97 ARG cc_start: 0.8558 (mtm110) cc_final: 0.8172 (mtm110) REVERT: C 98 GLU cc_start: 0.6972 (tp30) cc_final: 0.5589 (tp30) REVERT: C 102 ASP cc_start: 0.7721 (m-30) cc_final: 0.6682 (m-30) REVERT: C 126 LYS cc_start: 0.8514 (ttpp) cc_final: 0.7995 (ttpp) REVERT: C 127 MET cc_start: 0.7700 (mmm) cc_final: 0.7092 (mmm) REVERT: C 130 ASP cc_start: 0.6989 (m-30) cc_final: 0.6525 (m-30) REVERT: C 132 TYR cc_start: 0.8109 (m-80) cc_final: 0.7509 (m-80) REVERT: C 133 ARG cc_start: 0.8526 (ttp-110) cc_final: 0.7984 (ttp-110) REVERT: C 153 LYS cc_start: 0.8573 (tppt) cc_final: 0.7719 (tppt) REVERT: C 155 TYR cc_start: 0.7435 (m-10) cc_final: 0.7037 (m-80) REVERT: C 174 LEU cc_start: 0.8027 (mt) cc_final: 0.7737 (mt) REVERT: C 204 ASP cc_start: 0.7991 (t0) cc_final: 0.7743 (t0) REVERT: C 218 LYS cc_start: 0.7685 (mmpt) cc_final: 0.7421 (mmpt) REVERT: C 224 MET cc_start: 0.7457 (ptm) cc_final: 0.6161 (ptm) REVERT: C 225 GLN cc_start: 0.7463 (mm110) cc_final: 0.6615 (mm110) REVERT: D 6 LYS cc_start: 0.8303 (ttpp) cc_final: 0.8063 (ttpp) REVERT: D 10 VAL cc_start: 0.8870 (t) cc_final: 0.8649 (t) REVERT: D 14 LYS cc_start: 0.8798 (mttt) cc_final: 0.8433 (mttm) REVERT: D 20 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6686 (tm-30) REVERT: D 25 MET cc_start: 0.7496 (pmm) cc_final: 0.7214 (pmm) REVERT: D 29 MET cc_start: 0.8564 (tpp) cc_final: 0.8158 (tpp) REVERT: D 30 LYS cc_start: 0.8025 (mtmm) cc_final: 0.7490 (mttm) REVERT: D 32 VAL cc_start: 0.8280 (t) cc_final: 0.8075 (t) REVERT: D 34 GLU cc_start: 0.7729 (pp20) cc_final: 0.7302 (pp20) REVERT: D 43 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8413 (mt-10) REVERT: D 52 LYS cc_start: 0.8426 (tptm) cc_final: 0.8010 (tptm) REVERT: D 59 ARG cc_start: 0.7986 (mtp-110) cc_final: 0.7731 (mtp180) REVERT: D 65 ILE cc_start: 0.8691 (pt) cc_final: 0.8401 (pt) REVERT: D 66 SER cc_start: 0.8108 (m) cc_final: 0.7545 (m) REVERT: D 84 MET cc_start: 0.7422 (ptp) cc_final: 0.6899 (ptp) REVERT: D 87 GLU cc_start: 0.8125 (pt0) cc_final: 0.7820 (pt0) REVERT: D 91 LYS cc_start: 0.8690 (tppt) cc_final: 0.7968 (tppt) REVERT: D 93 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7913 (mt-10) REVERT: D 94 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8447 (ttpt) REVERT: D 97 ARG cc_start: 0.8689 (mtm110) cc_final: 0.8219 (ttm110) REVERT: D 102 ASP cc_start: 0.7429 (m-30) cc_final: 0.7124 (m-30) REVERT: D 119 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7561 (tp30) REVERT: D 127 MET cc_start: 0.7703 (mmm) cc_final: 0.7304 (mmp) REVERT: D 130 ASP cc_start: 0.7120 (m-30) cc_final: 0.6644 (m-30) REVERT: D 133 ARG cc_start: 0.8411 (ttp-110) cc_final: 0.7999 (ttp-110) REVERT: D 153 LYS cc_start: 0.8370 (tppt) cc_final: 0.7497 (tppt) REVERT: D 155 TYR cc_start: 0.7304 (m-80) cc_final: 0.7071 (m-80) REVERT: D 170 HIS cc_start: 0.8075 (t-90) cc_final: 0.7764 (t-90) REVERT: D 174 LEU cc_start: 0.8176 (mt) cc_final: 0.7908 (mt) REVERT: D 192 ASP cc_start: 0.8196 (p0) cc_final: 0.7726 (p0) REVERT: D 193 LYS cc_start: 0.8124 (mttt) cc_final: 0.7804 (mttt) REVERT: D 195 CYS cc_start: 0.7892 (m) cc_final: 0.7611 (m) REVERT: D 204 ASP cc_start: 0.7537 (t0) cc_final: 0.7331 (t0) REVERT: D 220 SER cc_start: 0.7241 (m) cc_final: 0.6965 (m) REVERT: E 121 CYS cc_start: 0.7556 (m) cc_final: 0.7265 (m) REVERT: E 125 TYR cc_start: 0.7824 (m-80) cc_final: 0.6907 (m-80) REVERT: E 160 ARG cc_start: 0.7004 (mpp80) cc_final: 0.6739 (mpp80) REVERT: E 168 LYS cc_start: 0.8357 (ttmm) cc_final: 0.7905 (ttmm) REVERT: E 175 LYS cc_start: 0.8666 (ptmt) cc_final: 0.8125 (ptmt) REVERT: E 187 MET cc_start: 0.4312 (ttm) cc_final: 0.3807 (ttm) REVERT: E 206 LEU cc_start: 0.6659 (tp) cc_final: 0.6318 (tp) REVERT: E 215 LEU cc_start: 0.5302 (tp) cc_final: 0.4949 (tt) REVERT: E 219 MET cc_start: 0.7609 (mtp) cc_final: 0.7201 (mtp) REVERT: E 234 ARG cc_start: 0.7335 (ttm-80) cc_final: 0.7042 (ttm-80) REVERT: E 236 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7431 (tm-30) REVERT: E 249 MET cc_start: 0.8176 (ppp) cc_final: 0.7903 (ppp) REVERT: E 253 LEU cc_start: 0.8762 (mt) cc_final: 0.8498 (mt) REVERT: E 255 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7317 (tm-30) REVERT: E 256 MET cc_start: 0.7614 (ptm) cc_final: 0.6898 (ptm) REVERT: E 316 TYR cc_start: 0.7665 (t80) cc_final: 0.7294 (t80) REVERT: E 324 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7568 (mmtt) REVERT: E 340 LYS cc_start: 0.8728 (mttp) cc_final: 0.8318 (tptp) REVERT: E 344 LYS cc_start: 0.8515 (tmmt) cc_final: 0.8215 (mttt) REVERT: E 356 MET cc_start: 0.7020 (ppp) cc_final: 0.6816 (ppp) REVERT: E 360 PHE cc_start: 0.8411 (p90) cc_final: 0.8149 (p90) REVERT: E 371 PHE cc_start: 0.7559 (m-80) cc_final: 0.7221 (m-80) REVERT: F 88 LYS cc_start: 0.8467 (mmmt) cc_final: 0.7963 (mmmt) REVERT: F 110 GLN cc_start: 0.8290 (mm-40) cc_final: 0.8065 (mp10) REVERT: F 187 MET cc_start: 0.3352 (ttt) cc_final: 0.1466 (ttt) REVERT: F 195 ASN cc_start: 0.7735 (t0) cc_final: 0.7415 (t0) REVERT: F 206 LEU cc_start: 0.6457 (tp) cc_final: 0.6026 (tp) REVERT: F 219 MET cc_start: 0.7530 (mtp) cc_final: 0.7248 (mtp) REVERT: F 227 ARG cc_start: 0.7193 (mtm180) cc_final: 0.6817 (mtm180) REVERT: F 249 MET cc_start: 0.8247 (ppp) cc_final: 0.7954 (ppp) REVERT: F 253 LEU cc_start: 0.8728 (mt) cc_final: 0.8480 (mt) REVERT: F 256 MET cc_start: 0.7770 (ptm) cc_final: 0.7376 (ptm) REVERT: F 267 ASP cc_start: 0.7732 (p0) cc_final: 0.7215 (p0) REVERT: F 316 TYR cc_start: 0.7698 (t80) cc_final: 0.7272 (t80) REVERT: F 318 VAL cc_start: 0.8349 (p) cc_final: 0.8084 (m) REVERT: F 319 ASN cc_start: 0.7753 (t0) cc_final: 0.6401 (t0) REVERT: F 320 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7544 (mm-30) REVERT: F 324 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7520 (mmtt) REVERT: F 344 LYS cc_start: 0.8267 (tmmt) cc_final: 0.8006 (tmmt) REVERT: F 371 PHE cc_start: 0.7552 (m-80) cc_final: 0.7075 (m-80) outliers start: 0 outliers final: 0 residues processed: 632 average time/residue: 0.3178 time to fit residues: 273.1344 Evaluate side-chains 624 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN E 243 GLN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12876 Z= 0.278 Angle : 0.737 12.202 17364 Z= 0.391 Chirality : 0.049 0.261 1918 Planarity : 0.005 0.049 2216 Dihedral : 5.510 37.031 1740 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.67 (0.21), residues: 1538 helix: 0.23 (0.16), residues: 896 sheet: -2.48 (0.49), residues: 80 loop : -1.08 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP D 62 HIS 0.010 0.002 HIS C 170 PHE 0.026 0.002 PHE D 202 TYR 0.044 0.002 TYR D 101 ARG 0.024 0.001 ARG D 144 *********************** 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 660 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 TRP cc_start: 0.8473 (m100) cc_final: 0.8095 (m100) REVERT: A 362 THR cc_start: 0.7808 (m) cc_final: 0.7515 (m) REVERT: A 367 LYS cc_start: 0.7433 (mmtt) cc_final: 0.6558 (mmtt) REVERT: A 387 PHE cc_start: 0.7865 (t80) cc_final: 0.6969 (t80) REVERT: A 391 ARG cc_start: 0.8045 (mmt90) cc_final: 0.7608 (mmm-85) REVERT: A 399 LYS cc_start: 0.8224 (mmtp) cc_final: 0.8023 (mmtp) REVERT: A 412 MET cc_start: 0.6337 (ppp) cc_final: 0.5791 (ppp) REVERT: A 417 LEU cc_start: 0.7746 (pt) cc_final: 0.7210 (pt) REVERT: A 439 LYS cc_start: 0.8369 (mppt) cc_final: 0.7722 (mppt) REVERT: A 444 GLN cc_start: 0.7490 (pt0) cc_final: 0.7232 (pt0) REVERT: A 445 LEU cc_start: 0.8393 (tp) cc_final: 0.8089 (tp) REVERT: A 457 ASP cc_start: 0.7013 (t0) cc_final: 0.6790 (t0) REVERT: A 460 HIS cc_start: 0.7969 (m90) cc_final: 0.7672 (m-70) REVERT: A 511 TRP cc_start: 0.6918 (m-90) cc_final: 0.6598 (m-90) REVERT: A 518 ARG cc_start: 0.8134 (ptp-110) cc_final: 0.7693 (ptp-110) REVERT: A 534 TYR cc_start: 0.8090 (t80) cc_final: 0.7677 (t80) REVERT: A 541 LEU cc_start: 0.8466 (mt) cc_final: 0.8103 (mt) REVERT: A 563 ARG cc_start: 0.8610 (mmm-85) cc_final: 0.8000 (ttm-80) REVERT: A 572 LYS cc_start: 0.8084 (mmmm) cc_final: 0.7606 (mmmm) REVERT: A 592 VAL cc_start: 0.8073 (t) cc_final: 0.7523 (m) REVERT: A 601 GLN cc_start: 0.8136 (tt0) cc_final: 0.7791 (tm-30) REVERT: B 342 TRP cc_start: 0.8496 (m100) cc_final: 0.8214 (m100) REVERT: B 348 GLU cc_start: 0.7133 (pt0) cc_final: 0.6740 (pt0) REVERT: B 362 THR cc_start: 0.7633 (m) cc_final: 0.7302 (m) REVERT: B 367 LYS cc_start: 0.7635 (mmtt) cc_final: 0.6738 (mmtt) REVERT: B 369 HIS cc_start: 0.7945 (m90) cc_final: 0.7711 (m-70) REVERT: B 375 LYS cc_start: 0.7235 (ttpp) cc_final: 0.7002 (ttpp) REVERT: B 398 ARG cc_start: 0.7910 (mtp180) cc_final: 0.7179 (ptm160) REVERT: B 399 LYS cc_start: 0.8275 (mmtp) cc_final: 0.8036 (mmtp) REVERT: B 412 MET cc_start: 0.6230 (ppp) cc_final: 0.5658 (ppp) REVERT: B 417 LEU cc_start: 0.7674 (pt) cc_final: 0.7430 (pt) REVERT: B 419 ILE cc_start: 0.6963 (mm) cc_final: 0.6618 (mm) REVERT: B 422 GLN cc_start: 0.8002 (tt0) cc_final: 0.7420 (pt0) REVERT: B 429 LEU cc_start: 0.8184 (tp) cc_final: 0.7840 (tp) REVERT: B 431 LYS cc_start: 0.8187 (mptt) cc_final: 0.7796 (mptt) REVERT: B 439 LYS cc_start: 0.8507 (mppt) cc_final: 0.7963 (mppt) REVERT: B 442 MET cc_start: 0.6556 (mpp) cc_final: 0.6271 (mpp) REVERT: B 458 TYR cc_start: 0.8187 (t80) cc_final: 0.7716 (t80) REVERT: B 466 HIS cc_start: 0.8279 (t-90) cc_final: 0.7953 (t-90) REVERT: B 470 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7960 (mtpt) REVERT: B 471 SER cc_start: 0.7679 (p) cc_final: 0.7306 (p) REVERT: B 483 LYS cc_start: 0.8135 (mttp) cc_final: 0.7309 (mttp) REVERT: B 484 ILE cc_start: 0.7831 (mt) cc_final: 0.7623 (mt) REVERT: B 511 TRP cc_start: 0.7070 (m-90) cc_final: 0.6709 (m-90) REVERT: B 528 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7126 (mm-40) REVERT: B 541 LEU cc_start: 0.8533 (mt) cc_final: 0.8217 (mt) REVERT: B 542 MET cc_start: 0.6831 (mtp) cc_final: 0.6587 (mtp) REVERT: B 545 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7335 (mt-10) REVERT: B 554 ARG cc_start: 0.7778 (tmm-80) cc_final: 0.7493 (tmm-80) REVERT: B 560 MET cc_start: 0.8065 (tpp) cc_final: 0.7345 (tpp) REVERT: B 563 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.7675 (ttm-80) REVERT: B 567 SER cc_start: 0.8170 (t) cc_final: 0.7957 (t) REVERT: B 583 ARG cc_start: 0.8338 (ptp-170) cc_final: 0.8009 (ptp-110) REVERT: B 593 LYS cc_start: 0.7855 (ttpp) cc_final: 0.7275 (tptp) REVERT: B 618 ARG cc_start: 0.7453 (ptm160) cc_final: 0.7222 (ptm160) REVERT: C 25 MET cc_start: 0.7430 (pmm) cc_final: 0.7056 (pmm) REVERT: C 29 MET cc_start: 0.8808 (mmt) cc_final: 0.8475 (mmm) REVERT: C 43 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8137 (mt-10) REVERT: C 59 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.7762 (mtp-110) REVERT: C 82 GLN cc_start: 0.8437 (pp30) cc_final: 0.7999 (pp30) REVERT: C 84 MET cc_start: 0.7224 (ptp) cc_final: 0.6796 (ptp) REVERT: C 87 GLU cc_start: 0.8062 (pt0) cc_final: 0.7728 (pt0) REVERT: C 91 LYS cc_start: 0.8614 (tppt) cc_final: 0.7502 (tppt) REVERT: C 93 GLU cc_start: 0.8519 (tt0) cc_final: 0.8034 (tt0) REVERT: C 94 LYS cc_start: 0.8603 (ttpt) cc_final: 0.8262 (ttpt) REVERT: C 95 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7552 (mt-10) REVERT: C 97 ARG cc_start: 0.8600 (mtm110) cc_final: 0.8245 (mtm110) REVERT: C 98 GLU cc_start: 0.7112 (tp30) cc_final: 0.5753 (tp30) REVERT: C 102 ASP cc_start: 0.7794 (m-30) cc_final: 0.6750 (m-30) REVERT: C 126 LYS cc_start: 0.8585 (ttpp) cc_final: 0.8251 (ttpp) REVERT: C 128 LYS cc_start: 0.8134 (tttt) cc_final: 0.7667 (tttt) REVERT: C 132 TYR cc_start: 0.8261 (m-80) cc_final: 0.7505 (m-80) REVERT: C 133 ARG cc_start: 0.8519 (ttp-110) cc_final: 0.7530 (ttp80) REVERT: C 153 LYS cc_start: 0.8619 (tppt) cc_final: 0.7764 (tppt) REVERT: C 155 TYR cc_start: 0.7511 (m-10) cc_final: 0.7291 (m-80) REVERT: C 174 LEU cc_start: 0.8087 (mt) cc_final: 0.7803 (mt) REVERT: C 197 LEU cc_start: 0.8423 (mm) cc_final: 0.8208 (mm) REVERT: C 218 LYS cc_start: 0.7707 (mmpt) cc_final: 0.7420 (mmpt) REVERT: C 224 MET cc_start: 0.7466 (ptm) cc_final: 0.6243 (ptm) REVERT: C 225 GLN cc_start: 0.7457 (mm110) cc_final: 0.6627 (mm110) REVERT: D 6 LYS cc_start: 0.8336 (ttpp) cc_final: 0.8115 (ttpp) REVERT: D 14 LYS cc_start: 0.8839 (mttt) cc_final: 0.8466 (mttm) REVERT: D 20 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6948 (tm-30) REVERT: D 25 MET cc_start: 0.7602 (pmm) cc_final: 0.7321 (pmm) REVERT: D 29 MET cc_start: 0.8632 (tpp) cc_final: 0.8168 (tpp) REVERT: D 30 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7568 (mtmm) REVERT: D 32 VAL cc_start: 0.8421 (t) cc_final: 0.8181 (t) REVERT: D 34 GLU cc_start: 0.7852 (pp20) cc_final: 0.7397 (pp20) REVERT: D 43 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8370 (mt-10) REVERT: D 52 LYS cc_start: 0.8478 (tptm) cc_final: 0.8070 (tptm) REVERT: D 65 ILE cc_start: 0.8745 (pt) cc_final: 0.8520 (pt) REVERT: D 66 SER cc_start: 0.8111 (m) cc_final: 0.7499 (m) REVERT: D 84 MET cc_start: 0.7501 (ptp) cc_final: 0.6950 (ptp) REVERT: D 87 GLU cc_start: 0.8120 (pt0) cc_final: 0.7805 (pt0) REVERT: D 91 LYS cc_start: 0.8718 (tppt) cc_final: 0.8060 (tppt) REVERT: D 97 ARG cc_start: 0.8710 (mtm110) cc_final: 0.8456 (mtm110) REVERT: D 102 ASP cc_start: 0.7524 (m-30) cc_final: 0.7186 (m-30) REVERT: D 119 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7587 (tp30) REVERT: D 127 MET cc_start: 0.7853 (mmm) cc_final: 0.7418 (mmp) REVERT: D 128 LYS cc_start: 0.8015 (tttt) cc_final: 0.7614 (tttt) REVERT: D 130 ASP cc_start: 0.7125 (m-30) cc_final: 0.6495 (m-30) REVERT: D 133 ARG cc_start: 0.8466 (ttp-110) cc_final: 0.7961 (ttp-110) REVERT: D 153 LYS cc_start: 0.8451 (tppt) cc_final: 0.7583 (tppt) REVERT: D 155 TYR cc_start: 0.7447 (m-80) cc_final: 0.7007 (m-80) REVERT: D 170 HIS cc_start: 0.8173 (t-90) cc_final: 0.7957 (t-90) REVERT: D 172 ILE cc_start: 0.8593 (tt) cc_final: 0.8053 (tt) REVERT: D 174 LEU cc_start: 0.8267 (mt) cc_final: 0.7990 (mt) REVERT: D 192 ASP cc_start: 0.8183 (p0) cc_final: 0.7804 (p0) REVERT: D 193 LYS cc_start: 0.8173 (mttt) cc_final: 0.7830 (mttt) REVERT: D 195 CYS cc_start: 0.8032 (m) cc_final: 0.7782 (m) REVERT: D 220 SER cc_start: 0.7334 (m) cc_final: 0.7109 (m) REVERT: E 97 LYS cc_start: 0.7945 (mttt) cc_final: 0.7689 (tttt) REVERT: E 121 CYS cc_start: 0.7378 (m) cc_final: 0.7071 (m) REVERT: E 125 TYR cc_start: 0.7975 (m-80) cc_final: 0.7095 (m-80) REVERT: E 144 GLU cc_start: 0.7496 (pp20) cc_final: 0.6691 (pp20) REVERT: E 146 MET cc_start: 0.4950 (tpt) cc_final: 0.4179 (tpt) REVERT: E 160 ARG cc_start: 0.7029 (mpp80) cc_final: 0.6707 (mpp80) REVERT: E 168 LYS cc_start: 0.8430 (ttmm) cc_final: 0.7989 (ttmm) REVERT: E 175 LYS cc_start: 0.8757 (ptmt) cc_final: 0.8226 (ptmt) REVERT: E 187 MET cc_start: 0.4107 (ttm) cc_final: 0.3093 (ttm) REVERT: E 192 LYS cc_start: 0.7733 (ttpt) cc_final: 0.7443 (ttpt) REVERT: E 206 LEU cc_start: 0.6777 (tp) cc_final: 0.6511 (tp) REVERT: E 212 SER cc_start: 0.7474 (p) cc_final: 0.7231 (p) REVERT: E 215 LEU cc_start: 0.5097 (tp) cc_final: 0.4533 (tt) REVERT: E 219 MET cc_start: 0.7632 (mtp) cc_final: 0.7208 (mtp) REVERT: E 236 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7531 (tm-30) REVERT: E 249 MET cc_start: 0.8244 (ppp) cc_final: 0.8035 (ppp) REVERT: E 253 LEU cc_start: 0.8791 (mt) cc_final: 0.8574 (mt) REVERT: E 256 MET cc_start: 0.7662 (ptm) cc_final: 0.7333 (ptm) REVERT: E 316 TYR cc_start: 0.7687 (t80) cc_final: 0.7323 (t80) REVERT: E 319 ASN cc_start: 0.8038 (t0) cc_final: 0.6858 (t0) REVERT: E 320 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7633 (mm-30) REVERT: E 324 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7605 (mmtt) REVERT: E 340 LYS cc_start: 0.8774 (mttp) cc_final: 0.8342 (tptp) REVERT: E 344 LYS cc_start: 0.8576 (tmmt) cc_final: 0.8336 (mttt) REVERT: E 356 MET cc_start: 0.7076 (ppp) cc_final: 0.6618 (ppp) REVERT: E 362 LYS cc_start: 0.8855 (mppt) cc_final: 0.8622 (mmtt) REVERT: E 363 ARG cc_start: 0.8624 (mmp80) cc_final: 0.8349 (mmp80) REVERT: E 371 PHE cc_start: 0.7702 (m-80) cc_final: 0.7347 (m-80) REVERT: F 88 LYS cc_start: 0.8473 (mmmt) cc_final: 0.7980 (mmmt) REVERT: F 175 LYS cc_start: 0.8708 (ptmt) cc_final: 0.8213 (ptmt) REVERT: F 187 MET cc_start: 0.3467 (ttt) cc_final: 0.2465 (ttt) REVERT: F 189 ARG cc_start: 0.7737 (tpp-160) cc_final: 0.7024 (tpp-160) REVERT: F 195 ASN cc_start: 0.7929 (t0) cc_final: 0.7494 (t0) REVERT: F 206 LEU cc_start: 0.6413 (tp) cc_final: 0.5779 (tp) REVERT: F 227 ARG cc_start: 0.7307 (mtm180) cc_final: 0.6843 (mtm180) REVERT: F 249 MET cc_start: 0.8299 (ppp) cc_final: 0.8026 (ppp) REVERT: F 253 LEU cc_start: 0.8744 (mt) cc_final: 0.8518 (mt) REVERT: F 256 MET cc_start: 0.7823 (ptm) cc_final: 0.7422 (ptm) REVERT: F 267 ASP cc_start: 0.7814 (p0) cc_final: 0.7283 (p0) REVERT: F 313 LEU cc_start: 0.8036 (mt) cc_final: 0.7829 (mt) REVERT: F 316 TYR cc_start: 0.7697 (t80) cc_final: 0.7318 (t80) REVERT: F 319 ASN cc_start: 0.7797 (t0) cc_final: 0.6412 (t0) REVERT: F 320 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7640 (mm-30) REVERT: F 324 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7550 (mmtt) REVERT: F 344 LYS cc_start: 0.8327 (tmmt) cc_final: 0.8080 (tmmt) REVERT: F 371 PHE cc_start: 0.7663 (m-80) cc_final: 0.7170 (m-80) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.3084 time to fit residues: 273.2680 Evaluate side-chains 643 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 643 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 0.0270 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS A 553 ASN ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN D 200 GLN E 195 ASN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12876 Z= 0.209 Angle : 0.723 10.757 17364 Z= 0.373 Chirality : 0.047 0.214 1918 Planarity : 0.005 0.055 2216 Dihedral : 5.527 41.020 1740 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1538 helix: 0.24 (0.16), residues: 894 sheet: -2.59 (0.49), residues: 80 loop : -0.99 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 368 HIS 0.010 0.001 HIS F 358 PHE 0.025 0.002 PHE F 371 TYR 0.045 0.003 TYR B 532 ARG 0.021 0.001 ARG D 63 ********************** 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 642 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 642 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: A 342 TRP cc_start: 0.8332 (m100) cc_final: 0.7969 (m100) REVERT: A 362 THR cc_start: 0.7682 (m) cc_final: 0.7355 (m) REVERT: A 367 LYS cc_start: 0.7467 (mmtt) cc_final: 0.6573 (mmtt) REVERT: A 375 LYS cc_start: 0.7247 (tmtt) cc_final: 0.6960 (tmtt) REVERT: A 387 PHE cc_start: 0.7792 (t80) cc_final: 0.6914 (t80) REVERT: A 391 ARG cc_start: 0.8003 (mmt90) cc_final: 0.7652 (mmm-85) REVERT: A 399 LYS cc_start: 0.8184 (mmtp) cc_final: 0.7964 (mmtp) REVERT: A 404 ASN cc_start: 0.7396 (m110) cc_final: 0.6898 (m110) REVERT: A 412 MET cc_start: 0.6277 (ppp) cc_final: 0.5712 (ppp) REVERT: A 417 LEU cc_start: 0.7821 (pt) cc_final: 0.7580 (pt) REVERT: A 439 LYS cc_start: 0.8259 (mppt) cc_final: 0.7599 (mppt) REVERT: A 445 LEU cc_start: 0.8304 (tp) cc_final: 0.8062 (tp) REVERT: A 484 ILE cc_start: 0.7779 (mt) cc_final: 0.7497 (mt) REVERT: A 518 ARG cc_start: 0.8005 (ptp-110) cc_final: 0.7747 (ptp-110) REVERT: A 534 TYR cc_start: 0.8061 (t80) cc_final: 0.7679 (t80) REVERT: A 541 LEU cc_start: 0.8481 (mt) cc_final: 0.8059 (mt) REVERT: A 560 MET cc_start: 0.7583 (tpp) cc_final: 0.6966 (tpp) REVERT: A 563 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.7982 (ttm-80) REVERT: A 572 LYS cc_start: 0.8001 (mmmm) cc_final: 0.7510 (mmmm) REVERT: A 592 VAL cc_start: 0.8093 (t) cc_final: 0.7547 (m) REVERT: A 601 GLN cc_start: 0.8098 (tt0) cc_final: 0.7753 (tm-30) REVERT: B 342 TRP cc_start: 0.8408 (m100) cc_final: 0.8089 (m100) REVERT: B 345 GLU cc_start: 0.6277 (mp0) cc_final: 0.5857 (mp0) REVERT: B 362 THR cc_start: 0.7647 (m) cc_final: 0.7307 (m) REVERT: B 367 LYS cc_start: 0.7608 (mmtt) cc_final: 0.6650 (mmtt) REVERT: B 398 ARG cc_start: 0.7878 (mtp180) cc_final: 0.7103 (ptm160) REVERT: B 399 LYS cc_start: 0.8194 (mmtp) cc_final: 0.7930 (mmtp) REVERT: B 412 MET cc_start: 0.6303 (ppp) cc_final: 0.5692 (ppp) REVERT: B 417 LEU cc_start: 0.7781 (pt) cc_final: 0.7507 (pt) REVERT: B 419 ILE cc_start: 0.6870 (mm) cc_final: 0.6398 (mm) REVERT: B 422 GLN cc_start: 0.7858 (tt0) cc_final: 0.7505 (pt0) REVERT: B 429 LEU cc_start: 0.8121 (tp) cc_final: 0.7867 (tp) REVERT: B 431 LYS cc_start: 0.8167 (mptt) cc_final: 0.7712 (mptt) REVERT: B 439 LYS cc_start: 0.8385 (mppt) cc_final: 0.7886 (mppt) REVERT: B 458 TYR cc_start: 0.8175 (t80) cc_final: 0.7736 (t80) REVERT: B 470 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7846 (mtpt) REVERT: B 471 SER cc_start: 0.7438 (p) cc_final: 0.7021 (p) REVERT: B 483 LYS cc_start: 0.8170 (mttp) cc_final: 0.7329 (mttp) REVERT: B 484 ILE cc_start: 0.7759 (mt) cc_final: 0.7472 (mt) REVERT: B 516 VAL cc_start: 0.8581 (t) cc_final: 0.8343 (t) REVERT: B 542 MET cc_start: 0.6750 (mtp) cc_final: 0.6331 (mtp) REVERT: B 545 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 554 ARG cc_start: 0.7779 (tmm-80) cc_final: 0.7520 (tmm-80) REVERT: B 560 MET cc_start: 0.8000 (tpp) cc_final: 0.7312 (tpp) REVERT: B 563 ARG cc_start: 0.8202 (mmm-85) cc_final: 0.7597 (ttm-80) REVERT: B 567 SER cc_start: 0.8103 (t) cc_final: 0.7771 (t) REVERT: B 583 ARG cc_start: 0.8342 (ptp-170) cc_final: 0.7966 (ptp-110) REVERT: B 618 ARG cc_start: 0.7475 (ptm160) cc_final: 0.7223 (ptm160) REVERT: C 6 LYS cc_start: 0.8522 (ttpp) cc_final: 0.8222 (ttpp) REVERT: C 25 MET cc_start: 0.7393 (pmm) cc_final: 0.7062 (pmm) REVERT: C 29 MET cc_start: 0.8769 (mmt) cc_final: 0.8553 (mmm) REVERT: C 30 LYS cc_start: 0.7965 (mtmm) cc_final: 0.7681 (mttt) REVERT: C 43 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8171 (mt-10) REVERT: C 52 LYS cc_start: 0.8392 (tptt) cc_final: 0.8162 (tptt) REVERT: C 82 GLN cc_start: 0.8399 (pp30) cc_final: 0.7958 (pp30) REVERT: C 84 MET cc_start: 0.7139 (ptp) cc_final: 0.6689 (ptp) REVERT: C 87 GLU cc_start: 0.8029 (pt0) cc_final: 0.7672 (pt0) REVERT: C 91 LYS cc_start: 0.8606 (tppt) cc_final: 0.7570 (tppt) REVERT: C 92 VAL cc_start: 0.8927 (m) cc_final: 0.8663 (m) REVERT: C 93 GLU cc_start: 0.8498 (tt0) cc_final: 0.7990 (tt0) REVERT: C 94 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8258 (ttpt) REVERT: C 95 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7534 (mt-10) REVERT: C 97 ARG cc_start: 0.8576 (mtm110) cc_final: 0.8261 (mtm110) REVERT: C 98 GLU cc_start: 0.6984 (tp30) cc_final: 0.6190 (tp30) REVERT: C 114 LYS cc_start: 0.7790 (mttt) cc_final: 0.7554 (mttt) REVERT: C 125 LEU cc_start: 0.8024 (mt) cc_final: 0.7818 (mt) REVERT: C 126 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8369 (ttpp) REVERT: C 132 TYR cc_start: 0.8102 (m-80) cc_final: 0.7558 (m-80) REVERT: C 133 ARG cc_start: 0.8495 (ttp-110) cc_final: 0.7851 (ttp-110) REVERT: C 153 LYS cc_start: 0.8545 (tppt) cc_final: 0.7678 (tppt) REVERT: C 155 TYR cc_start: 0.7442 (m-10) cc_final: 0.7137 (m-80) REVERT: C 174 LEU cc_start: 0.7985 (mt) cc_final: 0.7713 (mt) REVERT: C 195 CYS cc_start: 0.8097 (m) cc_final: 0.7869 (m) REVERT: C 218 LYS cc_start: 0.7722 (mmpt) cc_final: 0.7392 (mmpt) REVERT: C 224 MET cc_start: 0.7506 (ptm) cc_final: 0.6227 (ptm) REVERT: C 225 GLN cc_start: 0.7441 (mm110) cc_final: 0.6592 (mm110) REVERT: D 10 VAL cc_start: 0.8880 (t) cc_final: 0.8643 (t) REVERT: D 14 LYS cc_start: 0.8825 (mttt) cc_final: 0.8449 (mttm) REVERT: D 20 GLU cc_start: 0.6945 (tm-30) cc_final: 0.6584 (tm-30) REVERT: D 25 MET cc_start: 0.7534 (pmm) cc_final: 0.7293 (pmm) REVERT: D 29 MET cc_start: 0.8614 (tpp) cc_final: 0.8206 (mmm) REVERT: D 30 LYS cc_start: 0.8057 (mtmm) cc_final: 0.7503 (mttm) REVERT: D 32 VAL cc_start: 0.8367 (t) cc_final: 0.8123 (t) REVERT: D 34 GLU cc_start: 0.7780 (pp20) cc_final: 0.7317 (pp20) REVERT: D 43 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8318 (mt-10) REVERT: D 52 LYS cc_start: 0.8469 (tptm) cc_final: 0.8036 (tptm) REVERT: D 59 ARG cc_start: 0.7967 (mtp-110) cc_final: 0.7674 (mtp180) REVERT: D 65 ILE cc_start: 0.8673 (pt) cc_final: 0.8437 (pt) REVERT: D 66 SER cc_start: 0.8048 (m) cc_final: 0.7477 (m) REVERT: D 84 MET cc_start: 0.7401 (ptp) cc_final: 0.6867 (ptp) REVERT: D 87 GLU cc_start: 0.8107 (pt0) cc_final: 0.7766 (pt0) REVERT: D 91 LYS cc_start: 0.8692 (tppt) cc_final: 0.8063 (tppt) REVERT: D 93 GLU cc_start: 0.8156 (tt0) cc_final: 0.7770 (tt0) REVERT: D 97 ARG cc_start: 0.8615 (mtm110) cc_final: 0.8238 (ttm110) REVERT: D 102 ASP cc_start: 0.7471 (m-30) cc_final: 0.7146 (m-30) REVERT: D 119 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7527 (tp30) REVERT: D 125 LEU cc_start: 0.8000 (mt) cc_final: 0.7769 (mt) REVERT: D 127 MET cc_start: 0.7779 (mmm) cc_final: 0.7370 (mmp) REVERT: D 130 ASP cc_start: 0.7103 (m-30) cc_final: 0.6685 (m-30) REVERT: D 132 TYR cc_start: 0.7820 (m-80) cc_final: 0.7585 (m-80) REVERT: D 133 ARG cc_start: 0.8410 (ttp-110) cc_final: 0.7801 (ttp-110) REVERT: D 153 LYS cc_start: 0.8379 (tppt) cc_final: 0.7475 (tppt) REVERT: D 172 ILE cc_start: 0.8574 (tt) cc_final: 0.8051 (tt) REVERT: D 174 LEU cc_start: 0.8185 (mt) cc_final: 0.7928 (mt) REVERT: D 192 ASP cc_start: 0.8072 (p0) cc_final: 0.7669 (p0) REVERT: D 193 LYS cc_start: 0.8109 (mttt) cc_final: 0.7775 (mttt) REVERT: D 195 CYS cc_start: 0.7971 (m) cc_final: 0.7683 (m) REVERT: D 220 SER cc_start: 0.7284 (m) cc_final: 0.7011 (m) REVERT: E 121 CYS cc_start: 0.7469 (m) cc_final: 0.7186 (m) REVERT: E 125 TYR cc_start: 0.7907 (m-80) cc_final: 0.7001 (m-80) REVERT: E 144 GLU cc_start: 0.7330 (pp20) cc_final: 0.6581 (pp20) REVERT: E 160 ARG cc_start: 0.6983 (mpp80) cc_final: 0.6722 (mpp80) REVERT: E 175 LYS cc_start: 0.8709 (ptmt) cc_final: 0.8162 (ptmt) REVERT: E 187 MET cc_start: 0.3819 (ttm) cc_final: 0.1562 (ttm) REVERT: E 189 ARG cc_start: 0.7231 (tpp-160) cc_final: 0.5715 (tpp80) REVERT: E 192 LYS cc_start: 0.7567 (ttpt) cc_final: 0.7317 (ttpt) REVERT: E 206 LEU cc_start: 0.6751 (tp) cc_final: 0.6439 (tp) REVERT: E 215 LEU cc_start: 0.5279 (tp) cc_final: 0.4912 (tt) REVERT: E 219 MET cc_start: 0.7588 (mtp) cc_final: 0.7151 (mtp) REVERT: E 236 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7481 (tm-30) REVERT: E 249 MET cc_start: 0.8167 (ppp) cc_final: 0.7945 (ppp) REVERT: E 253 LEU cc_start: 0.8788 (mt) cc_final: 0.8550 (mt) REVERT: E 256 MET cc_start: 0.7597 (ptm) cc_final: 0.7367 (ptm) REVERT: E 316 TYR cc_start: 0.7674 (t80) cc_final: 0.7265 (t80) REVERT: E 319 ASN cc_start: 0.7930 (t0) cc_final: 0.6749 (t0) REVERT: E 320 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7642 (mm-30) REVERT: E 324 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7619 (mmtt) REVERT: E 340 LYS cc_start: 0.8744 (mttp) cc_final: 0.8377 (tptp) REVERT: E 344 LYS cc_start: 0.8574 (tmmt) cc_final: 0.8276 (mttt) REVERT: E 356 MET cc_start: 0.7027 (ppp) cc_final: 0.6531 (ppp) REVERT: E 371 PHE cc_start: 0.7683 (m-80) cc_final: 0.7119 (m-80) REVERT: F 88 LYS cc_start: 0.8466 (mmmt) cc_final: 0.7972 (mmmt) REVERT: F 175 LYS cc_start: 0.8638 (ptmt) cc_final: 0.8165 (ptmt) REVERT: F 187 MET cc_start: 0.3184 (ttt) cc_final: 0.2474 (ttt) REVERT: F 195 ASN cc_start: 0.7852 (t0) cc_final: 0.7498 (t0) REVERT: F 206 LEU cc_start: 0.6395 (tp) cc_final: 0.5903 (tp) REVERT: F 227 ARG cc_start: 0.7177 (mtm180) cc_final: 0.6783 (mtm180) REVERT: F 249 MET cc_start: 0.8209 (ppp) cc_final: 0.7945 (ppp) REVERT: F 253 LEU cc_start: 0.8732 (mt) cc_final: 0.8461 (mt) REVERT: F 256 MET cc_start: 0.7782 (ptm) cc_final: 0.7367 (ptm) REVERT: F 267 ASP cc_start: 0.7794 (p0) cc_final: 0.7260 (p0) REVERT: F 316 TYR cc_start: 0.7669 (t80) cc_final: 0.7273 (t80) REVERT: F 319 ASN cc_start: 0.7732 (t0) cc_final: 0.6348 (t0) REVERT: F 320 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7598 (mm-30) REVERT: F 324 LYS cc_start: 0.7970 (mmtt) cc_final: 0.7530 (mmtt) REVERT: F 344 LYS cc_start: 0.8298 (tmmt) cc_final: 0.8045 (tmmt) REVERT: F 371 PHE cc_start: 0.7564 (m-80) cc_final: 0.7116 (m-80) outliers start: 0 outliers final: 0 residues processed: 642 average time/residue: 0.3149 time to fit residues: 272.4983 Evaluate side-chains 635 residues out of total 1388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 635 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 37 optimal weight: 0.0050 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 122 optimal weight: 0.0020 chunk 51 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 15 optimal weight: 0.0040 chunk 22 optimal weight: 0.6980 chunk 107 optimal weight: 8.9990 overall best weight: 0.2814 ------------------------------------------------------------------------------- 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 444 GLN A 477 HIS B 369 HIS ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 200 GLN ** E 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.137705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.113103 restraints weight = 27475.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.117459 restraints weight = 15176.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.120457 restraints weight = 9823.180| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12876 Z= 0.196 Angle : 0.714 11.501 17364 Z= 0.369 Chirality : 0.046 0.186 1918 Planarity : 0.004 0.054 2216 Dihedral : 5.423 44.111 1740 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.21), residues: 1538 helix: 0.29 (0.16), residues: 894 sheet: -3.28 (0.40), residues: 110 loop : -0.84 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 368 HIS 0.020 0.001 HIS E 358 PHE 0.029 0.002 PHE F 360 TYR 0.040 0.002 TYR D 101 ARG 0.013 0.001 ARG D 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4437.61 seconds wall clock time: 80 minutes 38.21 seconds (4838.21 seconds total)