Starting phenix.real_space_refine on Fri Mar 15 19:52:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chf_16660/03_2024/8chf_16660_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chf_16660/03_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_16660/03_2024/8chf_16660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chf_16660/03_2024/8chf_16660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chf_16660/03_2024/8chf_16660_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chf_16660/03_2024/8chf_16660_updated.pdb" } 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 Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 255": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.98, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.17 Conformation dependent library (CDL) restraints added in 2.2 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... running ksdssp... Secondary structure from input PDB file: 68 helices and 6 sheets defined 53.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 442 through 461 Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 527 through 543 Processing helix chain 'A' and resid 554 through 562 removed outlier: 3.545A pdb=" N PHE A 559 " --> pdb=" O ASP A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 579 through 588 Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 599 through 611 Processing helix chain 'B' and resid 384 through 398 Processing helix chain 'B' and resid 429 through 434 Processing helix chain 'B' and resid 442 through 461 Processing helix chain 'B' and resid 514 through 518 Processing helix chain 'B' and resid 527 through 543 Processing helix chain 'B' and resid 554 through 562 removed outlier: 3.546A pdb=" N PHE B 559 " --> pdb=" O ASP B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'B' and resid 579 through 588 Processing helix chain 'B' and resid 593 through 595 No H-bonds generated for 'chain 'B' and resid 593 through 595' Processing helix chain 'B' and resid 599 through 611 Processing helix chain 'C' and resid 5 through 17 Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 41 through 71 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 110 Processing helix chain 'C' and resid 118 through 138 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 165 Processing helix chain 'C' and resid 171 through 186 Processing helix chain 'C' and resid 191 through 207 Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 214 through 235 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 17 Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 41 through 71 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 110 Processing helix chain 'D' and resid 118 through 138 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 165 Processing helix chain 'D' and resid 171 through 186 Processing helix chain 'D' and resid 191 through 207 Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 214 through 235 removed outlier: 4.274A pdb=" N ASP D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 119 removed outlier: 4.283A pdb=" N GLN E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE E 112 " --> pdb=" O ARG E 108 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ARG E 113 " --> pdb=" O ASN E 109 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 158 Processing helix chain 'E' and resid 163 through 183 Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'E' and resid 232 through 236 Processing helix chain 'E' and resid 242 through 258 Processing helix chain 'E' and resid 268 through 272 Processing helix chain 'E' and resid 310 through 319 Processing helix chain 'E' and resid 332 through 342 Processing helix chain 'E' and resid 346 through 348 No H-bonds generated for 'chain 'E' and resid 346 through 348' Processing helix chain 'E' and resid 352 through 357 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 371 through 378 Processing helix chain 'F' and resid 105 through 119 removed outlier: 4.284A pdb=" N GLN F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE F 111 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE F 112 " --> pdb=" O ARG F 108 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ARG F 113 " --> pdb=" O ASN F 109 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU F 114 " --> pdb=" O GLN F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 158 Processing helix chain 'F' and resid 163 through 183 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 213 through 220 Processing helix chain 'F' and resid 232 through 236 Processing helix chain 'F' and resid 242 through 258 Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 310 through 319 Processing helix chain 'F' and resid 332 through 342 Processing helix chain 'F' and resid 346 through 348 No H-bonds generated for 'chain 'F' and resid 346 through 348' Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 371 through 378 Processing sheet with id= A, first strand: chain 'A' and resid 408 through 412 removed outlier: 6.741A pdb=" N VAL A 420 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR A 411 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 418 " --> pdb=" O TYR A 411 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 356 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 408 through 412 removed outlier: 6.741A pdb=" N VAL B 420 " --> pdb=" O MET B 409 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TYR B 411 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 418 " --> pdb=" O TYR B 411 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY B 356 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 94 through 96 Processing sheet with id= D, 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= E, first strand: chain 'F' and resid 94 through 96 Processing sheet with id= F, 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) 592 hydrogen bonds defined for protein. 1770 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: 3.28 Time building geometry restraints manager: 5.58 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: 97.29 - 104.66: 223 104.66 - 112.03: 6357 112.03 - 119.41: 4514 119.41 - 126.78: 6110 126.78 - 134.16: 160 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: 364 2.69 - 3.24: 14170 3.24 - 3.79: 21537 3.79 - 4.35: 27380 4.35 - 4.90: 42174 Nonbonded interactions: 105625 Sorted by model distance: nonbonded pdb=" OD2 ASP E 65 " pdb=" OG SER E 135 " model vdw 2.136 2.440 nonbonded pdb=" OD2 ASP F 65 " pdb=" OG SER F 135 " model vdw 2.137 2.440 nonbonded pdb=" OD2 ASP B 555 " pdb=" OG SER F 228 " model vdw 2.178 2.440 nonbonded pdb=" OD2 ASP A 555 " pdb=" OG SER E 228 " model vdw 2.178 2.440 nonbonded pdb=" ND1 HIS E 188 " pdb=" O ASP E 190 " model vdw 2.216 2.520 ... (remaining 105620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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: 0.830 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: 4.120 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 35.170 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.000 ------------------------------------------------------------------------------- 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= 0.366 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 fitting. rotamer outliers: 0 poor density : 676 time to evaluate : 1.269 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: 0.2790 time to fit residues: 257.2118 Evaluate side-chains 658 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 658 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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: 2.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 444 GLN B 369 HIS ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 GLN E 109 ASN E 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12876 Z= 0.223 Angle : 0.642 11.067 17364 Z= 0.334 Chirality : 0.044 0.185 1918 Planarity : 0.005 0.100 2216 Dihedral : 6.416 113.466 1740 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1538 helix: 0.66 (0.17), residues: 882 sheet: -2.90 (0.46), residues: 88 loop : -1.11 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 368 HIS 0.007 0.002 HIS E 358 PHE 0.015 0.002 PHE A 387 TYR 0.040 0.003 TYR C 101 ARG 0.027 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 669 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 669 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 GLU cc_start: 0.6540 (mp0) cc_final: 0.6072 (mp0) REVERT: A 359 SER cc_start: 0.8146 (m) cc_final: 0.7650 (p) REVERT: A 368 TRP cc_start: 0.8206 (t60) cc_final: 0.7953 (t60) REVERT: A 387 PHE cc_start: 0.7898 (t80) cc_final: 0.7267 (t80) REVERT: A 391 ARG cc_start: 0.8059 (mmt90) cc_final: 0.7661 (mmm-85) REVERT: A 392 ASN cc_start: 0.8055 (m-40) cc_final: 0.7723 (m-40) REVERT: A 399 LYS cc_start: 0.8272 (mmtp) cc_final: 0.7777 (mmtp) REVERT: A 412 MET cc_start: 0.6671 (ppp) cc_final: 0.6010 (ppp) REVERT: A 416 ASN cc_start: 0.7498 (p0) cc_final: 0.6975 (p0) REVERT: A 423 TRP cc_start: 0.7796 (t-100) cc_final: 0.7564 (t60) REVERT: A 431 LYS cc_start: 0.8069 (mppt) cc_final: 0.7714 (mppt) REVERT: A 439 LYS cc_start: 0.8208 (mppt) cc_final: 0.7687 (mppt) REVERT: A 442 MET cc_start: 0.6952 (mpp) cc_final: 0.6613 (mpp) REVERT: A 445 LEU cc_start: 0.8235 (tp) cc_final: 0.7932 (tp) REVERT: A 451 GLN cc_start: 0.7920 (mt0) cc_final: 0.6728 (mt0) REVERT: A 457 ASP cc_start: 0.6818 (t0) cc_final: 0.6573 (t0) REVERT: A 458 TYR cc_start: 0.8130 (t80) cc_final: 0.7926 (t80) REVERT: A 516 VAL cc_start: 0.8743 (t) cc_final: 0.8334 (t) REVERT: A 517 ILE cc_start: 0.8656 (mt) cc_final: 0.8324 (mt) REVERT: A 518 ARG cc_start: 0.7808 (ptp-110) cc_final: 0.7042 (ptp-110) REVERT: A 528 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7397 (mm110) REVERT: A 541 LEU cc_start: 0.8308 (mt) cc_final: 0.7898 (mt) REVERT: A 542 MET cc_start: 0.6452 (mtp) cc_final: 0.5974 (mtp) REVERT: A 554 ARG cc_start: 0.7296 (tmm-80) cc_final: 0.7076 (tmm-80) REVERT: A 560 MET cc_start: 0.7878 (mmp) cc_final: 0.7603 (mmt) REVERT: A 590 LYS cc_start: 0.7782 (mmtm) cc_final: 0.7309 (mmtm) REVERT: A 592 VAL cc_start: 0.8246 (t) cc_final: 0.7852 (m) REVERT: B 367 LYS cc_start: 0.7561 (mmtt) cc_final: 0.6579 (mmtt) REVERT: B 393 GLU cc_start: 0.6943 (tp30) cc_final: 0.6465 (tp30) REVERT: B 399 LYS cc_start: 0.8269 (mmtp) cc_final: 0.7777 (mmtp) REVERT: B 412 MET cc_start: 0.6630 (ppp) cc_final: 0.6003 (ppp) REVERT: B 416 ASN cc_start: 0.7809 (p0) cc_final: 0.7338 (p0) REVERT: B 419 ILE cc_start: 0.7040 (mm) cc_final: 0.6793 (mm) REVERT: B 429 LEU cc_start: 0.8108 (tp) cc_final: 0.7823 (tp) REVERT: B 432 HIS cc_start: 0.6999 (m90) cc_final: 0.6364 (m90) REVERT: B 439 LYS cc_start: 0.8406 (mppt) cc_final: 0.7925 (mppt) REVERT: B 441 GLN cc_start: 0.7479 (mt0) cc_final: 0.7186 (mt0) REVERT: B 442 MET cc_start: 0.7070 (mpp) cc_final: 0.6818 (mpp) REVERT: B 458 TYR cc_start: 0.7992 (t80) cc_final: 0.7515 (t80) REVERT: B 460 HIS cc_start: 0.7603 (m170) cc_final: 0.7340 (m-70) REVERT: B 516 VAL cc_start: 0.8817 (t) cc_final: 0.8483 (t) REVERT: B 528 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7362 (mm110) REVERT: B 534 TYR cc_start: 0.7926 (t80) cc_final: 0.7606 (t80) REVERT: B 541 LEU cc_start: 0.8300 (mt) cc_final: 0.8066 (mt) REVERT: B 542 MET cc_start: 0.6508 (mtp) cc_final: 0.6207 (mtp) REVERT: B 545 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7282 (mt-10) REVERT: B 551 ILE cc_start: 0.8673 (mp) cc_final: 0.8434 (mp) REVERT: B 554 ARG cc_start: 0.7298 (tmm-80) cc_final: 0.7031 (tmm-80) REVERT: B 583 ARG cc_start: 0.8214 (ptp-170) cc_final: 0.7879 (ptp-110) REVERT: B 590 LYS cc_start: 0.7776 (mmtm) cc_final: 0.7286 (mmtm) REVERT: B 592 VAL cc_start: 0.8126 (t) cc_final: 0.7671 (m) REVERT: B 615 LYS cc_start: 0.7851 (mttm) cc_final: 0.7486 (mttm) REVERT: B 622 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6774 (tm-30) REVERT: C 20 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6927 (tm-30) REVERT: C 25 MET cc_start: 0.7557 (pmm) cc_final: 0.7132 (pmm) REVERT: C 29 MET cc_start: 0.8846 (tpp) cc_final: 0.8472 (mmm) REVERT: C 43 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8313 (mt-10) REVERT: C 49 VAL cc_start: 0.7917 (t) cc_final: 0.7385 (t) REVERT: C 52 LYS cc_start: 0.8420 (tptm) cc_final: 0.8171 (tptm) REVERT: C 53 ASN cc_start: 0.8046 (m-40) cc_final: 0.7723 (m-40) REVERT: C 59 ARG cc_start: 0.7992 (mtp-110) cc_final: 0.7744 (mtp180) REVERT: C 87 GLU cc_start: 0.8092 (pt0) cc_final: 0.7865 (pt0) REVERT: C 91 LYS cc_start: 0.8477 (tppt) cc_final: 0.7563 (tppt) REVERT: C 94 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8188 (ttpt) REVERT: C 95 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7344 (mt-10) REVERT: C 97 ARG cc_start: 0.8539 (mtm110) cc_final: 0.8259 (mtm110) REVERT: C 98 GLU cc_start: 0.6842 (tp30) cc_final: 0.5625 (tp30) REVERT: C 102 ASP cc_start: 0.7677 (m-30) cc_final: 0.6734 (m-30) REVERT: C 103 VAL cc_start: 0.8320 (t) cc_final: 0.8011 (t) REVERT: C 125 LEU cc_start: 0.8135 (mt) cc_final: 0.7872 (mt) REVERT: C 126 LYS cc_start: 0.8613 (tttm) cc_final: 0.8325 (tttm) REVERT: C 127 MET cc_start: 0.7849 (mmm) cc_final: 0.7419 (mmp) REVERT: C 132 TYR cc_start: 0.8110 (m-80) cc_final: 0.7274 (m-80) REVERT: C 133 ARG cc_start: 0.8451 (ttp-110) cc_final: 0.7888 (ttp-110) REVERT: C 149 GLU cc_start: 0.8149 (tp30) cc_final: 0.7731 (tp30) REVERT: C 150 ASP cc_start: 0.8061 (m-30) cc_final: 0.7819 (m-30) REVERT: C 155 TYR cc_start: 0.7187 (m-10) cc_final: 0.6817 (m-80) REVERT: C 159 PHE cc_start: 0.8026 (t80) cc_final: 0.7788 (t80) REVERT: C 180 PHE cc_start: 0.8211 (m-80) cc_final: 0.7577 (m-80) REVERT: C 195 CYS cc_start: 0.7985 (m) cc_final: 0.7740 (m) REVERT: C 197 LEU cc_start: 0.8468 (mm) cc_final: 0.8254 (mm) REVERT: C 200 GLN cc_start: 0.8679 (pt0) cc_final: 0.8474 (pt0) REVERT: C 224 MET cc_start: 0.7241 (ptm) cc_final: 0.6290 (ptm) REVERT: C 225 GLN cc_start: 0.7539 (mm110) cc_final: 0.6817 (mm110) REVERT: C 227 LEU cc_start: 0.8549 (mt) cc_final: 0.8341 (mt) REVERT: D 10 VAL cc_start: 0.8844 (t) cc_final: 0.8643 (t) REVERT: D 14 LYS cc_start: 0.8796 (mttt) cc_final: 0.8513 (mttt) REVERT: D 20 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7191 (tm-30) REVERT: D 25 MET cc_start: 0.7605 (pmm) cc_final: 0.7327 (pmm) REVERT: D 29 MET cc_start: 0.8629 (tpp) cc_final: 0.8305 (mmm) REVERT: D 34 GLU cc_start: 0.7823 (pp20) cc_final: 0.7497 (pp20) REVERT: D 43 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8495 (mt-10) REVERT: D 49 VAL cc_start: 0.7977 (t) cc_final: 0.7425 (t) REVERT: D 53 ASN cc_start: 0.7871 (m-40) cc_final: 0.7487 (m-40) REVERT: D 65 ILE cc_start: 0.8683 (pt) cc_final: 0.8374 (pt) REVERT: D 66 SER cc_start: 0.8080 (m) cc_final: 0.7329 (m) REVERT: D 87 GLU cc_start: 0.8102 (pt0) cc_final: 0.7851 (pt0) REVERT: D 91 LYS cc_start: 0.8596 (tppt) cc_final: 0.7980 (tppt) REVERT: D 93 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8062 (mt-10) REVERT: D 97 ARG cc_start: 0.8825 (mtm110) cc_final: 0.8411 (mtm110) REVERT: D 119 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7818 (tp30) REVERT: D 125 LEU cc_start: 0.8081 (mt) cc_final: 0.7813 (mt) REVERT: D 127 MET cc_start: 0.7962 (mmm) cc_final: 0.7355 (mmp) REVERT: D 130 ASP cc_start: 0.7431 (m-30) cc_final: 0.6306 (m-30) REVERT: D 132 TYR cc_start: 0.8128 (m-80) cc_final: 0.7864 (m-80) REVERT: D 133 ARG cc_start: 0.8418 (ttp-110) cc_final: 0.7594 (ttp80) REVERT: D 153 LYS cc_start: 0.8534 (tppt) cc_final: 0.7691 (tppt) REVERT: D 155 TYR cc_start: 0.7020 (m-10) cc_final: 0.6754 (m-80) REVERT: D 180 PHE cc_start: 0.8244 (m-80) cc_final: 0.7478 (m-80) REVERT: D 192 ASP cc_start: 0.8298 (p0) cc_final: 0.7451 (p0) REVERT: D 193 LYS cc_start: 0.8212 (mttt) cc_final: 0.7689 (mptt) REVERT: D 195 CYS cc_start: 0.7887 (m) cc_final: 0.7605 (m) REVERT: D 220 SER cc_start: 0.7221 (m) cc_final: 0.6799 (m) REVERT: D 224 MET cc_start: 0.7272 (ptm) cc_final: 0.6330 (ptm) REVERT: D 225 GLN cc_start: 0.7505 (mm110) cc_final: 0.6779 (mm110) REVERT: E 88 LYS cc_start: 0.8416 (mmmt) cc_final: 0.7970 (mmmt) REVERT: E 121 CYS cc_start: 0.7801 (m) cc_final: 0.7527 (m) REVERT: E 160 ARG cc_start: 0.7626 (mpp80) cc_final: 0.6023 (mtt180) REVERT: E 175 LYS cc_start: 0.8658 (ptmt) cc_final: 0.8097 (ptmt) REVERT: E 187 MET cc_start: 0.6560 (mtt) cc_final: 0.5886 (mtm) REVERT: E 219 MET cc_start: 0.7658 (mtp) cc_final: 0.7307 (mtp) REVERT: E 249 MET cc_start: 0.8164 (ppp) cc_final: 0.7946 (ppp) REVERT: E 253 LEU cc_start: 0.8790 (mt) cc_final: 0.8535 (mt) REVERT: E 256 MET cc_start: 0.7699 (ptm) cc_final: 0.7331 (ptm) REVERT: E 267 ASP cc_start: 0.7278 (p0) cc_final: 0.6963 (p0) REVERT: E 270 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7357 (mt-10) REVERT: E 311 PHE cc_start: 0.6939 (t80) cc_final: 0.6370 (t80) REVERT: E 316 TYR cc_start: 0.7732 (t80) cc_final: 0.7295 (t80) REVERT: E 319 ASN cc_start: 0.7771 (t0) cc_final: 0.6569 (t0) REVERT: E 320 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7553 (mm-30) REVERT: E 333 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8368 (mt-10) REVERT: E 344 LYS cc_start: 0.8397 (tttt) cc_final: 0.7973 (mttt) REVERT: E 353 LYS cc_start: 0.8019 (mmpt) cc_final: 0.7789 (mmpt) REVERT: F 88 LYS cc_start: 0.8503 (mmmt) cc_final: 0.7976 (mmmt) REVERT: F 96 ARG cc_start: 0.7396 (ptm160) cc_final: 0.6769 (ptm160) REVERT: F 125 TYR cc_start: 0.8089 (m-80) cc_final: 0.7221 (m-80) REVERT: F 168 LYS cc_start: 0.8537 (ttmm) cc_final: 0.8024 (ttmm) REVERT: F 175 LYS cc_start: 0.8646 (ptmt) cc_final: 0.8112 (ptmt) REVERT: F 187 MET cc_start: 0.6309 (mtm) cc_final: 0.5874 (mtm) REVERT: F 195 ASN cc_start: 0.7207 (t0) cc_final: 0.6970 (t0) REVERT: F 206 LEU cc_start: 0.6587 (tp) cc_final: 0.6253 (tp) REVERT: F 219 MET cc_start: 0.7573 (mtp) cc_final: 0.7245 (mtp) REVERT: F 256 MET cc_start: 0.7698 (ptm) cc_final: 0.7428 (ptm) REVERT: F 267 ASP cc_start: 0.7266 (p0) cc_final: 0.6790 (p0) REVERT: F 316 TYR cc_start: 0.7753 (t80) cc_final: 0.7244 (t80) REVERT: F 318 VAL cc_start: 0.8459 (p) cc_final: 0.8206 (m) REVERT: F 319 ASN cc_start: 0.7663 (t0) cc_final: 0.6310 (t0) REVERT: F 320 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7462 (mm-30) REVERT: F 333 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8297 (mt-10) REVERT: F 353 LYS cc_start: 0.8038 (mmpt) cc_final: 0.7824 (mmpt) outliers start: 0 outliers final: 0 residues processed: 669 average time/residue: 0.2737 time to fit residues: 249.6251 Evaluate side-chains 654 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 654 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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: 0.9980 chunk 43 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN C 200 GLN D 200 GLN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12876 Z= 0.285 Angle : 0.684 11.112 17364 Z= 0.363 Chirality : 0.046 0.187 1918 Planarity : 0.005 0.075 2216 Dihedral : 5.951 87.364 1740 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.14 % Allowed : 5.12 % Favored : 94.74 % 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: -0.58 (0.20), residues: 1538 helix: 0.51 (0.16), residues: 876 sheet: -2.87 (0.47), residues: 88 loop : -1.28 (0.25), residues: 574 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 0.017 0.002 PHE F 360 TYR 0.029 0.002 TYR C 101 ARG 0.013 0.001 ARG E 181 *********************** 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 684 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 682 time to evaluate : 1.401 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 359 SER cc_start: 0.8070 (m) cc_final: 0.7589 (p) REVERT: A 367 LYS cc_start: 0.7321 (mmtt) cc_final: 0.6595 (mmtt) REVERT: A 391 ARG cc_start: 0.8075 (mmt90) cc_final: 0.7705 (tpp80) REVERT: A 392 ASN cc_start: 0.8071 (m-40) cc_final: 0.7741 (m-40) REVERT: A 399 LYS cc_start: 0.8192 (mmtp) cc_final: 0.7818 (mmtp) REVERT: A 411 TYR cc_start: 0.6907 (p90) cc_final: 0.6630 (p90) REVERT: A 412 MET cc_start: 0.6408 (ppp) cc_final: 0.5866 (ppp) REVERT: A 413 THR cc_start: 0.7861 (p) cc_final: 0.7604 (p) REVERT: A 414 LYS cc_start: 0.8225 (tppt) cc_final: 0.7661 (mmmt) REVERT: A 425 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6583 (mm-30) REVERT: A 429 LEU cc_start: 0.7949 (tp) cc_final: 0.7706 (tp) REVERT: A 439 LYS cc_start: 0.8336 (mppt) cc_final: 0.7790 (mppt) REVERT: A 442 MET cc_start: 0.7131 (mpp) cc_final: 0.6656 (mpp) REVERT: A 444 GLN cc_start: 0.7661 (mt0) cc_final: 0.7263 (mt0) REVERT: A 445 LEU cc_start: 0.8314 (tp) cc_final: 0.8003 (tp) REVERT: A 460 HIS cc_start: 0.7862 (m90) cc_final: 0.7437 (m-70) REVERT: A 463 ASN cc_start: 0.6659 (m-40) cc_final: 0.6380 (m-40) REVERT: A 466 HIS cc_start: 0.8297 (t-90) cc_final: 0.8004 (t70) REVERT: A 483 LYS cc_start: 0.8059 (mttm) cc_final: 0.7689 (mttm) REVERT: A 517 ILE cc_start: 0.8777 (mt) cc_final: 0.8418 (mt) REVERT: A 518 ARG cc_start: 0.7994 (ptp-110) cc_final: 0.7370 (ptp-110) REVERT: A 527 PHE cc_start: 0.8653 (m-10) cc_final: 0.8374 (m-10) REVERT: A 541 LEU cc_start: 0.8242 (mt) cc_final: 0.8039 (mt) REVERT: A 554 ARG cc_start: 0.7385 (tmm-80) cc_final: 0.7129 (tmm-80) REVERT: A 560 MET cc_start: 0.8111 (mmp) cc_final: 0.7848 (mmt) REVERT: A 590 LYS cc_start: 0.7841 (mmtm) cc_final: 0.7383 (mmtm) REVERT: A 592 VAL cc_start: 0.8200 (t) cc_final: 0.7742 (m) REVERT: A 601 GLN cc_start: 0.8069 (tt0) cc_final: 0.7756 (tm-30) REVERT: A 610 GLN cc_start: 0.8047 (mm110) cc_final: 0.7633 (mm110) REVERT: A 622 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7111 (tm-30) REVERT: B 345 GLU cc_start: 0.6186 (mp0) cc_final: 0.5794 (mp0) REVERT: B 367 LYS cc_start: 0.7550 (mmtt) cc_final: 0.6625 (mmtt) REVERT: B 383 THR cc_start: 0.8322 (p) cc_final: 0.7685 (p) REVERT: B 385 GLU cc_start: 0.9013 (pm20) cc_final: 0.8812 (pm20) REVERT: B 393 GLU cc_start: 0.7099 (tp30) cc_final: 0.6572 (tp30) REVERT: B 399 LYS cc_start: 0.8306 (mmtp) cc_final: 0.7876 (mmtp) REVERT: B 412 MET cc_start: 0.6268 (ppp) cc_final: 0.5678 (ppp) REVERT: B 413 THR cc_start: 0.7799 (p) cc_final: 0.7595 (p) REVERT: B 414 LYS cc_start: 0.8300 (tppt) cc_final: 0.7996 (mmmt) REVERT: B 416 ASN cc_start: 0.7765 (p0) cc_final: 0.7517 (p0) REVERT: B 419 ILE cc_start: 0.7024 (mm) cc_final: 0.6717 (mm) REVERT: B 422 GLN cc_start: 0.7646 (tt0) cc_final: 0.7358 (pt0) REVERT: B 425 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6870 (mm-30) REVERT: B 429 LEU cc_start: 0.8150 (tp) cc_final: 0.7916 (tp) REVERT: B 432 HIS cc_start: 0.7145 (m90) cc_final: 0.6737 (m90) REVERT: B 439 LYS cc_start: 0.8564 (mppt) cc_final: 0.8144 (mppt) REVERT: B 442 MET cc_start: 0.7115 (mpp) cc_final: 0.6647 (mpp) REVERT: B 456 MET cc_start: 0.6886 (mmm) cc_final: 0.6079 (mmm) REVERT: B 458 TYR cc_start: 0.8103 (t80) cc_final: 0.7692 (t80) REVERT: B 460 HIS cc_start: 0.7492 (m170) cc_final: 0.7019 (m170) REVERT: B 463 ASN cc_start: 0.6973 (m-40) cc_final: 0.6668 (m-40) REVERT: B 483 LYS cc_start: 0.8080 (mttm) cc_final: 0.6870 (mttm) REVERT: B 484 ILE cc_start: 0.7922 (mt) cc_final: 0.7683 (mt) REVERT: B 493 LYS cc_start: 0.7609 (mmtm) cc_final: 0.6940 (mmtm) REVERT: B 511 TRP cc_start: 0.7182 (m-90) cc_final: 0.6980 (m-90) REVERT: B 516 VAL cc_start: 0.8832 (t) cc_final: 0.8256 (t) REVERT: B 517 ILE cc_start: 0.8754 (mt) cc_final: 0.8393 (mt) REVERT: B 528 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7181 (mm110) REVERT: B 534 TYR cc_start: 0.7880 (t80) cc_final: 0.7582 (t80) REVERT: B 542 MET cc_start: 0.6586 (mtp) cc_final: 0.6346 (mtp) REVERT: B 545 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7281 (mt-10) REVERT: B 554 ARG cc_start: 0.7428 (tmm-80) cc_final: 0.7203 (tmm-80) REVERT: B 556 GLN cc_start: 0.8250 (tt0) cc_final: 0.8032 (tt0) REVERT: B 560 MET cc_start: 0.7720 (tpp) cc_final: 0.7326 (tpp) REVERT: B 583 ARG cc_start: 0.8261 (ptp-170) cc_final: 0.7906 (ptp-110) REVERT: B 592 VAL cc_start: 0.8082 (t) cc_final: 0.7566 (m) REVERT: B 622 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6805 (tm-30) REVERT: C 10 VAL cc_start: 0.8837 (t) cc_final: 0.8496 (t) REVERT: C 14 LYS cc_start: 0.8679 (pttm) cc_final: 0.8455 (ptpp) REVERT: C 20 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7033 (tm-30) REVERT: C 25 MET cc_start: 0.7565 (pmm) cc_final: 0.7186 (pmm) REVERT: C 29 MET cc_start: 0.8862 (tpp) cc_final: 0.8360 (mmm) REVERT: C 43 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8178 (mt-10) REVERT: C 52 LYS cc_start: 0.8476 (tptm) cc_final: 0.8071 (tptm) REVERT: C 87 GLU cc_start: 0.8041 (pt0) cc_final: 0.7750 (pt0) REVERT: C 91 LYS cc_start: 0.8540 (tppt) cc_final: 0.7576 (tppt) REVERT: C 94 LYS cc_start: 0.8577 (ttpt) cc_final: 0.8243 (ttpt) REVERT: C 95 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7371 (mt-10) REVERT: C 97 ARG cc_start: 0.8549 (mtm110) cc_final: 0.8179 (mtm110) REVERT: C 98 GLU cc_start: 0.6955 (tp30) cc_final: 0.5631 (tp30) REVERT: C 102 ASP cc_start: 0.7755 (m-30) cc_final: 0.6691 (m-30) REVERT: C 125 LEU cc_start: 0.8181 (mt) cc_final: 0.7917 (mt) REVERT: C 126 LYS cc_start: 0.8643 (tttm) cc_final: 0.8125 (tttm) REVERT: C 127 MET cc_start: 0.7926 (mmm) cc_final: 0.7367 (mmp) REVERT: C 132 TYR cc_start: 0.8244 (m-80) cc_final: 0.7514 (m-80) REVERT: C 133 ARG cc_start: 0.8401 (ttp-110) cc_final: 0.7660 (ttp80) REVERT: C 149 GLU cc_start: 0.8235 (tp30) cc_final: 0.7880 (tp30) REVERT: C 150 ASP cc_start: 0.8135 (m-30) cc_final: 0.7853 (m-30) REVERT: C 153 LYS cc_start: 0.8787 (tppt) cc_final: 0.7977 (tppt) REVERT: C 155 TYR cc_start: 0.7434 (m-10) cc_final: 0.7037 (m-80) REVERT: C 159 PHE cc_start: 0.8071 (t80) cc_final: 0.7856 (t80) REVERT: C 172 ILE cc_start: 0.8500 (tt) cc_final: 0.8234 (tt) REVERT: C 174 LEU cc_start: 0.8116 (mt) cc_final: 0.7678 (mt) REVERT: C 180 PHE cc_start: 0.8265 (m-80) cc_final: 0.7686 (m-80) REVERT: C 218 LYS cc_start: 0.7464 (mmpt) cc_final: 0.7254 (mmpt) REVERT: C 224 MET cc_start: 0.7386 (ptm) cc_final: 0.6338 (ptm) REVERT: C 225 GLN cc_start: 0.7518 (mm110) cc_final: 0.6720 (mm110) REVERT: C 226 LEU cc_start: 0.8244 (tt) cc_final: 0.7824 (tt) REVERT: D 14 LYS cc_start: 0.8822 (mttt) cc_final: 0.8452 (mttt) REVERT: D 20 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7135 (tm-30) REVERT: D 29 MET cc_start: 0.8611 (tpp) cc_final: 0.8268 (mmm) REVERT: D 30 LYS cc_start: 0.8013 (mtmm) cc_final: 0.7671 (mttm) REVERT: D 34 GLU cc_start: 0.7914 (pp20) cc_final: 0.7569 (pp20) REVERT: D 43 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8371 (mt-10) REVERT: D 52 LYS cc_start: 0.8531 (tptm) cc_final: 0.8024 (tptm) REVERT: D 59 ARG cc_start: 0.7863 (mtp-110) cc_final: 0.7637 (mtp180) REVERT: D 65 ILE cc_start: 0.8666 (pt) cc_final: 0.8336 (pt) REVERT: D 66 SER cc_start: 0.8078 (m) cc_final: 0.7374 (m) REVERT: D 87 GLU cc_start: 0.8130 (pt0) cc_final: 0.7829 (pt0) REVERT: D 91 LYS cc_start: 0.8637 (tppt) cc_final: 0.8035 (tppt) REVERT: D 93 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8081 (mt-10) REVERT: D 97 ARG cc_start: 0.8828 (mtm110) cc_final: 0.8372 (mtm110) REVERT: D 102 ASP cc_start: 0.7513 (m-30) cc_final: 0.7194 (m-30) REVERT: D 119 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7899 (tp30) REVERT: D 125 LEU cc_start: 0.8150 (mt) cc_final: 0.7890 (mt) REVERT: D 127 MET cc_start: 0.7968 (mmm) cc_final: 0.7340 (mmp) REVERT: D 130 ASP cc_start: 0.7144 (m-30) cc_final: 0.6934 (m-30) REVERT: D 133 ARG cc_start: 0.8196 (ttp-110) cc_final: 0.7515 (ttp80) REVERT: D 153 LYS cc_start: 0.8576 (tppt) cc_final: 0.7642 (tppt) REVERT: D 155 TYR cc_start: 0.7288 (m-10) cc_final: 0.6884 (m-80) REVERT: D 174 LEU cc_start: 0.8169 (mt) cc_final: 0.7864 (mt) REVERT: D 176 LEU cc_start: 0.8803 (tt) cc_final: 0.7860 (tt) REVERT: D 180 PHE cc_start: 0.8280 (m-80) cc_final: 0.7543 (m-80) REVERT: D 192 ASP cc_start: 0.8338 (p0) cc_final: 0.7525 (p0) REVERT: D 193 LYS cc_start: 0.8239 (mttt) cc_final: 0.7700 (mptt) REVERT: D 195 CYS cc_start: 0.8028 (m) cc_final: 0.7763 (m) REVERT: D 220 SER cc_start: 0.7282 (m) cc_final: 0.6970 (m) REVERT: D 224 MET cc_start: 0.7521 (ptm) cc_final: 0.6439 (ptm) REVERT: D 225 GLN cc_start: 0.7609 (mm110) cc_final: 0.6833 (mm110) REVERT: E 88 LYS cc_start: 0.8417 (mmmt) cc_final: 0.7971 (mmmt) REVERT: E 121 CYS cc_start: 0.7779 (m) cc_final: 0.7397 (m) REVERT: E 125 TYR cc_start: 0.8027 (m-80) cc_final: 0.7141 (m-80) REVERT: E 146 MET cc_start: 0.6866 (tpp) cc_final: 0.6562 (tpp) REVERT: E 168 LYS cc_start: 0.8382 (ttmm) cc_final: 0.7962 (ttmm) REVERT: E 175 LYS cc_start: 0.8764 (ptmt) cc_final: 0.8241 (ptmt) REVERT: E 187 MET cc_start: 0.6394 (mtt) cc_final: 0.5974 (mtm) REVERT: E 236 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7407 (tm-30) REVERT: E 249 MET cc_start: 0.8163 (ppp) cc_final: 0.7948 (ppp) REVERT: E 253 LEU cc_start: 0.8776 (mt) cc_final: 0.8521 (mt) REVERT: E 256 MET cc_start: 0.7761 (ptm) cc_final: 0.7452 (ptm) REVERT: E 267 ASP cc_start: 0.7571 (p0) cc_final: 0.7173 (p0) REVERT: E 270 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7481 (mt-10) REVERT: E 311 PHE cc_start: 0.7008 (t80) cc_final: 0.6486 (t80) REVERT: E 312 GLU cc_start: 0.7758 (pp20) cc_final: 0.7356 (pp20) REVERT: E 313 LEU cc_start: 0.8215 (mt) cc_final: 0.7970 (mt) REVERT: E 316 TYR cc_start: 0.7734 (t80) cc_final: 0.7327 (t80) REVERT: E 319 ASN cc_start: 0.7990 (t0) cc_final: 0.6725 (t0) REVERT: E 320 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7679 (mm-30) REVERT: E 333 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8241 (mt-10) REVERT: E 334 PHE cc_start: 0.8473 (t80) cc_final: 0.8243 (t80) REVERT: E 344 LYS cc_start: 0.8551 (tttt) cc_final: 0.8174 (mttt) REVERT: F 88 LYS cc_start: 0.8486 (mmmt) cc_final: 0.7987 (mmmt) REVERT: F 96 ARG cc_start: 0.7396 (ptm160) cc_final: 0.6712 (ptm160) REVERT: F 110 GLN cc_start: 0.8308 (mm-40) cc_final: 0.8053 (mp10) REVERT: F 125 TYR cc_start: 0.8092 (m-80) cc_final: 0.7255 (m-80) REVERT: F 163 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7925 (mt-10) REVERT: F 175 LYS cc_start: 0.8752 (ptmt) cc_final: 0.8207 (ptmt) REVERT: F 195 ASN cc_start: 0.7485 (t0) cc_final: 0.7132 (t0) REVERT: F 206 LEU cc_start: 0.6504 (tp) cc_final: 0.6183 (tp) REVERT: F 227 ARG cc_start: 0.7389 (mtm180) cc_final: 0.7077 (mtm180) REVERT: F 236 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7525 (tm-30) REVERT: F 249 MET cc_start: 0.8167 (ppp) cc_final: 0.7966 (ppp) REVERT: F 253 LEU cc_start: 0.8774 (mt) cc_final: 0.8545 (mt) REVERT: F 256 MET cc_start: 0.7834 (ptm) cc_final: 0.7470 (ptm) REVERT: F 267 ASP cc_start: 0.7514 (p0) cc_final: 0.7101 (p0) REVERT: F 314 LEU cc_start: 0.8477 (mp) cc_final: 0.8261 (mp) REVERT: F 316 TYR cc_start: 0.7767 (t80) cc_final: 0.7299 (t80) REVERT: F 318 VAL cc_start: 0.8437 (p) cc_final: 0.8166 (m) REVERT: F 319 ASN cc_start: 0.7848 (t0) cc_final: 0.6490 (t0) REVERT: F 320 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7564 (mm-30) REVERT: F 333 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8410 (mt-10) REVERT: F 362 LYS cc_start: 0.8894 (tptp) cc_final: 0.8426 (tptp) outliers start: 2 outliers final: 1 residues processed: 683 average time/residue: 0.2937 time to fit residues: 274.4438 Evaluate side-chains 679 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 678 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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: 5.9990 chunk 105 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 0.0570 chunk 94 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS C 200 GLN D 11 GLN D 200 GLN E 109 ASN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2832 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= 0.197 Angle : 0.627 10.765 17364 Z= 0.325 Chirality : 0.044 0.183 1918 Planarity : 0.004 0.066 2216 Dihedral : 5.633 72.303 1740 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1538 helix: 0.67 (0.17), residues: 882 sheet: -2.92 (0.46), residues: 88 loop : -1.17 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 368 HIS 0.010 0.002 HIS F 188 PHE 0.015 0.002 PHE B 599 TYR 0.023 0.002 TYR B 532 ARG 0.008 0.001 ARG F 181 *********************** 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 671 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 671 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 SER cc_start: 0.8059 (m) cc_final: 0.7578 (p) REVERT: A 367 LYS cc_start: 0.7413 (mmtt) cc_final: 0.6576 (mmtt) REVERT: A 387 PHE cc_start: 0.7894 (t80) cc_final: 0.7658 (t80) REVERT: A 391 ARG cc_start: 0.8065 (mmt90) cc_final: 0.7574 (tpp-160) REVERT: A 397 LEU cc_start: 0.8494 (mt) cc_final: 0.8146 (mm) REVERT: A 399 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7858 (mmtp) REVERT: A 412 MET cc_start: 0.6590 (ppp) cc_final: 0.5934 (ppp) REVERT: A 413 THR cc_start: 0.7820 (p) cc_final: 0.7544 (p) REVERT: A 414 LYS cc_start: 0.8150 (tppt) cc_final: 0.7702 (mmmt) REVERT: A 422 GLN cc_start: 0.7608 (pm20) cc_final: 0.7304 (pm20) REVERT: A 439 LYS cc_start: 0.8302 (mppt) cc_final: 0.7678 (mppt) REVERT: A 441 GLN cc_start: 0.6991 (mt0) cc_final: 0.6294 (mt0) REVERT: A 442 MET cc_start: 0.7097 (mpp) cc_final: 0.6598 (mpp) REVERT: A 444 GLN cc_start: 0.7584 (mt0) cc_final: 0.6745 (mt0) REVERT: A 445 LEU cc_start: 0.8337 (tp) cc_final: 0.8039 (tp) REVERT: A 458 TYR cc_start: 0.8228 (t80) cc_final: 0.8027 (t80) REVERT: A 460 HIS cc_start: 0.7700 (m90) cc_final: 0.7291 (m-70) REVERT: A 463 ASN cc_start: 0.6611 (m-40) cc_final: 0.6314 (m-40) REVERT: A 466 HIS cc_start: 0.8247 (t-90) cc_final: 0.8035 (t70) REVERT: A 517 ILE cc_start: 0.8763 (mt) cc_final: 0.8227 (mt) REVERT: A 518 ARG cc_start: 0.7852 (ptp-110) cc_final: 0.7421 (ptp-110) REVERT: A 527 PHE cc_start: 0.8497 (m-10) cc_final: 0.8221 (m-80) REVERT: A 528 GLN cc_start: 0.7574 (mm-40) cc_final: 0.6850 (mm-40) REVERT: A 541 LEU cc_start: 0.8329 (mt) cc_final: 0.7969 (mt) REVERT: A 554 ARG cc_start: 0.7302 (tmm-80) cc_final: 0.7027 (tmm-80) REVERT: A 563 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.8052 (mmm-85) REVERT: A 567 SER cc_start: 0.7999 (t) cc_final: 0.7674 (t) REVERT: A 590 LYS cc_start: 0.7781 (mmtm) cc_final: 0.7333 (mmtm) REVERT: A 592 VAL cc_start: 0.8201 (t) cc_final: 0.7740 (m) REVERT: B 345 GLU cc_start: 0.6189 (mp0) cc_final: 0.5874 (mp0) REVERT: B 362 THR cc_start: 0.7481 (m) cc_final: 0.7277 (m) REVERT: B 367 LYS cc_start: 0.7547 (mmtt) cc_final: 0.6537 (mmtt) REVERT: B 393 GLU cc_start: 0.7153 (tp30) cc_final: 0.6620 (tp30) REVERT: B 399 LYS cc_start: 0.8266 (mmtp) cc_final: 0.7846 (mmtp) REVERT: B 409 MET cc_start: 0.5774 (mtm) cc_final: 0.5566 (mtm) REVERT: B 411 TYR cc_start: 0.7054 (p90) cc_final: 0.6848 (p90) REVERT: B 412 MET cc_start: 0.6445 (ppp) cc_final: 0.5847 (ppp) REVERT: B 414 LYS cc_start: 0.8255 (tppt) cc_final: 0.8028 (tptp) REVERT: B 419 ILE cc_start: 0.6867 (mm) cc_final: 0.6516 (mm) REVERT: B 422 GLN cc_start: 0.7736 (tt0) cc_final: 0.7270 (pt0) REVERT: B 425 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6829 (mm-30) REVERT: B 429 LEU cc_start: 0.8119 (tp) cc_final: 0.7872 (tp) REVERT: B 432 HIS cc_start: 0.7131 (m90) cc_final: 0.6827 (m90) REVERT: B 439 LYS cc_start: 0.8491 (mppt) cc_final: 0.8109 (mppt) REVERT: B 441 GLN cc_start: 0.7257 (mt0) cc_final: 0.7035 (mp10) REVERT: B 442 MET cc_start: 0.6962 (mpp) cc_final: 0.6655 (mpp) REVERT: B 456 MET cc_start: 0.6968 (mmm) cc_final: 0.6026 (mmm) REVERT: B 460 HIS cc_start: 0.7556 (m170) cc_final: 0.6844 (m-70) REVERT: B 470 LYS cc_start: 0.8317 (mtpt) cc_final: 0.7799 (mtpt) REVERT: B 471 SER cc_start: 0.7559 (p) cc_final: 0.7107 (p) REVERT: B 483 LYS cc_start: 0.8028 (mttm) cc_final: 0.6923 (mttm) REVERT: B 511 TRP cc_start: 0.7113 (m-90) cc_final: 0.6811 (m-90) REVERT: B 517 ILE cc_start: 0.8757 (mt) cc_final: 0.8043 (mt) REVERT: B 518 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.7085 (mtm-85) REVERT: B 528 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7077 (mm-40) REVERT: B 534 TYR cc_start: 0.7897 (t80) cc_final: 0.7599 (t80) REVERT: B 542 MET cc_start: 0.6480 (mtp) cc_final: 0.6250 (mtp) REVERT: B 545 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7288 (mt-10) REVERT: B 554 ARG cc_start: 0.7368 (tmm-80) cc_final: 0.7119 (tmm-80) REVERT: B 556 GLN cc_start: 0.8242 (tt0) cc_final: 0.8009 (tt0) REVERT: B 560 MET cc_start: 0.7707 (tpp) cc_final: 0.7424 (tpp) REVERT: B 567 SER cc_start: 0.8064 (t) cc_final: 0.7597 (t) REVERT: B 583 ARG cc_start: 0.8248 (ptp-170) cc_final: 0.7937 (ptp-110) REVERT: B 603 LEU cc_start: 0.8334 (tp) cc_final: 0.8122 (tp) REVERT: B 622 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6769 (tm-30) REVERT: C 9 LEU cc_start: 0.8198 (mt) cc_final: 0.7984 (mt) REVERT: C 25 MET cc_start: 0.7521 (pmm) cc_final: 0.7184 (pmm) REVERT: C 29 MET cc_start: 0.8827 (tpp) cc_final: 0.8374 (mmm) REVERT: C 43 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8409 (mp0) REVERT: C 52 LYS cc_start: 0.8464 (tptm) cc_final: 0.8214 (tptm) REVERT: C 87 GLU cc_start: 0.8065 (pt0) cc_final: 0.7745 (pt0) REVERT: C 91 LYS cc_start: 0.8503 (tppt) cc_final: 0.7540 (tppt) REVERT: C 94 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8260 (ttpt) REVERT: C 95 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7283 (mt-10) REVERT: C 98 GLU cc_start: 0.6891 (tp30) cc_final: 0.5588 (tp30) REVERT: C 102 ASP cc_start: 0.7719 (m-30) cc_final: 0.6618 (m-30) REVERT: C 125 LEU cc_start: 0.8112 (mt) cc_final: 0.7870 (mt) REVERT: C 126 LYS cc_start: 0.8668 (tttm) cc_final: 0.8175 (tttm) REVERT: C 127 MET cc_start: 0.7855 (mmm) cc_final: 0.7196 (mmm) REVERT: C 130 ASP cc_start: 0.6928 (m-30) cc_final: 0.6205 (m-30) REVERT: C 132 TYR cc_start: 0.8173 (m-80) cc_final: 0.7335 (m-80) REVERT: C 133 ARG cc_start: 0.8211 (ttp-110) cc_final: 0.7530 (ttp80) REVERT: C 134 TYR cc_start: 0.7925 (m-10) cc_final: 0.7380 (m-80) REVERT: C 135 LEU cc_start: 0.8500 (mt) cc_final: 0.8249 (mt) REVERT: C 149 GLU cc_start: 0.8192 (tp30) cc_final: 0.7831 (tp30) REVERT: C 150 ASP cc_start: 0.8060 (m-30) cc_final: 0.7825 (m-30) REVERT: C 153 LYS cc_start: 0.8705 (tppt) cc_final: 0.7892 (tppt) REVERT: C 174 LEU cc_start: 0.8094 (mt) cc_final: 0.7738 (mt) REVERT: C 202 PHE cc_start: 0.8590 (t80) cc_final: 0.8350 (t80) REVERT: C 224 MET cc_start: 0.7365 (ptm) cc_final: 0.6342 (ptm) REVERT: C 225 GLN cc_start: 0.7523 (mm110) cc_final: 0.6675 (mm110) REVERT: C 226 LEU cc_start: 0.8271 (tt) cc_final: 0.7813 (tt) REVERT: D 14 LYS cc_start: 0.8822 (mttt) cc_final: 0.8431 (mttt) REVERT: D 20 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6947 (tm-30) REVERT: D 25 MET cc_start: 0.7582 (pmm) cc_final: 0.7276 (pmm) REVERT: D 29 MET cc_start: 0.8599 (tpp) cc_final: 0.8241 (mmm) REVERT: D 30 LYS cc_start: 0.7975 (mtmm) cc_final: 0.7683 (mttm) REVERT: D 34 GLU cc_start: 0.7896 (pp20) cc_final: 0.7533 (pp20) REVERT: D 43 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8299 (mt-10) REVERT: D 52 LYS cc_start: 0.8471 (tptm) cc_final: 0.7921 (tptm) REVERT: D 59 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7575 (mtp180) REVERT: D 65 ILE cc_start: 0.8635 (pt) cc_final: 0.8305 (pt) REVERT: D 66 SER cc_start: 0.8030 (m) cc_final: 0.7313 (m) REVERT: D 84 MET cc_start: 0.7624 (ptp) cc_final: 0.7103 (ptp) REVERT: D 87 GLU cc_start: 0.8129 (pt0) cc_final: 0.7795 (pt0) REVERT: D 91 LYS cc_start: 0.8627 (tppt) cc_final: 0.7969 (tppt) REVERT: D 93 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8051 (mt-10) REVERT: D 102 ASP cc_start: 0.7488 (m-30) cc_final: 0.7172 (m-30) REVERT: D 119 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7808 (tp30) REVERT: D 125 LEU cc_start: 0.8069 (mt) cc_final: 0.7821 (mt) REVERT: D 127 MET cc_start: 0.7860 (mmm) cc_final: 0.7273 (mmp) REVERT: D 130 ASP cc_start: 0.7024 (m-30) cc_final: 0.6593 (m-30) REVERT: D 133 ARG cc_start: 0.8182 (ttp-110) cc_final: 0.7880 (ttp-110) REVERT: D 153 LYS cc_start: 0.8517 (tppt) cc_final: 0.7565 (tppt) REVERT: D 155 TYR cc_start: 0.7312 (m-10) cc_final: 0.7027 (m-80) REVERT: D 174 LEU cc_start: 0.8140 (mt) cc_final: 0.7912 (mt) REVERT: D 192 ASP cc_start: 0.8267 (p0) cc_final: 0.7536 (p0) REVERT: D 193 LYS cc_start: 0.8197 (mttt) cc_final: 0.7715 (mptt) REVERT: D 220 SER cc_start: 0.7268 (m) cc_final: 0.6961 (m) REVERT: D 224 MET cc_start: 0.7518 (ptm) cc_final: 0.6389 (ptm) REVERT: D 225 GLN cc_start: 0.7604 (mm110) cc_final: 0.6760 (mm110) REVERT: D 226 LEU cc_start: 0.8438 (tt) cc_final: 0.7938 (tt) REVERT: E 88 LYS cc_start: 0.8401 (mmmt) cc_final: 0.7962 (mmmt) REVERT: E 125 TYR cc_start: 0.7988 (m-80) cc_final: 0.7076 (m-80) REVERT: E 144 GLU cc_start: 0.7178 (pt0) cc_final: 0.6537 (pt0) REVERT: E 146 MET cc_start: 0.6781 (tpp) cc_final: 0.6513 (tpp) REVERT: E 160 ARG cc_start: 0.7279 (mpp80) cc_final: 0.6665 (mpp80) REVERT: E 168 LYS cc_start: 0.8326 (ttmm) cc_final: 0.7814 (ttmm) REVERT: E 175 LYS cc_start: 0.8729 (ptmt) cc_final: 0.8213 (ptmt) REVERT: E 187 MET cc_start: 0.6282 (mtt) cc_final: 0.5956 (mtm) REVERT: E 236 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7379 (tm-30) REVERT: E 249 MET cc_start: 0.8084 (ppp) cc_final: 0.7874 (ppp) REVERT: E 253 LEU cc_start: 0.8767 (mt) cc_final: 0.8510 (mt) REVERT: E 255 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7400 (tm-30) REVERT: E 256 MET cc_start: 0.7733 (ptm) cc_final: 0.6957 (ptm) REVERT: E 267 ASP cc_start: 0.7739 (p0) cc_final: 0.7400 (p0) REVERT: E 316 TYR cc_start: 0.7690 (t80) cc_final: 0.7295 (t80) REVERT: E 319 ASN cc_start: 0.7922 (t0) cc_final: 0.6682 (t0) REVERT: E 320 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7704 (mm-30) REVERT: E 333 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8400 (mt-10) REVERT: E 344 LYS cc_start: 0.8508 (tttt) cc_final: 0.8123 (mttt) REVERT: E 353 LYS cc_start: 0.8000 (mptt) cc_final: 0.7792 (mptt) REVERT: F 88 LYS cc_start: 0.8482 (mmmt) cc_final: 0.7985 (mmmt) REVERT: F 96 ARG cc_start: 0.7360 (ptm160) cc_final: 0.6730 (ptm160) REVERT: F 110 GLN cc_start: 0.8207 (mm-40) cc_final: 0.8004 (mp10) REVERT: F 125 TYR cc_start: 0.8033 (m-80) cc_final: 0.7215 (m-80) REVERT: F 163 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7900 (mt-10) REVERT: F 175 LYS cc_start: 0.8744 (ptmt) cc_final: 0.8232 (ptmt) REVERT: F 195 ASN cc_start: 0.7302 (t0) cc_final: 0.7086 (t0) REVERT: F 206 LEU cc_start: 0.6463 (tp) cc_final: 0.6173 (tp) REVERT: F 227 ARG cc_start: 0.7326 (mtm180) cc_final: 0.7032 (mtm180) REVERT: F 253 LEU cc_start: 0.8720 (mt) cc_final: 0.8509 (mt) REVERT: F 256 MET cc_start: 0.7827 (ptm) cc_final: 0.7425 (ptm) REVERT: F 267 ASP cc_start: 0.7507 (p0) cc_final: 0.7035 (p0) REVERT: F 316 TYR cc_start: 0.7713 (t80) cc_final: 0.7282 (t80) REVERT: F 318 VAL cc_start: 0.8384 (p) cc_final: 0.8114 (m) REVERT: F 319 ASN cc_start: 0.7805 (t0) cc_final: 0.6424 (t0) REVERT: F 320 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7540 (mm-30) REVERT: F 324 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7585 (mmtt) REVERT: F 333 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8298 (mt-10) outliers start: 0 outliers final: 0 residues processed: 671 average time/residue: 0.2826 time to fit residues: 257.6079 Evaluate side-chains 661 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 661 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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: 4.9990 chunk 84 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN D 11 GLN D 117 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12876 Z= 0.284 Angle : 0.690 11.004 17364 Z= 0.364 Chirality : 0.046 0.182 1918 Planarity : 0.005 0.050 2216 Dihedral : 5.632 55.345 1740 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 25.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.07 % Allowed : 2.67 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.20), residues: 1538 helix: 0.52 (0.16), residues: 882 sheet: -2.45 (0.61), residues: 48 loop : -1.29 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 368 HIS 0.012 0.002 HIS B 466 PHE 0.024 0.002 PHE B 599 TYR 0.023 0.002 TYR C 131 ARG 0.008 0.001 ARG F 181 *********************** 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 671 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 670 time to evaluate : 1.443 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 342 TRP cc_start: 0.8496 (m100) cc_final: 0.8242 (m100) REVERT: A 359 SER cc_start: 0.8106 (m) cc_final: 0.7573 (p) REVERT: A 367 LYS cc_start: 0.7518 (mmtt) cc_final: 0.6637 (mmtt) REVERT: A 387 PHE cc_start: 0.7946 (t80) cc_final: 0.7708 (t80) REVERT: A 390 PHE cc_start: 0.7604 (t80) cc_final: 0.7146 (t80) REVERT: A 391 ARG cc_start: 0.8160 (mmt90) cc_final: 0.7547 (tpp80) REVERT: A 397 LEU cc_start: 0.8513 (mt) cc_final: 0.8221 (mm) REVERT: A 412 MET cc_start: 0.6597 (ppp) cc_final: 0.5975 (ppp) REVERT: A 414 LYS cc_start: 0.8165 (tppt) cc_final: 0.7736 (mmmt) REVERT: A 417 LEU cc_start: 0.7807 (pt) cc_final: 0.7383 (pt) REVERT: A 419 ILE cc_start: 0.6983 (mm) cc_final: 0.6641 (mm) REVERT: A 423 TRP cc_start: 0.7857 (t60) cc_final: 0.7643 (t60) REVERT: A 429 LEU cc_start: 0.7875 (tp) cc_final: 0.7588 (tp) REVERT: A 439 LYS cc_start: 0.8434 (mppt) cc_final: 0.7810 (mppt) REVERT: A 441 GLN cc_start: 0.6902 (mt0) cc_final: 0.6238 (mt0) REVERT: A 442 MET cc_start: 0.7117 (mpp) cc_final: 0.6635 (mpp) REVERT: A 444 GLN cc_start: 0.7566 (mt0) cc_final: 0.6711 (mt0) REVERT: A 445 LEU cc_start: 0.8311 (tp) cc_final: 0.8045 (tp) REVERT: A 460 HIS cc_start: 0.7811 (m90) cc_final: 0.7605 (m-70) REVERT: A 463 ASN cc_start: 0.6669 (m-40) cc_final: 0.6399 (m-40) REVERT: A 518 ARG cc_start: 0.7946 (ptp-110) cc_final: 0.7599 (ptp-110) REVERT: A 528 GLN cc_start: 0.7650 (mm-40) cc_final: 0.6889 (mm110) REVERT: A 534 TYR cc_start: 0.7967 (t80) cc_final: 0.7747 (t80) REVERT: A 536 ILE cc_start: 0.8212 (mm) cc_final: 0.7915 (mm) REVERT: A 541 LEU cc_start: 0.8403 (mt) cc_final: 0.7963 (mt) REVERT: A 554 ARG cc_start: 0.7404 (tmm-80) cc_final: 0.7119 (tmm-80) REVERT: A 560 MET cc_start: 0.7780 (tpp) cc_final: 0.7538 (tpp) REVERT: A 563 ARG cc_start: 0.8481 (mmm-85) cc_final: 0.8189 (mmm-85) REVERT: A 572 LYS cc_start: 0.8023 (mmmm) cc_final: 0.7576 (mmmm) REVERT: A 576 ASN cc_start: 0.7534 (t0) cc_final: 0.7325 (t0) REVERT: A 592 VAL cc_start: 0.8085 (t) cc_final: 0.7595 (m) REVERT: A 601 GLN cc_start: 0.8112 (tt0) cc_final: 0.7781 (tm-30) REVERT: A 610 GLN cc_start: 0.8095 (mm110) cc_final: 0.7730 (mm110) REVERT: B 342 TRP cc_start: 0.8482 (m100) cc_final: 0.8249 (m100) REVERT: B 345 GLU cc_start: 0.6258 (mp0) cc_final: 0.5839 (mp0) REVERT: B 362 THR cc_start: 0.7600 (m) cc_final: 0.7362 (m) REVERT: B 367 LYS cc_start: 0.7615 (mmtt) cc_final: 0.6634 (mmtt) REVERT: B 383 THR cc_start: 0.8514 (p) cc_final: 0.7971 (p) REVERT: B 385 GLU cc_start: 0.9022 (pm20) cc_final: 0.8683 (pm20) REVERT: B 393 GLU cc_start: 0.7246 (tp30) cc_final: 0.6660 (tp30) REVERT: B 399 LYS cc_start: 0.8305 (mmtp) cc_final: 0.8030 (mmtp) REVERT: B 409 MET cc_start: 0.6049 (mtm) cc_final: 0.5653 (mtm) REVERT: B 412 MET cc_start: 0.6491 (ppp) cc_final: 0.5858 (ppp) REVERT: B 414 LYS cc_start: 0.8254 (tppt) cc_final: 0.8034 (tptp) REVERT: B 419 ILE cc_start: 0.6994 (mm) cc_final: 0.6725 (mm) REVERT: B 429 LEU cc_start: 0.8161 (tp) cc_final: 0.7876 (tp) REVERT: B 439 LYS cc_start: 0.8621 (mppt) cc_final: 0.8241 (mppt) REVERT: B 441 GLN cc_start: 0.7173 (mt0) cc_final: 0.6867 (mp10) REVERT: B 442 MET cc_start: 0.7165 (mpp) cc_final: 0.6775 (mpp) REVERT: B 456 MET cc_start: 0.6937 (mmm) cc_final: 0.6142 (mmm) REVERT: B 458 TYR cc_start: 0.8287 (t80) cc_final: 0.7765 (t80) REVERT: B 460 HIS cc_start: 0.7628 (m170) cc_final: 0.7213 (m-70) REVERT: B 470 LYS cc_start: 0.8445 (mtpt) cc_final: 0.7851 (mtpt) REVERT: B 471 SER cc_start: 0.7867 (p) cc_final: 0.7345 (p) REVERT: B 484 ILE cc_start: 0.7822 (mt) cc_final: 0.7013 (mt) REVERT: B 517 ILE cc_start: 0.8864 (mt) cc_final: 0.8476 (mt) REVERT: B 518 ARG cc_start: 0.7691 (mtm-85) cc_final: 0.7271 (mtm-85) REVERT: B 528 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7056 (mm-40) REVERT: B 531 VAL cc_start: 0.7560 (t) cc_final: 0.7359 (t) REVERT: B 534 TYR cc_start: 0.7906 (t80) cc_final: 0.7595 (t80) REVERT: B 541 LEU cc_start: 0.8505 (mt) cc_final: 0.8130 (mt) REVERT: B 545 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7395 (mt-10) REVERT: B 554 ARG cc_start: 0.7472 (tmm-80) cc_final: 0.7238 (tmm-80) REVERT: B 556 GLN cc_start: 0.8281 (tt0) cc_final: 0.8075 (tt0) REVERT: B 560 MET cc_start: 0.7963 (tpp) cc_final: 0.7493 (tpp) REVERT: B 567 SER cc_start: 0.8240 (t) cc_final: 0.7935 (t) REVERT: B 572 LYS cc_start: 0.8244 (mmmm) cc_final: 0.7906 (mmmm) REVERT: B 574 TYR cc_start: 0.8048 (m-10) cc_final: 0.7764 (m-10) REVERT: B 583 ARG cc_start: 0.8208 (ptp-170) cc_final: 0.7936 (ptp-170) REVERT: B 593 LYS cc_start: 0.7882 (ttpp) cc_final: 0.7215 (tptp) REVERT: B 594 GLU cc_start: 0.7649 (pm20) cc_final: 0.7367 (pm20) REVERT: B 618 ARG cc_start: 0.7502 (ptm160) cc_final: 0.7261 (ptm160) REVERT: B 622 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6749 (tm-30) REVERT: C 14 LYS cc_start: 0.8354 (pttm) cc_final: 0.8142 (pttm) REVERT: C 20 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7050 (tm-30) REVERT: C 25 MET cc_start: 0.7397 (pmm) cc_final: 0.7034 (pmm) REVERT: C 29 MET cc_start: 0.8866 (tpp) cc_final: 0.8416 (mmm) REVERT: C 30 LYS cc_start: 0.8053 (mtmm) cc_final: 0.7719 (mttt) REVERT: C 43 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8330 (mt-10) REVERT: C 52 LYS cc_start: 0.8468 (tptm) cc_final: 0.8182 (tptm) REVERT: C 87 GLU cc_start: 0.8106 (pt0) cc_final: 0.7753 (pt0) REVERT: C 91 LYS cc_start: 0.8564 (tppt) cc_final: 0.7638 (tppt) REVERT: C 94 LYS cc_start: 0.8566 (ttpt) cc_final: 0.8287 (ttpt) REVERT: C 95 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7385 (mt-10) REVERT: C 98 GLU cc_start: 0.7111 (tp30) cc_final: 0.5748 (tp30) REVERT: C 102 ASP cc_start: 0.7820 (m-30) cc_final: 0.6807 (m-30) REVERT: C 125 LEU cc_start: 0.8156 (mt) cc_final: 0.7899 (mt) REVERT: C 126 LYS cc_start: 0.8716 (tttm) cc_final: 0.8116 (tttm) REVERT: C 127 MET cc_start: 0.7862 (mmm) cc_final: 0.7247 (mmp) REVERT: C 132 TYR cc_start: 0.8247 (m-80) cc_final: 0.7737 (m-80) REVERT: C 135 LEU cc_start: 0.8682 (mt) cc_final: 0.8458 (mt) REVERT: C 150 ASP cc_start: 0.8058 (m-30) cc_final: 0.7798 (m-30) REVERT: C 153 LYS cc_start: 0.8657 (tppt) cc_final: 0.7814 (tppt) REVERT: C 155 TYR cc_start: 0.7226 (m-80) cc_final: 0.6765 (m-80) REVERT: C 174 LEU cc_start: 0.8163 (mt) cc_final: 0.7839 (mt) REVERT: C 176 LEU cc_start: 0.8574 (tt) cc_final: 0.7397 (tt) REVERT: C 180 PHE cc_start: 0.8218 (m-80) cc_final: 0.7744 (m-80) REVERT: C 202 PHE cc_start: 0.8649 (t80) cc_final: 0.8402 (t80) REVERT: C 206 ILE cc_start: 0.8088 (mt) cc_final: 0.7888 (mt) REVERT: C 224 MET cc_start: 0.7420 (ptm) cc_final: 0.6303 (ptm) REVERT: C 225 GLN cc_start: 0.7472 (mm110) cc_final: 0.6619 (mm110) REVERT: D 14 LYS cc_start: 0.8845 (mttt) cc_final: 0.8472 (mttt) REVERT: D 20 GLU cc_start: 0.7377 (tm-30) cc_final: 0.6984 (tm-30) REVERT: D 25 MET cc_start: 0.7544 (pmm) cc_final: 0.7247 (pmm) REVERT: D 29 MET cc_start: 0.8637 (tpp) cc_final: 0.8212 (mmm) REVERT: D 30 LYS cc_start: 0.8057 (mtmm) cc_final: 0.7737 (mttt) REVERT: D 34 GLU cc_start: 0.7997 (pp20) cc_final: 0.7676 (pp20) REVERT: D 43 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8337 (mt-10) REVERT: D 52 LYS cc_start: 0.8487 (tptm) cc_final: 0.7967 (tptm) REVERT: D 59 ARG cc_start: 0.7814 (mtp-110) cc_final: 0.7547 (mtp180) REVERT: D 63 ARG cc_start: 0.7761 (tpp-160) cc_final: 0.7534 (tpp-160) REVERT: D 65 ILE cc_start: 0.8654 (pt) cc_final: 0.8318 (pt) REVERT: D 66 SER cc_start: 0.8088 (m) cc_final: 0.7382 (m) REVERT: D 84 MET cc_start: 0.7613 (ptp) cc_final: 0.7124 (ptp) REVERT: D 87 GLU cc_start: 0.8160 (pt0) cc_final: 0.7839 (pt0) REVERT: D 91 LYS cc_start: 0.8682 (tppt) cc_final: 0.7928 (tppt) REVERT: D 93 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8114 (mt-10) REVERT: D 102 ASP cc_start: 0.7612 (m-30) cc_final: 0.7329 (m-30) REVERT: D 119 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7907 (tp30) REVERT: D 127 MET cc_start: 0.7907 (mmm) cc_final: 0.7590 (mmm) REVERT: D 128 LYS cc_start: 0.8118 (tttt) cc_final: 0.7615 (tttt) REVERT: D 130 ASP cc_start: 0.7044 (m-30) cc_final: 0.6677 (m-30) REVERT: D 133 ARG cc_start: 0.8228 (ttp-110) cc_final: 0.7872 (ttp-110) REVERT: D 153 LYS cc_start: 0.8467 (tppt) cc_final: 0.7547 (tppt) REVERT: D 155 TYR cc_start: 0.7443 (m-10) cc_final: 0.6830 (m-80) REVERT: D 174 LEU cc_start: 0.8242 (mt) cc_final: 0.7976 (mt) REVERT: D 176 LEU cc_start: 0.8678 (tt) cc_final: 0.7535 (tt) REVERT: D 180 PHE cc_start: 0.8271 (m-80) cc_final: 0.7692 (m-80) REVERT: D 220 SER cc_start: 0.7339 (m) cc_final: 0.7059 (m) REVERT: D 224 MET cc_start: 0.7656 (ptm) cc_final: 0.6475 (ptm) REVERT: D 225 GLN cc_start: 0.7614 (mm110) cc_final: 0.6799 (mm110) REVERT: D 226 LEU cc_start: 0.8433 (tt) cc_final: 0.8008 (tt) REVERT: E 125 TYR cc_start: 0.8024 (m-80) cc_final: 0.7187 (m-80) REVERT: E 160 ARG cc_start: 0.7308 (mpp80) cc_final: 0.6799 (mpp80) REVERT: E 168 LYS cc_start: 0.8341 (ttmm) cc_final: 0.7844 (ttmm) REVERT: E 175 LYS cc_start: 0.8788 (ptmt) cc_final: 0.8248 (ptmt) REVERT: E 192 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7387 (ttpt) REVERT: E 206 LEU cc_start: 0.6736 (tp) cc_final: 0.6265 (tp) REVERT: E 236 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7516 (tm-30) REVERT: E 249 MET cc_start: 0.8144 (ppp) cc_final: 0.7932 (ppp) REVERT: E 253 LEU cc_start: 0.8746 (mt) cc_final: 0.8489 (mt) REVERT: E 256 MET cc_start: 0.7759 (ptm) cc_final: 0.7352 (ptm) REVERT: E 267 ASP cc_start: 0.7842 (p0) cc_final: 0.7531 (p0) REVERT: E 316 TYR cc_start: 0.7707 (t80) cc_final: 0.7334 (t80) REVERT: E 319 ASN cc_start: 0.8045 (t0) cc_final: 0.6752 (t0) REVERT: E 320 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7664 (mm-30) REVERT: E 324 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7716 (mmtt) REVERT: E 333 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8436 (mt-10) REVERT: E 344 LYS cc_start: 0.8541 (tttt) cc_final: 0.8181 (mttt) REVERT: E 353 LYS cc_start: 0.8113 (mptt) cc_final: 0.7886 (mptt) REVERT: E 356 MET cc_start: 0.7083 (ppp) cc_final: 0.6556 (ppp) REVERT: F 88 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8022 (mmmt) REVERT: F 96 ARG cc_start: 0.7244 (ptm160) cc_final: 0.6601 (ptm160) REVERT: F 125 TYR cc_start: 0.8024 (m-80) cc_final: 0.7348 (m-80) REVERT: F 163 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8083 (mt-10) REVERT: F 175 LYS cc_start: 0.8798 (ptmt) cc_final: 0.8298 (ptmt) REVERT: F 195 ASN cc_start: 0.7630 (t0) cc_final: 0.7272 (t0) REVERT: F 206 LEU cc_start: 0.6383 (tp) cc_final: 0.6028 (tp) REVERT: F 219 MET cc_start: 0.7470 (mtp) cc_final: 0.7091 (mtp) REVERT: F 234 ARG cc_start: 0.7566 (ttm-80) cc_final: 0.6681 (ttm-80) REVERT: F 253 LEU cc_start: 0.8709 (mt) cc_final: 0.8504 (mt) REVERT: F 256 MET cc_start: 0.7877 (ptm) cc_final: 0.7583 (ptm) REVERT: F 267 ASP cc_start: 0.7568 (p0) cc_final: 0.7122 (p0) REVERT: F 316 TYR cc_start: 0.7712 (t80) cc_final: 0.7286 (t80) REVERT: F 319 ASN cc_start: 0.7839 (t0) cc_final: 0.6446 (t0) REVERT: F 320 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7581 (mm-30) REVERT: F 333 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8404 (mt-10) REVERT: F 353 LYS cc_start: 0.8087 (mptt) cc_final: 0.7877 (mptt) outliers start: 1 outliers final: 1 residues processed: 671 average time/residue: 0.2893 time to fit residues: 262.5051 Evaluate side-chains 670 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 669 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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: 0.0060 chunk 134 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 HIS ** 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 11 GLN D 117 ASN D 200 GLN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3499 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= 0.189 Angle : 0.667 17.928 17364 Z= 0.332 Chirality : 0.044 0.184 1918 Planarity : 0.004 0.055 2216 Dihedral : 5.444 46.382 1740 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1538 helix: 0.69 (0.17), residues: 880 sheet: -3.00 (0.46), residues: 88 loop : -1.14 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 368 HIS 0.008 0.001 HIS E 358 PHE 0.029 0.002 PHE D 202 TYR 0.033 0.002 TYR C 155 ARG 0.006 0.000 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 668 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 668 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 SER cc_start: 0.8077 (m) cc_final: 0.7582 (p) REVERT: A 367 LYS cc_start: 0.7502 (mmtt) cc_final: 0.6609 (mmtt) REVERT: A 387 PHE cc_start: 0.7892 (t80) cc_final: 0.7671 (t80) REVERT: A 391 ARG cc_start: 0.8142 (mmt90) cc_final: 0.7596 (tpp80) REVERT: A 397 LEU cc_start: 0.8512 (mt) cc_final: 0.8254 (mm) REVERT: A 409 MET cc_start: 0.5913 (mtt) cc_final: 0.5705 (mtt) REVERT: A 412 MET cc_start: 0.6290 (ppp) cc_final: 0.5807 (ppp) REVERT: A 419 ILE cc_start: 0.6935 (mm) cc_final: 0.6663 (mm) REVERT: A 422 GLN cc_start: 0.7726 (pm20) cc_final: 0.7458 (pm20) REVERT: A 439 LYS cc_start: 0.8358 (mppt) cc_final: 0.7687 (mppt) REVERT: A 441 GLN cc_start: 0.6894 (mt0) cc_final: 0.6193 (mt0) REVERT: A 442 MET cc_start: 0.6915 (mpp) cc_final: 0.6519 (mpp) REVERT: A 444 GLN cc_start: 0.7669 (mt0) cc_final: 0.6697 (mt0) REVERT: A 445 LEU cc_start: 0.8314 (tp) cc_final: 0.7975 (tp) REVERT: A 456 MET cc_start: 0.7134 (tpt) cc_final: 0.6825 (tpt) REVERT: A 458 TYR cc_start: 0.8272 (t80) cc_final: 0.7903 (t80) REVERT: A 460 HIS cc_start: 0.7710 (m90) cc_final: 0.7421 (m-70) REVERT: A 463 ASN cc_start: 0.6535 (m-40) cc_final: 0.6229 (m-40) REVERT: A 518 ARG cc_start: 0.7794 (ptp-110) cc_final: 0.7463 (ptp-110) REVERT: A 534 TYR cc_start: 0.7924 (t80) cc_final: 0.7647 (t80) REVERT: A 536 ILE cc_start: 0.8116 (mm) cc_final: 0.7888 (mm) REVERT: A 541 LEU cc_start: 0.8303 (mt) cc_final: 0.7710 (mt) REVERT: A 542 MET cc_start: 0.6378 (mtp) cc_final: 0.6094 (mtp) REVERT: A 554 ARG cc_start: 0.7360 (tmm-80) cc_final: 0.7113 (tmm-80) REVERT: A 556 GLN cc_start: 0.8219 (tt0) cc_final: 0.7965 (tt0) REVERT: A 560 MET cc_start: 0.7685 (tpp) cc_final: 0.6816 (tpp) REVERT: A 567 SER cc_start: 0.8175 (t) cc_final: 0.7723 (t) REVERT: A 572 LYS cc_start: 0.7950 (mmmm) cc_final: 0.7523 (mmmm) REVERT: A 574 TYR cc_start: 0.7472 (m-10) cc_final: 0.7112 (m-10) REVERT: A 590 LYS cc_start: 0.7769 (mmtm) cc_final: 0.7290 (mmtm) REVERT: A 592 VAL cc_start: 0.8082 (t) cc_final: 0.7574 (m) REVERT: A 601 GLN cc_start: 0.8058 (tt0) cc_final: 0.7621 (tm-30) REVERT: B 342 TRP cc_start: 0.8538 (m100) cc_final: 0.8214 (m100) REVERT: B 345 GLU cc_start: 0.6169 (mp0) cc_final: 0.5737 (mp0) REVERT: B 362 THR cc_start: 0.7641 (m) cc_final: 0.7364 (m) REVERT: B 367 LYS cc_start: 0.7616 (mmtt) cc_final: 0.6550 (mmtt) REVERT: B 369 HIS cc_start: 0.7885 (m-70) cc_final: 0.7603 (m-70) REVERT: B 383 THR cc_start: 0.8538 (p) cc_final: 0.8047 (p) REVERT: B 385 GLU cc_start: 0.9013 (pm20) cc_final: 0.8723 (pm20) REVERT: B 393 GLU cc_start: 0.7264 (tp30) cc_final: 0.6668 (tp30) REVERT: B 399 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7765 (mmtp) REVERT: B 409 MET cc_start: 0.5803 (mtm) cc_final: 0.5335 (mtm) REVERT: B 411 TYR cc_start: 0.7013 (p90) cc_final: 0.6764 (p90) REVERT: B 412 MET cc_start: 0.6146 (ppp) cc_final: 0.5556 (ppp) REVERT: B 419 ILE cc_start: 0.6934 (mm) cc_final: 0.6569 (mm) REVERT: B 439 LYS cc_start: 0.8524 (mppt) cc_final: 0.8126 (mppt) REVERT: B 441 GLN cc_start: 0.7125 (mt0) cc_final: 0.6836 (mp10) REVERT: B 442 MET cc_start: 0.6992 (mpp) cc_final: 0.6611 (mpp) REVERT: B 456 MET cc_start: 0.6930 (mmm) cc_final: 0.6083 (mmm) REVERT: B 458 TYR cc_start: 0.8180 (t80) cc_final: 0.7659 (t80) REVERT: B 459 LEU cc_start: 0.8725 (mm) cc_final: 0.8481 (mm) REVERT: B 460 HIS cc_start: 0.7607 (m170) cc_final: 0.7206 (m-70) REVERT: B 470 LYS cc_start: 0.8335 (mtpt) cc_final: 0.7724 (mtpt) REVERT: B 471 SER cc_start: 0.7595 (p) cc_final: 0.7170 (p) REVERT: B 484 ILE cc_start: 0.7872 (mt) cc_final: 0.7007 (mt) REVERT: B 517 ILE cc_start: 0.8685 (mt) cc_final: 0.8420 (mt) REVERT: B 528 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7298 (mm-40) REVERT: B 534 TYR cc_start: 0.7845 (t80) cc_final: 0.7567 (t80) REVERT: B 541 LEU cc_start: 0.8453 (mt) cc_final: 0.8030 (mt) REVERT: B 542 MET cc_start: 0.6600 (mtp) cc_final: 0.6292 (mtp) REVERT: B 545 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7420 (mt-10) REVERT: B 554 ARG cc_start: 0.7420 (tmm-80) cc_final: 0.7157 (tmm-80) REVERT: B 556 GLN cc_start: 0.8235 (tt0) cc_final: 0.7970 (tt0) REVERT: B 560 MET cc_start: 0.7899 (tpp) cc_final: 0.7434 (tpp) REVERT: B 567 SER cc_start: 0.8116 (t) cc_final: 0.7729 (t) REVERT: B 572 LYS cc_start: 0.8135 (mmmm) cc_final: 0.7675 (mmmm) REVERT: B 574 TYR cc_start: 0.7951 (m-10) cc_final: 0.7667 (m-10) REVERT: B 583 ARG cc_start: 0.8215 (ptp-170) cc_final: 0.7846 (ptp-110) REVERT: B 594 GLU cc_start: 0.7561 (pm20) cc_final: 0.7322 (pm20) REVERT: B 618 ARG cc_start: 0.7497 (ptm160) cc_final: 0.7256 (ptm160) REVERT: B 622 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6735 (tm-30) REVERT: C 14 LYS cc_start: 0.8338 (pttm) cc_final: 0.8077 (pttm) REVERT: C 25 MET cc_start: 0.7286 (pmm) cc_final: 0.6921 (pmm) REVERT: C 29 MET cc_start: 0.8830 (tpp) cc_final: 0.8428 (mmm) REVERT: C 30 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7709 (mttt) REVERT: C 43 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8176 (mt-10) REVERT: C 51 TYR cc_start: 0.7703 (m-10) cc_final: 0.7492 (m-10) REVERT: C 52 LYS cc_start: 0.8427 (tptm) cc_final: 0.8147 (tptm) REVERT: C 84 MET cc_start: 0.7344 (ptp) cc_final: 0.7036 (ptp) REVERT: C 87 GLU cc_start: 0.8050 (pt0) cc_final: 0.7672 (pt0) REVERT: C 91 LYS cc_start: 0.8524 (tppt) cc_final: 0.7660 (tppt) REVERT: C 94 LYS cc_start: 0.8560 (ttpt) cc_final: 0.8217 (ttpt) REVERT: C 95 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7432 (mt-10) REVERT: C 97 ARG cc_start: 0.8557 (mtm110) cc_final: 0.8140 (mtm110) REVERT: C 98 GLU cc_start: 0.7005 (tp30) cc_final: 0.5632 (tp30) REVERT: C 102 ASP cc_start: 0.7758 (m-30) cc_final: 0.6647 (m-30) REVERT: C 103 VAL cc_start: 0.8416 (t) cc_final: 0.7992 (t) REVERT: C 125 LEU cc_start: 0.7995 (mt) cc_final: 0.7766 (mt) REVERT: C 126 LYS cc_start: 0.8612 (tttm) cc_final: 0.8175 (tttm) REVERT: C 127 MET cc_start: 0.7666 (mmm) cc_final: 0.7181 (mmp) REVERT: C 132 TYR cc_start: 0.8127 (m-80) cc_final: 0.7614 (m-80) REVERT: C 133 ARG cc_start: 0.7155 (ptp90) cc_final: 0.6916 (ptt-90) REVERT: C 135 LEU cc_start: 0.8575 (mt) cc_final: 0.8334 (mt) REVERT: C 150 ASP cc_start: 0.8049 (m-30) cc_final: 0.7756 (m-30) REVERT: C 153 LYS cc_start: 0.8642 (tppt) cc_final: 0.7819 (tppt) REVERT: C 174 LEU cc_start: 0.8076 (mt) cc_final: 0.7784 (mt) REVERT: C 197 LEU cc_start: 0.8449 (mm) cc_final: 0.8221 (mm) REVERT: C 200 GLN cc_start: 0.8640 (pt0) cc_final: 0.8364 (pt0) REVERT: C 202 PHE cc_start: 0.8576 (t80) cc_final: 0.8353 (t80) REVERT: C 204 ASP cc_start: 0.7951 (t0) cc_final: 0.7668 (t0) REVERT: D 6 LYS cc_start: 0.8441 (ttpt) cc_final: 0.8239 (ttpt) REVERT: D 10 VAL cc_start: 0.8892 (t) cc_final: 0.8672 (t) REVERT: D 14 LYS cc_start: 0.8836 (mttt) cc_final: 0.8447 (mttt) REVERT: D 20 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6702 (tm-30) REVERT: D 25 MET cc_start: 0.7345 (pmm) cc_final: 0.7034 (pmm) REVERT: D 29 MET cc_start: 0.8612 (tpp) cc_final: 0.8224 (mmm) REVERT: D 30 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7529 (mttm) REVERT: D 32 VAL cc_start: 0.8369 (t) cc_final: 0.8154 (t) REVERT: D 34 GLU cc_start: 0.7814 (pp20) cc_final: 0.7397 (pp20) REVERT: D 43 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8328 (mt-10) REVERT: D 52 LYS cc_start: 0.8448 (tptm) cc_final: 0.7922 (tptm) REVERT: D 59 ARG cc_start: 0.7745 (mtp-110) cc_final: 0.7505 (mtp180) REVERT: D 65 ILE cc_start: 0.8610 (pt) cc_final: 0.8263 (pt) REVERT: D 66 SER cc_start: 0.8051 (m) cc_final: 0.7381 (m) REVERT: D 84 MET cc_start: 0.7401 (ptp) cc_final: 0.6880 (ptp) REVERT: D 87 GLU cc_start: 0.8150 (pt0) cc_final: 0.7842 (pt0) REVERT: D 91 LYS cc_start: 0.8640 (tppt) cc_final: 0.7865 (tppt) REVERT: D 97 ARG cc_start: 0.8769 (mtm110) cc_final: 0.8534 (mtm110) REVERT: D 102 ASP cc_start: 0.7523 (m-30) cc_final: 0.7254 (m-30) REVERT: D 119 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7808 (tp30) REVERT: D 127 MET cc_start: 0.7796 (mmm) cc_final: 0.7537 (mmm) REVERT: D 128 LYS cc_start: 0.8072 (tttt) cc_final: 0.7555 (tttt) REVERT: D 130 ASP cc_start: 0.6946 (m-30) cc_final: 0.6663 (m-30) REVERT: D 133 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7894 (ttp-110) REVERT: D 153 LYS cc_start: 0.8371 (tppt) cc_final: 0.7443 (tppt) REVERT: D 155 TYR cc_start: 0.7308 (m-10) cc_final: 0.6751 (m-80) REVERT: D 174 LEU cc_start: 0.8200 (mt) cc_final: 0.7951 (mt) REVERT: D 176 LEU cc_start: 0.8626 (tt) cc_final: 0.7476 (tt) REVERT: D 180 PHE cc_start: 0.8201 (m-80) cc_final: 0.7707 (m-80) REVERT: D 192 ASP cc_start: 0.8272 (p0) cc_final: 0.7929 (p0) REVERT: D 193 LYS cc_start: 0.8365 (mttt) cc_final: 0.8119 (mttt) REVERT: D 195 CYS cc_start: 0.7928 (m) cc_final: 0.7721 (m) REVERT: D 204 ASP cc_start: 0.7520 (t0) cc_final: 0.7263 (t0) REVERT: D 220 SER cc_start: 0.7250 (m) cc_final: 0.6949 (m) REVERT: D 224 MET cc_start: 0.7679 (ptm) cc_final: 0.7352 (ptm) REVERT: E 125 TYR cc_start: 0.8015 (m-80) cc_final: 0.7143 (m-80) REVERT: E 160 ARG cc_start: 0.7232 (mpp80) cc_final: 0.6823 (mpp80) REVERT: E 168 LYS cc_start: 0.8319 (ttmm) cc_final: 0.7776 (ttmm) REVERT: E 175 LYS cc_start: 0.8763 (ptmt) cc_final: 0.8222 (ptmt) REVERT: E 192 LYS cc_start: 0.7561 (ttpt) cc_final: 0.7326 (ttpt) REVERT: E 206 LEU cc_start: 0.6742 (tp) cc_final: 0.6331 (tp) REVERT: E 236 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7463 (tm-30) REVERT: E 253 LEU cc_start: 0.8734 (mt) cc_final: 0.8473 (mt) REVERT: E 256 MET cc_start: 0.7712 (ptm) cc_final: 0.7270 (ptm) REVERT: E 267 ASP cc_start: 0.7839 (p0) cc_final: 0.7477 (p0) REVERT: E 274 MET cc_start: 0.6041 (ppp) cc_final: 0.5836 (ppp) REVERT: E 316 TYR cc_start: 0.7650 (t80) cc_final: 0.7265 (t80) REVERT: E 319 ASN cc_start: 0.7941 (t0) cc_final: 0.6639 (t0) REVERT: E 320 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7626 (mm-30) REVERT: E 324 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7682 (mmtt) REVERT: E 333 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8285 (mt-10) REVERT: E 344 LYS cc_start: 0.8503 (tttt) cc_final: 0.8127 (mttt) REVERT: E 353 LYS cc_start: 0.8067 (mptt) cc_final: 0.7779 (mptt) REVERT: E 356 MET cc_start: 0.7068 (ppp) cc_final: 0.6517 (ppp) REVERT: E 360 PHE cc_start: 0.7823 (p90) cc_final: 0.7567 (p90) REVERT: F 88 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8015 (mmmt) REVERT: F 96 ARG cc_start: 0.7261 (ptm160) cc_final: 0.6559 (ptm160) REVERT: F 125 TYR cc_start: 0.8039 (m-80) cc_final: 0.7317 (m-80) REVERT: F 175 LYS cc_start: 0.8769 (ptmt) cc_final: 0.8281 (ptmt) REVERT: F 195 ASN cc_start: 0.7547 (t0) cc_final: 0.7318 (t0) REVERT: F 206 LEU cc_start: 0.6464 (tp) cc_final: 0.6111 (tp) REVERT: F 219 MET cc_start: 0.7360 (mtp) cc_final: 0.7098 (mtp) REVERT: F 227 ARG cc_start: 0.7322 (mtm180) cc_final: 0.6952 (mtm180) REVERT: F 234 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.6723 (ttm-80) REVERT: F 253 LEU cc_start: 0.8700 (mt) cc_final: 0.8494 (mt) REVERT: F 256 MET cc_start: 0.7858 (ptm) cc_final: 0.7528 (ptm) REVERT: F 267 ASP cc_start: 0.7582 (p0) cc_final: 0.7152 (p0) REVERT: F 316 TYR cc_start: 0.7663 (t80) cc_final: 0.7256 (t80) REVERT: F 319 ASN cc_start: 0.7791 (t0) cc_final: 0.6473 (t0) REVERT: F 320 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7631 (mm-30) REVERT: F 324 LYS cc_start: 0.8062 (mmtt) cc_final: 0.7564 (mmtt) REVERT: F 333 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8320 (mt-10) outliers start: 0 outliers final: 0 residues processed: 668 average time/residue: 0.2838 time to fit residues: 256.0143 Evaluate side-chains 666 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 666 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 0.2980 chunk 84 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 225 GLN D 117 ASN ** D 200 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12876 Z= 0.242 Angle : 0.673 11.261 17364 Z= 0.348 Chirality : 0.045 0.176 1918 Planarity : 0.004 0.052 2216 Dihedral : 5.424 37.308 1740 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -0.29 (0.21), residues: 1538 helix: 0.70 (0.17), residues: 878 sheet: -2.07 (0.59), residues: 60 loop : -1.28 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 368 HIS 0.007 0.001 HIS E 358 PHE 0.027 0.002 PHE C 180 TYR 0.029 0.002 TYR C 131 ARG 0.009 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 661 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 661 time to evaluate : 1.756 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 367 LYS cc_start: 0.7584 (mmtt) cc_final: 0.6681 (mmtt) REVERT: A 387 PHE cc_start: 0.7918 (t80) cc_final: 0.7682 (t80) REVERT: A 390 PHE cc_start: 0.7622 (t80) cc_final: 0.7020 (t80) REVERT: A 391 ARG cc_start: 0.8178 (mmt90) cc_final: 0.7666 (tpp80) REVERT: A 409 MET cc_start: 0.6077 (mtt) cc_final: 0.5824 (mtt) REVERT: A 412 MET cc_start: 0.6417 (ppp) cc_final: 0.5884 (ppp) REVERT: A 417 LEU cc_start: 0.7938 (pt) cc_final: 0.7544 (pt) REVERT: A 419 ILE cc_start: 0.6979 (mm) cc_final: 0.6538 (mm) REVERT: A 422 GLN cc_start: 0.7586 (pm20) cc_final: 0.7255 (pm20) REVERT: A 429 LEU cc_start: 0.7893 (tp) cc_final: 0.7603 (tp) REVERT: A 439 LYS cc_start: 0.8399 (mppt) cc_final: 0.7740 (mppt) REVERT: A 441 GLN cc_start: 0.6906 (mt0) cc_final: 0.6208 (mt0) REVERT: A 442 MET cc_start: 0.6990 (mpp) cc_final: 0.6582 (mpp) REVERT: A 444 GLN cc_start: 0.7646 (mt0) cc_final: 0.6703 (mt0) REVERT: A 445 LEU cc_start: 0.8338 (tp) cc_final: 0.7971 (tp) REVERT: A 456 MET cc_start: 0.7200 (tpt) cc_final: 0.6718 (tpt) REVERT: A 458 TYR cc_start: 0.8259 (t80) cc_final: 0.7927 (t80) REVERT: A 459 LEU cc_start: 0.8792 (mm) cc_final: 0.8573 (mm) REVERT: A 460 HIS cc_start: 0.7745 (m90) cc_final: 0.7286 (m-70) REVERT: A 463 ASN cc_start: 0.6651 (m-40) cc_final: 0.6324 (m-40) REVERT: A 518 ARG cc_start: 0.7815 (ptp-110) cc_final: 0.7463 (ptp-110) REVERT: A 527 PHE cc_start: 0.8546 (m-10) cc_final: 0.8307 (m-80) REVERT: A 534 TYR cc_start: 0.7984 (t80) cc_final: 0.7674 (t80) REVERT: A 536 ILE cc_start: 0.8152 (mm) cc_final: 0.7831 (mm) REVERT: A 541 LEU cc_start: 0.8342 (mt) cc_final: 0.7793 (mt) REVERT: A 542 MET cc_start: 0.6496 (mtp) cc_final: 0.6155 (mtp) REVERT: A 556 GLN cc_start: 0.8323 (tt0) cc_final: 0.8034 (tt0) REVERT: A 560 MET cc_start: 0.7783 (tpp) cc_final: 0.7521 (tpp) REVERT: A 572 LYS cc_start: 0.8032 (mmmm) cc_final: 0.7571 (mmmm) REVERT: A 574 TYR cc_start: 0.7652 (m-10) cc_final: 0.7220 (m-10) REVERT: A 575 LYS cc_start: 0.8011 (pptt) cc_final: 0.7785 (pptt) REVERT: A 592 VAL cc_start: 0.8054 (t) cc_final: 0.7558 (m) REVERT: A 601 GLN cc_start: 0.8109 (tt0) cc_final: 0.7700 (tm-30) REVERT: B 342 TRP cc_start: 0.8536 (m100) cc_final: 0.8204 (m100) REVERT: B 345 GLU cc_start: 0.6266 (mp0) cc_final: 0.5788 (mp0) REVERT: B 362 THR cc_start: 0.7655 (m) cc_final: 0.7375 (m) REVERT: B 367 LYS cc_start: 0.7667 (mmtt) cc_final: 0.6632 (mmtt) REVERT: B 369 HIS cc_start: 0.7916 (m-70) cc_final: 0.7591 (m-70) REVERT: B 383 THR cc_start: 0.8541 (p) cc_final: 0.8003 (p) REVERT: B 385 GLU cc_start: 0.9006 (pm20) cc_final: 0.8704 (pm20) REVERT: B 393 GLU cc_start: 0.7342 (tp30) cc_final: 0.6711 (tp30) REVERT: B 399 LYS cc_start: 0.8214 (mmtp) cc_final: 0.8008 (mmtp) REVERT: B 409 MET cc_start: 0.5891 (mtm) cc_final: 0.5495 (mtm) REVERT: B 412 MET cc_start: 0.6313 (ppp) cc_final: 0.5716 (ppp) REVERT: B 417 LEU cc_start: 0.7927 (pt) cc_final: 0.7719 (pt) REVERT: B 419 ILE cc_start: 0.6993 (mm) cc_final: 0.6652 (mm) REVERT: B 422 GLN cc_start: 0.7850 (tt0) cc_final: 0.7354 (pt0) REVERT: B 429 LEU cc_start: 0.8111 (tp) cc_final: 0.7810 (tp) REVERT: B 439 LYS cc_start: 0.8588 (mppt) cc_final: 0.8186 (mppt) REVERT: B 441 GLN cc_start: 0.7108 (mt0) cc_final: 0.6836 (mp10) REVERT: B 442 MET cc_start: 0.7045 (mpp) cc_final: 0.6685 (mpp) REVERT: B 456 MET cc_start: 0.7008 (mmm) cc_final: 0.6058 (mmm) REVERT: B 458 TYR cc_start: 0.8219 (t80) cc_final: 0.7734 (t80) REVERT: B 460 HIS cc_start: 0.7625 (m170) cc_final: 0.7290 (m-70) REVERT: B 470 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7661 (mtpt) REVERT: B 471 SER cc_start: 0.7780 (p) cc_final: 0.7362 (p) REVERT: B 484 ILE cc_start: 0.7842 (mt) cc_final: 0.7078 (mt) REVERT: B 517 ILE cc_start: 0.8711 (mt) cc_final: 0.8422 (mt) REVERT: B 518 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7576 (mtm-85) REVERT: B 528 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7312 (mm-40) REVERT: B 534 TYR cc_start: 0.7843 (t80) cc_final: 0.7555 (t80) REVERT: B 541 LEU cc_start: 0.8520 (mt) cc_final: 0.8072 (mt) REVERT: B 542 MET cc_start: 0.6653 (mtp) cc_final: 0.6409 (mtp) REVERT: B 545 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7418 (mt-10) REVERT: B 554 ARG cc_start: 0.7480 (tmm-80) cc_final: 0.7195 (tmm-80) REVERT: B 556 GLN cc_start: 0.8328 (tt0) cc_final: 0.8125 (tt0) REVERT: B 560 MET cc_start: 0.7918 (tpp) cc_final: 0.7413 (tpp) REVERT: B 574 TYR cc_start: 0.8057 (m-10) cc_final: 0.7683 (m-10) REVERT: B 583 ARG cc_start: 0.8238 (ptp-170) cc_final: 0.7918 (ptp-110) REVERT: B 592 VAL cc_start: 0.7986 (t) cc_final: 0.7753 (t) REVERT: B 594 GLU cc_start: 0.7554 (pm20) cc_final: 0.7323 (pm20) REVERT: B 603 LEU cc_start: 0.8379 (tp) cc_final: 0.8137 (tp) REVERT: B 622 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6696 (tm-30) REVERT: C 14 LYS cc_start: 0.8374 (pttm) cc_final: 0.8122 (pttm) REVERT: C 25 MET cc_start: 0.7337 (pmm) cc_final: 0.6970 (pmm) REVERT: C 29 MET cc_start: 0.8860 (tpp) cc_final: 0.8392 (mmm) REVERT: C 30 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7776 (mttt) REVERT: C 52 LYS cc_start: 0.8460 (tptm) cc_final: 0.8192 (tptm) REVERT: C 84 MET cc_start: 0.7523 (ptp) cc_final: 0.7300 (ptp) REVERT: C 87 GLU cc_start: 0.8158 (pt0) cc_final: 0.7828 (pt0) REVERT: C 91 LYS cc_start: 0.8573 (tppt) cc_final: 0.7610 (tppt) REVERT: C 94 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8239 (ttpt) REVERT: C 95 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7436 (mt-10) REVERT: C 97 ARG cc_start: 0.8562 (mtm110) cc_final: 0.8156 (mtm110) REVERT: C 98 GLU cc_start: 0.7063 (tp30) cc_final: 0.5670 (tp30) REVERT: C 102 ASP cc_start: 0.7776 (m-30) cc_final: 0.6601 (m-30) REVERT: C 103 VAL cc_start: 0.8411 (t) cc_final: 0.8048 (t) REVERT: C 126 LYS cc_start: 0.8682 (tttm) cc_final: 0.8008 (tttm) REVERT: C 127 MET cc_start: 0.7717 (mmm) cc_final: 0.7090 (mmp) REVERT: C 128 LYS cc_start: 0.8064 (tttt) cc_final: 0.7589 (tttt) REVERT: C 130 ASP cc_start: 0.6887 (m-30) cc_final: 0.5741 (m-30) REVERT: C 149 GLU cc_start: 0.8116 (tp30) cc_final: 0.7848 (tp30) REVERT: C 153 LYS cc_start: 0.8675 (tppt) cc_final: 0.7890 (tppt) REVERT: C 172 ILE cc_start: 0.8512 (tt) cc_final: 0.8247 (tt) REVERT: C 174 LEU cc_start: 0.8072 (mt) cc_final: 0.7863 (mt) REVERT: D 14 LYS cc_start: 0.8868 (mttt) cc_final: 0.8472 (mttt) REVERT: D 20 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6828 (tm-30) REVERT: D 25 MET cc_start: 0.7439 (pmm) cc_final: 0.7119 (pmm) REVERT: D 29 MET cc_start: 0.8620 (tpp) cc_final: 0.8191 (mmm) REVERT: D 30 LYS cc_start: 0.8050 (mtmm) cc_final: 0.7544 (mttm) REVERT: D 32 VAL cc_start: 0.8388 (t) cc_final: 0.8166 (t) REVERT: D 34 GLU cc_start: 0.7871 (pp20) cc_final: 0.7437 (pp20) REVERT: D 43 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8349 (mt-10) REVERT: D 52 LYS cc_start: 0.8469 (tptm) cc_final: 0.7944 (tptm) REVERT: D 59 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7549 (mtp180) REVERT: D 65 ILE cc_start: 0.8621 (pt) cc_final: 0.8354 (pt) REVERT: D 66 SER cc_start: 0.8047 (m) cc_final: 0.7446 (m) REVERT: D 84 MET cc_start: 0.7512 (ptp) cc_final: 0.7016 (ptp) REVERT: D 87 GLU cc_start: 0.8150 (pt0) cc_final: 0.7864 (pt0) REVERT: D 91 LYS cc_start: 0.8666 (tppt) cc_final: 0.7893 (tppt) REVERT: D 93 GLU cc_start: 0.8222 (tt0) cc_final: 0.7931 (tt0) REVERT: D 102 ASP cc_start: 0.7565 (m-30) cc_final: 0.7305 (m-30) REVERT: D 119 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7860 (tp30) REVERT: D 127 MET cc_start: 0.7882 (mmm) cc_final: 0.7607 (mmm) REVERT: D 128 LYS cc_start: 0.8130 (tttt) cc_final: 0.7610 (tttt) REVERT: D 130 ASP cc_start: 0.6969 (m-30) cc_final: 0.6654 (m-30) REVERT: D 133 ARG cc_start: 0.8322 (ttp-110) cc_final: 0.7999 (ttp-110) REVERT: D 153 LYS cc_start: 0.8402 (tppt) cc_final: 0.7466 (tppt) REVERT: D 155 TYR cc_start: 0.7414 (m-10) cc_final: 0.7081 (m-80) REVERT: D 174 LEU cc_start: 0.8136 (mt) cc_final: 0.7918 (mt) REVERT: D 192 ASP cc_start: 0.8207 (p0) cc_final: 0.7874 (p0) REVERT: D 193 LYS cc_start: 0.8356 (mttt) cc_final: 0.8015 (mttt) REVERT: D 204 ASP cc_start: 0.7604 (t0) cc_final: 0.7367 (t0) REVERT: D 224 MET cc_start: 0.7680 (ptm) cc_final: 0.7433 (ptm) REVERT: D 226 LEU cc_start: 0.8398 (tt) cc_final: 0.7959 (tt) REVERT: E 96 ARG cc_start: 0.7341 (ptm160) cc_final: 0.7097 (ptm160) REVERT: E 125 TYR cc_start: 0.7994 (m-80) cc_final: 0.7173 (m-80) REVERT: E 175 LYS cc_start: 0.8790 (ptmt) cc_final: 0.8257 (ptmt) REVERT: E 192 LYS cc_start: 0.7720 (ttpt) cc_final: 0.7424 (ttpt) REVERT: E 206 LEU cc_start: 0.6751 (tp) cc_final: 0.6377 (tp) REVERT: E 219 MET cc_start: 0.7633 (mtm) cc_final: 0.7411 (mtm) REVERT: E 236 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7460 (tm-30) REVERT: E 249 MET cc_start: 0.8147 (ppp) cc_final: 0.7938 (ppp) REVERT: E 253 LEU cc_start: 0.8724 (mt) cc_final: 0.8478 (mt) REVERT: E 256 MET cc_start: 0.7752 (ptm) cc_final: 0.7336 (ptm) REVERT: E 267 ASP cc_start: 0.7958 (p0) cc_final: 0.7644 (p0) REVERT: E 316 TYR cc_start: 0.7660 (t80) cc_final: 0.7304 (t80) REVERT: E 319 ASN cc_start: 0.8002 (t0) cc_final: 0.6673 (t0) REVERT: E 320 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7644 (mm-30) REVERT: E 324 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7684 (mmtt) REVERT: E 333 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8234 (mt-10) REVERT: E 344 LYS cc_start: 0.8525 (tttt) cc_final: 0.8139 (mttt) REVERT: E 353 LYS cc_start: 0.8166 (mptt) cc_final: 0.7905 (mptt) REVERT: E 356 MET cc_start: 0.7056 (ppp) cc_final: 0.6584 (ppp) REVERT: E 360 PHE cc_start: 0.7860 (p90) cc_final: 0.7413 (p90) REVERT: F 88 LYS cc_start: 0.8510 (mmmt) cc_final: 0.8010 (mmmt) REVERT: F 96 ARG cc_start: 0.7291 (ptm160) cc_final: 0.6524 (ptm160) REVERT: F 125 TYR cc_start: 0.8068 (m-80) cc_final: 0.7366 (m-80) REVERT: F 175 LYS cc_start: 0.8804 (ptmt) cc_final: 0.8340 (ptmt) REVERT: F 192 LYS cc_start: 0.7590 (ttpt) cc_final: 0.7287 (ttpt) REVERT: F 206 LEU cc_start: 0.6392 (tp) cc_final: 0.6009 (tp) REVERT: F 219 MET cc_start: 0.7397 (mtp) cc_final: 0.7117 (mtp) REVERT: F 227 ARG cc_start: 0.7361 (mtm180) cc_final: 0.6951 (mtm180) REVERT: F 249 MET cc_start: 0.8199 (ppp) cc_final: 0.7932 (ppp) REVERT: F 253 LEU cc_start: 0.8707 (mt) cc_final: 0.8450 (mt) REVERT: F 256 MET cc_start: 0.7841 (ptm) cc_final: 0.7547 (ptm) REVERT: F 267 ASP cc_start: 0.7573 (p0) cc_final: 0.7154 (p0) REVERT: F 316 TYR cc_start: 0.7667 (t80) cc_final: 0.7273 (t80) REVERT: F 319 ASN cc_start: 0.7831 (t0) cc_final: 0.6476 (t0) REVERT: F 320 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7549 (mm-30) REVERT: F 333 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8394 (mt-10) outliers start: 0 outliers final: 0 residues processed: 661 average time/residue: 0.2875 time to fit residues: 257.3245 Evaluate side-chains 658 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 658 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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: 0.6980 chunk 88 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 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 ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12876 Z= 0.204 Angle : 0.681 18.212 17364 Z= 0.345 Chirality : 0.045 0.245 1918 Planarity : 0.005 0.065 2216 Dihedral : 5.419 30.761 1740 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.21), residues: 1538 helix: 0.73 (0.17), residues: 874 sheet: -2.56 (0.54), residues: 68 loop : -1.08 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A 342 HIS 0.007 0.001 HIS E 358 PHE 0.032 0.002 PHE C 202 TYR 0.059 0.002 TYR D 101 ARG 0.011 0.001 ARG F 234 *********************** 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 664 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 664 time to evaluate : 1.380 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 359 SER cc_start: 0.8010 (m) cc_final: 0.7568 (p) REVERT: A 367 LYS cc_start: 0.7606 (mmtt) cc_final: 0.6610 (mmtt) REVERT: A 387 PHE cc_start: 0.7887 (t80) cc_final: 0.7646 (t80) REVERT: A 390 PHE cc_start: 0.7565 (t80) cc_final: 0.7004 (t80) REVERT: A 391 ARG cc_start: 0.8182 (mmt90) cc_final: 0.7663 (tpp80) REVERT: A 409 MET cc_start: 0.6149 (mtt) cc_final: 0.5897 (mtt) REVERT: A 412 MET cc_start: 0.6431 (ppp) cc_final: 0.5919 (ppp) REVERT: A 417 LEU cc_start: 0.7786 (pt) cc_final: 0.7377 (pt) REVERT: A 419 ILE cc_start: 0.6781 (mm) cc_final: 0.6392 (mm) REVERT: A 422 GLN cc_start: 0.7640 (pm20) cc_final: 0.7303 (pm20) REVERT: A 431 LYS cc_start: 0.7898 (mppt) cc_final: 0.7601 (mppt) REVERT: A 439 LYS cc_start: 0.8339 (mppt) cc_final: 0.7688 (mppt) REVERT: A 441 GLN cc_start: 0.6875 (mt0) cc_final: 0.6198 (mt0) REVERT: A 442 MET cc_start: 0.6927 (mpp) cc_final: 0.6527 (mpp) REVERT: A 444 GLN cc_start: 0.7674 (mt0) cc_final: 0.6667 (mt0) REVERT: A 445 LEU cc_start: 0.8327 (tp) cc_final: 0.8015 (tp) REVERT: A 456 MET cc_start: 0.7207 (tpt) cc_final: 0.6585 (tpt) REVERT: A 458 TYR cc_start: 0.8233 (t80) cc_final: 0.7865 (t80) REVERT: A 460 HIS cc_start: 0.7732 (m90) cc_final: 0.7236 (m90) REVERT: A 463 ASN cc_start: 0.6575 (m-40) cc_final: 0.6264 (m-40) REVERT: A 518 ARG cc_start: 0.7837 (ptp-110) cc_final: 0.7627 (ptp-110) REVERT: A 527 PHE cc_start: 0.8503 (m-10) cc_final: 0.8266 (m-80) REVERT: A 534 TYR cc_start: 0.7984 (t80) cc_final: 0.7658 (t80) REVERT: A 541 LEU cc_start: 0.8347 (mt) cc_final: 0.7760 (mt) REVERT: A 542 MET cc_start: 0.6503 (mtp) cc_final: 0.6196 (mtp) REVERT: A 560 MET cc_start: 0.7746 (tpp) cc_final: 0.6876 (tpp) REVERT: A 572 LYS cc_start: 0.7948 (mmmm) cc_final: 0.7487 (mmmm) REVERT: A 574 TYR cc_start: 0.7648 (m-10) cc_final: 0.7276 (m-10) REVERT: A 575 LYS cc_start: 0.8019 (pptt) cc_final: 0.7802 (pptt) REVERT: A 590 LYS cc_start: 0.7735 (mmtm) cc_final: 0.7238 (mmtm) REVERT: A 592 VAL cc_start: 0.8037 (t) cc_final: 0.7508 (m) REVERT: A 601 GLN cc_start: 0.8097 (tt0) cc_final: 0.7695 (tm-30) REVERT: B 342 TRP cc_start: 0.8537 (m100) cc_final: 0.8144 (m100) REVERT: B 345 GLU cc_start: 0.6230 (mp0) cc_final: 0.5736 (mp0) REVERT: B 362 THR cc_start: 0.7667 (m) cc_final: 0.7375 (m) REVERT: B 367 LYS cc_start: 0.7712 (mmtt) cc_final: 0.6646 (mmtt) REVERT: B 369 HIS cc_start: 0.7911 (m-70) cc_final: 0.7549 (m-70) REVERT: B 383 THR cc_start: 0.8536 (p) cc_final: 0.8051 (p) REVERT: B 385 GLU cc_start: 0.8992 (pm20) cc_final: 0.8714 (pm20) REVERT: B 393 GLU cc_start: 0.7331 (tp30) cc_final: 0.6733 (tp30) REVERT: B 399 LYS cc_start: 0.8138 (mmtp) cc_final: 0.7850 (mmtp) REVERT: B 409 MET cc_start: 0.5815 (mtm) cc_final: 0.5427 (mtm) REVERT: B 412 MET cc_start: 0.6333 (ppp) cc_final: 0.5738 (ppp) REVERT: B 419 ILE cc_start: 0.6954 (mm) cc_final: 0.6638 (mm) REVERT: B 422 GLN cc_start: 0.7777 (tt0) cc_final: 0.6833 (pt0) REVERT: B 429 LEU cc_start: 0.8087 (tp) cc_final: 0.7785 (tp) REVERT: B 439 LYS cc_start: 0.8549 (mppt) cc_final: 0.8123 (mppt) REVERT: B 441 GLN cc_start: 0.7100 (mt0) cc_final: 0.6819 (mp10) REVERT: B 442 MET cc_start: 0.7005 (mpp) cc_final: 0.6649 (mpp) REVERT: B 456 MET cc_start: 0.6932 (mmm) cc_final: 0.6072 (mmm) REVERT: B 458 TYR cc_start: 0.8203 (t80) cc_final: 0.7706 (t80) REVERT: B 459 LEU cc_start: 0.8750 (mm) cc_final: 0.8506 (mm) REVERT: B 460 HIS cc_start: 0.7653 (m170) cc_final: 0.7302 (m-70) REVERT: B 470 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7811 (mtpt) REVERT: B 471 SER cc_start: 0.7589 (p) cc_final: 0.7251 (p) REVERT: B 473 ASN cc_start: 0.7543 (m-40) cc_final: 0.7208 (m-40) REVERT: B 484 ILE cc_start: 0.7874 (mt) cc_final: 0.7059 (mt) REVERT: B 512 MET cc_start: 0.4614 (tmm) cc_final: 0.4385 (tmm) REVERT: B 517 ILE cc_start: 0.8668 (mt) cc_final: 0.7975 (mt) REVERT: B 528 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7197 (mm-40) REVERT: B 534 TYR cc_start: 0.7868 (t80) cc_final: 0.7589 (t80) REVERT: B 541 LEU cc_start: 0.8461 (mt) cc_final: 0.7992 (mt) REVERT: B 542 MET cc_start: 0.6685 (mtp) cc_final: 0.6429 (mtp) REVERT: B 545 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7408 (mt-10) REVERT: B 554 ARG cc_start: 0.7421 (tmm-80) cc_final: 0.7151 (tmm-80) REVERT: B 556 GLN cc_start: 0.8355 (tt0) cc_final: 0.8142 (tt0) REVERT: B 560 MET cc_start: 0.7870 (tpp) cc_final: 0.7396 (tpp) REVERT: B 567 SER cc_start: 0.8210 (t) cc_final: 0.7944 (t) REVERT: B 574 TYR cc_start: 0.8028 (m-10) cc_final: 0.7660 (m-10) REVERT: B 583 ARG cc_start: 0.8243 (ptp-170) cc_final: 0.7896 (ptp-110) REVERT: B 622 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6732 (tm-30) REVERT: C 14 LYS cc_start: 0.8461 (pttm) cc_final: 0.8162 (pttm) REVERT: C 20 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6667 (tm-30) REVERT: C 25 MET cc_start: 0.7408 (pmm) cc_final: 0.6978 (pmm) REVERT: C 29 MET cc_start: 0.8714 (mmt) cc_final: 0.8343 (mmm) REVERT: C 30 LYS cc_start: 0.8003 (mtmm) cc_final: 0.7713 (mttt) REVERT: C 52 LYS cc_start: 0.8467 (tptm) cc_final: 0.8187 (tptm) REVERT: C 84 MET cc_start: 0.7446 (ptp) cc_final: 0.7211 (ptp) REVERT: C 87 GLU cc_start: 0.8170 (pt0) cc_final: 0.7815 (pt0) REVERT: C 91 LYS cc_start: 0.8568 (tppt) cc_final: 0.7595 (tppt) REVERT: C 94 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8215 (ttpt) REVERT: C 95 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7417 (mt-10) REVERT: C 97 ARG cc_start: 0.8566 (mtm110) cc_final: 0.8152 (mtm110) REVERT: C 98 GLU cc_start: 0.7049 (tp30) cc_final: 0.5641 (tp30) REVERT: C 102 ASP cc_start: 0.7772 (m-30) cc_final: 0.6677 (m-30) REVERT: C 126 LYS cc_start: 0.8671 (tttm) cc_final: 0.8101 (tttm) REVERT: C 127 MET cc_start: 0.7633 (mmm) cc_final: 0.6817 (mmm) REVERT: C 128 LYS cc_start: 0.8082 (tttt) cc_final: 0.7605 (tttt) REVERT: C 149 GLU cc_start: 0.8040 (tp30) cc_final: 0.7815 (tp30) REVERT: C 153 LYS cc_start: 0.8645 (tppt) cc_final: 0.7864 (tppt) REVERT: C 155 TYR cc_start: 0.7435 (m-80) cc_final: 0.6932 (m-80) REVERT: C 180 PHE cc_start: 0.8194 (m-80) cc_final: 0.7637 (m-80) REVERT: C 204 ASP cc_start: 0.8042 (t0) cc_final: 0.7782 (t0) REVERT: C 226 LEU cc_start: 0.8251 (tt) cc_final: 0.7769 (tt) REVERT: D 10 VAL cc_start: 0.8902 (t) cc_final: 0.8655 (t) REVERT: D 14 LYS cc_start: 0.8872 (mttt) cc_final: 0.8473 (mttt) REVERT: D 20 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6656 (tm-30) REVERT: D 25 MET cc_start: 0.7365 (pmm) cc_final: 0.7098 (pmm) REVERT: D 29 MET cc_start: 0.8613 (tpp) cc_final: 0.8172 (mmm) REVERT: D 30 LYS cc_start: 0.8051 (mtmm) cc_final: 0.7552 (mttm) REVERT: D 32 VAL cc_start: 0.8363 (t) cc_final: 0.8152 (t) REVERT: D 34 GLU cc_start: 0.7858 (pp20) cc_final: 0.7407 (pp20) REVERT: D 43 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8394 (mt-10) REVERT: D 52 LYS cc_start: 0.8460 (tptm) cc_final: 0.7897 (tptm) REVERT: D 59 ARG cc_start: 0.7849 (mtp-110) cc_final: 0.7497 (mtp180) REVERT: D 65 ILE cc_start: 0.8620 (pt) cc_final: 0.8332 (pt) REVERT: D 66 SER cc_start: 0.8099 (m) cc_final: 0.7224 (m) REVERT: D 84 MET cc_start: 0.7424 (ptp) cc_final: 0.6877 (ptp) REVERT: D 87 GLU cc_start: 0.8118 (pt0) cc_final: 0.7795 (pt0) REVERT: D 91 LYS cc_start: 0.8647 (tppt) cc_final: 0.7876 (tppt) REVERT: D 97 ARG cc_start: 0.8513 (mtm110) cc_final: 0.7945 (mtm110) REVERT: D 101 TYR cc_start: 0.7810 (m-80) cc_final: 0.7433 (m-80) REVERT: D 102 ASP cc_start: 0.7582 (m-30) cc_final: 0.7303 (m-30) REVERT: D 119 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7854 (tp30) REVERT: D 127 MET cc_start: 0.7843 (mmm) cc_final: 0.7602 (mmm) REVERT: D 128 LYS cc_start: 0.8108 (tttt) cc_final: 0.7601 (tttt) REVERT: D 130 ASP cc_start: 0.6844 (m-30) cc_final: 0.6546 (m-30) REVERT: D 133 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.8004 (ttp-110) REVERT: D 153 LYS cc_start: 0.8358 (tppt) cc_final: 0.7399 (tppt) REVERT: D 155 TYR cc_start: 0.7273 (m-10) cc_final: 0.6695 (m-80) REVERT: D 167 GLN cc_start: 0.8268 (tp-100) cc_final: 0.8050 (tp-100) REVERT: D 170 HIS cc_start: 0.7989 (t-90) cc_final: 0.7780 (t-90) REVERT: D 174 LEU cc_start: 0.8089 (mt) cc_final: 0.7855 (mt) REVERT: D 176 LEU cc_start: 0.8650 (tt) cc_final: 0.8210 (tt) REVERT: D 180 PHE cc_start: 0.8243 (m-80) cc_final: 0.7349 (m-80) REVERT: D 192 ASP cc_start: 0.8144 (p0) cc_final: 0.7820 (p0) REVERT: D 193 LYS cc_start: 0.8306 (mttt) cc_final: 0.7991 (mttt) REVERT: D 204 ASP cc_start: 0.7573 (t0) cc_final: 0.7363 (t0) REVERT: D 220 SER cc_start: 0.7326 (m) cc_final: 0.7095 (m) REVERT: D 224 MET cc_start: 0.7704 (ptm) cc_final: 0.7404 (ptm) REVERT: D 226 LEU cc_start: 0.8392 (tt) cc_final: 0.7989 (tt) REVERT: E 96 ARG cc_start: 0.7357 (ptm160) cc_final: 0.7056 (ptm160) REVERT: E 125 TYR cc_start: 0.8004 (m-80) cc_final: 0.7160 (m-80) REVERT: E 160 ARG cc_start: 0.7078 (mpp80) cc_final: 0.6724 (mpp80) REVERT: E 168 LYS cc_start: 0.8348 (ttmm) cc_final: 0.7895 (ttmm) REVERT: E 175 LYS cc_start: 0.8773 (ptmt) cc_final: 0.8249 (ptmt) REVERT: E 187 MET cc_start: 0.4869 (ttt) cc_final: 0.3179 (ttt) REVERT: E 192 LYS cc_start: 0.7684 (ttpt) cc_final: 0.7429 (ttpt) REVERT: E 206 LEU cc_start: 0.6875 (tp) cc_final: 0.6472 (tp) REVERT: E 219 MET cc_start: 0.7558 (mtm) cc_final: 0.7344 (mtm) REVERT: E 236 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7474 (tm-30) REVERT: E 249 MET cc_start: 0.8157 (ppp) cc_final: 0.7938 (ppp) REVERT: E 253 LEU cc_start: 0.8729 (mt) cc_final: 0.8425 (mt) REVERT: E 256 MET cc_start: 0.7698 (ptm) cc_final: 0.7282 (ptm) REVERT: E 267 ASP cc_start: 0.7958 (p0) cc_final: 0.7641 (p0) REVERT: E 316 TYR cc_start: 0.7612 (t80) cc_final: 0.7299 (t80) REVERT: E 319 ASN cc_start: 0.7963 (t0) cc_final: 0.6635 (t0) REVERT: E 320 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7663 (mm-30) REVERT: E 324 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7669 (mmtt) REVERT: E 333 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8195 (mt-10) REVERT: E 344 LYS cc_start: 0.8514 (tttt) cc_final: 0.8113 (mttt) REVERT: E 353 LYS cc_start: 0.8234 (mptt) cc_final: 0.7940 (mptt) REVERT: E 356 MET cc_start: 0.7063 (ppp) cc_final: 0.6580 (ppp) REVERT: E 360 PHE cc_start: 0.7819 (p90) cc_final: 0.7378 (p90) REVERT: F 88 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8004 (mmmt) REVERT: F 96 ARG cc_start: 0.7345 (ptm160) cc_final: 0.6613 (ptm160) REVERT: F 125 TYR cc_start: 0.8022 (m-80) cc_final: 0.7306 (m-80) REVERT: F 175 LYS cc_start: 0.8799 (ptmt) cc_final: 0.8326 (ptmt) REVERT: F 192 LYS cc_start: 0.7484 (ttpt) cc_final: 0.7220 (ttpt) REVERT: F 219 MET cc_start: 0.7388 (mtp) cc_final: 0.7136 (mtp) REVERT: F 227 ARG cc_start: 0.7330 (mtm180) cc_final: 0.6902 (mtm180) REVERT: F 249 MET cc_start: 0.8110 (ppp) cc_final: 0.7865 (ppp) REVERT: F 253 LEU cc_start: 0.8710 (mt) cc_final: 0.8475 (mt) REVERT: F 256 MET cc_start: 0.7825 (ptm) cc_final: 0.7531 (ptm) REVERT: F 267 ASP cc_start: 0.7610 (p0) cc_final: 0.7205 (p0) REVERT: F 316 TYR cc_start: 0.7654 (t80) cc_final: 0.7260 (t80) REVERT: F 319 ASN cc_start: 0.7823 (t0) cc_final: 0.6432 (t0) REVERT: F 320 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7532 (mm-30) REVERT: F 344 LYS cc_start: 0.8368 (tmmt) cc_final: 0.8167 (tmmt) REVERT: F 353 LYS cc_start: 0.8072 (mptt) cc_final: 0.7764 (mptt) outliers start: 0 outliers final: 0 residues processed: 664 average time/residue: 0.2804 time to fit residues: 252.7685 Evaluate side-chains 658 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 658 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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: 10.0000 chunk 129 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 124 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN D 117 ASN D 200 GLN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12876 Z= 0.207 Angle : 0.685 14.316 17364 Z= 0.347 Chirality : 0.046 0.221 1918 Planarity : 0.004 0.054 2216 Dihedral : 5.351 31.741 1740 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -0.20 (0.21), residues: 1538 helix: 0.75 (0.17), residues: 874 sheet: -2.76 (0.52), residues: 72 loop : -1.03 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 342 HIS 0.008 0.001 HIS E 358 PHE 0.028 0.002 PHE C 202 TYR 0.047 0.002 TYR D 101 ARG 0.012 0.001 ARG F 234 *********************** 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 662 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 662 time to evaluate : 1.534 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 342 TRP cc_start: 0.8425 (m100) cc_final: 0.8169 (m100) REVERT: A 362 THR cc_start: 0.7873 (m) cc_final: 0.7602 (m) REVERT: A 367 LYS cc_start: 0.7628 (mmtt) cc_final: 0.6695 (mmtt) REVERT: A 387 PHE cc_start: 0.7878 (t80) cc_final: 0.7647 (t80) REVERT: A 390 PHE cc_start: 0.7538 (t80) cc_final: 0.7020 (t80) REVERT: A 391 ARG cc_start: 0.8181 (mmt90) cc_final: 0.7677 (tpp80) REVERT: A 407 LEU cc_start: 0.7185 (mp) cc_final: 0.6872 (mp) REVERT: A 409 MET cc_start: 0.6111 (mtt) cc_final: 0.5703 (mtt) REVERT: A 412 MET cc_start: 0.6446 (ppp) cc_final: 0.5927 (ppp) REVERT: A 417 LEU cc_start: 0.7763 (pt) cc_final: 0.7327 (pt) REVERT: A 419 ILE cc_start: 0.6793 (mm) cc_final: 0.6395 (mm) REVERT: A 431 LYS cc_start: 0.7824 (mppt) cc_final: 0.7529 (mppt) REVERT: A 439 LYS cc_start: 0.8325 (mppt) cc_final: 0.7669 (mppt) REVERT: A 441 GLN cc_start: 0.6860 (mt0) cc_final: 0.6188 (mt0) REVERT: A 442 MET cc_start: 0.6911 (mpp) cc_final: 0.6537 (mpp) REVERT: A 444 GLN cc_start: 0.7676 (mt0) cc_final: 0.6674 (mt0) REVERT: A 445 LEU cc_start: 0.8306 (tp) cc_final: 0.8007 (tp) REVERT: A 456 MET cc_start: 0.7204 (tpt) cc_final: 0.6932 (tpt) REVERT: A 458 TYR cc_start: 0.8204 (t80) cc_final: 0.7846 (t80) REVERT: A 459 LEU cc_start: 0.8779 (mm) cc_final: 0.8488 (mm) REVERT: A 460 HIS cc_start: 0.7685 (m90) cc_final: 0.7286 (m-70) REVERT: A 463 ASN cc_start: 0.6579 (m-40) cc_final: 0.6312 (m-40) REVERT: A 471 SER cc_start: 0.7614 (p) cc_final: 0.7376 (p) REVERT: A 527 PHE cc_start: 0.8482 (m-10) cc_final: 0.8265 (m-80) REVERT: A 534 TYR cc_start: 0.8035 (t80) cc_final: 0.7613 (t80) REVERT: A 541 LEU cc_start: 0.8341 (mt) cc_final: 0.7764 (mt) REVERT: A 542 MET cc_start: 0.6539 (mtp) cc_final: 0.6179 (mtp) REVERT: A 556 GLN cc_start: 0.8292 (tt0) cc_final: 0.7962 (tt0) REVERT: A 560 MET cc_start: 0.7721 (tpp) cc_final: 0.6866 (tpp) REVERT: A 572 LYS cc_start: 0.7935 (mmmm) cc_final: 0.7470 (mmmm) REVERT: A 574 TYR cc_start: 0.7642 (m-10) cc_final: 0.7271 (m-10) REVERT: A 575 LYS cc_start: 0.8008 (pptt) cc_final: 0.7796 (pptt) REVERT: A 592 VAL cc_start: 0.8060 (t) cc_final: 0.7521 (m) REVERT: A 601 GLN cc_start: 0.8094 (tt0) cc_final: 0.7681 (tm-30) REVERT: B 342 TRP cc_start: 0.8512 (m100) cc_final: 0.8150 (m100) REVERT: B 345 GLU cc_start: 0.6214 (mp0) cc_final: 0.5725 (mp0) REVERT: B 362 THR cc_start: 0.7643 (m) cc_final: 0.7367 (m) REVERT: B 367 LYS cc_start: 0.7736 (mmtt) cc_final: 0.6693 (mmtt) REVERT: B 369 HIS cc_start: 0.7909 (m-70) cc_final: 0.7539 (m-70) REVERT: B 383 THR cc_start: 0.8521 (p) cc_final: 0.8023 (p) REVERT: B 385 GLU cc_start: 0.8984 (pm20) cc_final: 0.8708 (pm20) REVERT: B 393 GLU cc_start: 0.7317 (tp30) cc_final: 0.6668 (tp30) REVERT: B 409 MET cc_start: 0.5734 (mtm) cc_final: 0.5406 (mtm) REVERT: B 412 MET cc_start: 0.6383 (ppp) cc_final: 0.5759 (ppp) REVERT: B 416 ASN cc_start: 0.7651 (p0) cc_final: 0.7441 (p0) REVERT: B 417 LEU cc_start: 0.8022 (pt) cc_final: 0.7816 (pt) REVERT: B 419 ILE cc_start: 0.6900 (mm) cc_final: 0.6593 (mm) REVERT: B 422 GLN cc_start: 0.7878 (tt0) cc_final: 0.6959 (pt0) REVERT: B 429 LEU cc_start: 0.8097 (tp) cc_final: 0.7770 (tp) REVERT: B 439 LYS cc_start: 0.8533 (mppt) cc_final: 0.8118 (mppt) REVERT: B 441 GLN cc_start: 0.7074 (mt0) cc_final: 0.6804 (mp10) REVERT: B 442 MET cc_start: 0.6999 (mpp) cc_final: 0.6653 (mpp) REVERT: B 456 MET cc_start: 0.6949 (mmm) cc_final: 0.6092 (mmm) REVERT: B 458 TYR cc_start: 0.8175 (t80) cc_final: 0.7637 (t80) REVERT: B 460 HIS cc_start: 0.7642 (m170) cc_final: 0.7260 (m-70) REVERT: B 470 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7764 (mtpt) REVERT: B 471 SER cc_start: 0.7635 (p) cc_final: 0.7259 (p) REVERT: B 473 ASN cc_start: 0.7562 (m-40) cc_final: 0.7137 (m-40) REVERT: B 484 ILE cc_start: 0.7803 (mt) cc_final: 0.7028 (mt) REVERT: B 517 ILE cc_start: 0.8697 (mt) cc_final: 0.7986 (mt) REVERT: B 518 ARG cc_start: 0.7722 (mtm-85) cc_final: 0.7514 (mtm-85) REVERT: B 534 TYR cc_start: 0.7828 (t80) cc_final: 0.7576 (t80) REVERT: B 541 LEU cc_start: 0.8469 (mt) cc_final: 0.7991 (mt) REVERT: B 542 MET cc_start: 0.6743 (mtp) cc_final: 0.6476 (mtp) REVERT: B 545 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7409 (mt-10) REVERT: B 554 ARG cc_start: 0.7436 (tmm-80) cc_final: 0.7151 (tmm-80) REVERT: B 556 GLN cc_start: 0.8347 (tt0) cc_final: 0.8121 (tt0) REVERT: B 560 MET cc_start: 0.7847 (tpp) cc_final: 0.7329 (tpp) REVERT: B 567 SER cc_start: 0.8184 (t) cc_final: 0.7957 (t) REVERT: B 574 TYR cc_start: 0.8006 (m-10) cc_final: 0.7644 (m-10) REVERT: B 583 ARG cc_start: 0.8219 (ptp-170) cc_final: 0.7896 (ptp-110) REVERT: B 593 LYS cc_start: 0.7700 (ttpp) cc_final: 0.7360 (tptp) REVERT: B 603 LEU cc_start: 0.8324 (tp) cc_final: 0.8121 (tp) REVERT: B 622 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6708 (tm-30) REVERT: C 6 LYS cc_start: 0.8594 (ttpt) cc_final: 0.8119 (ttpt) REVERT: C 12 ARG cc_start: 0.8447 (ttt180) cc_final: 0.8171 (ttt180) REVERT: C 14 LYS cc_start: 0.8427 (pttm) cc_final: 0.8105 (pttm) REVERT: C 25 MET cc_start: 0.7465 (pmm) cc_final: 0.6939 (pmm) REVERT: C 29 MET cc_start: 0.8747 (mmt) cc_final: 0.8385 (mmm) REVERT: C 32 VAL cc_start: 0.8608 (t) cc_final: 0.8378 (t) REVERT: C 34 GLU cc_start: 0.7781 (pp20) cc_final: 0.7299 (pp20) REVERT: C 52 LYS cc_start: 0.8466 (tptm) cc_final: 0.8186 (tptm) REVERT: C 87 GLU cc_start: 0.8144 (pt0) cc_final: 0.7810 (pt0) REVERT: C 91 LYS cc_start: 0.8570 (tppt) cc_final: 0.7591 (tppt) REVERT: C 92 VAL cc_start: 0.8965 (m) cc_final: 0.8624 (m) REVERT: C 94 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8209 (ttpt) REVERT: C 95 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7398 (mt-10) REVERT: C 97 ARG cc_start: 0.8574 (mtm110) cc_final: 0.8176 (mtm110) REVERT: C 98 GLU cc_start: 0.7034 (tp30) cc_final: 0.6147 (tp30) REVERT: C 126 LYS cc_start: 0.8686 (tttm) cc_final: 0.8096 (tttm) REVERT: C 127 MET cc_start: 0.7654 (mmm) cc_final: 0.6839 (mmm) REVERT: C 128 LYS cc_start: 0.8128 (tttt) cc_final: 0.7623 (tttt) REVERT: C 149 GLU cc_start: 0.8000 (tp30) cc_final: 0.7527 (tp30) REVERT: C 153 LYS cc_start: 0.8625 (tppt) cc_final: 0.7796 (tppt) REVERT: C 176 LEU cc_start: 0.8538 (tt) cc_final: 0.7662 (tt) REVERT: C 180 PHE cc_start: 0.8152 (m-80) cc_final: 0.7520 (m-80) REVERT: C 185 TYR cc_start: 0.8193 (t80) cc_final: 0.7992 (t80) REVERT: C 195 CYS cc_start: 0.8187 (m) cc_final: 0.7642 (t) REVERT: D 10 VAL cc_start: 0.8902 (t) cc_final: 0.8653 (t) REVERT: D 14 LYS cc_start: 0.8867 (mttt) cc_final: 0.8461 (mttt) REVERT: D 20 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6572 (tm-30) REVERT: D 25 MET cc_start: 0.7336 (pmm) cc_final: 0.6972 (pmm) REVERT: D 29 MET cc_start: 0.8606 (tpp) cc_final: 0.8188 (mmm) REVERT: D 30 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7530 (mtmm) REVERT: D 32 VAL cc_start: 0.8359 (t) cc_final: 0.8098 (t) REVERT: D 34 GLU cc_start: 0.7886 (pp20) cc_final: 0.7490 (pp20) REVERT: D 43 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8389 (mt-10) REVERT: D 52 LYS cc_start: 0.8457 (tptm) cc_final: 0.7920 (tptm) REVERT: D 59 ARG cc_start: 0.7851 (mtp-110) cc_final: 0.7528 (mtp180) REVERT: D 65 ILE cc_start: 0.8625 (pt) cc_final: 0.8316 (pt) REVERT: D 66 SER cc_start: 0.8046 (m) cc_final: 0.7274 (m) REVERT: D 84 MET cc_start: 0.7444 (ptp) cc_final: 0.6858 (ptp) REVERT: D 87 GLU cc_start: 0.8081 (pt0) cc_final: 0.7790 (pt0) REVERT: D 91 LYS cc_start: 0.8665 (tppt) cc_final: 0.7900 (tppt) REVERT: D 94 LYS cc_start: 0.8687 (ttpt) cc_final: 0.8366 (ttpt) REVERT: D 97 ARG cc_start: 0.8615 (mtm110) cc_final: 0.7774 (mtm110) REVERT: D 101 TYR cc_start: 0.7714 (m-80) cc_final: 0.7489 (m-80) REVERT: D 102 ASP cc_start: 0.7458 (m-30) cc_final: 0.7143 (m-30) REVERT: D 119 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7816 (tp30) REVERT: D 127 MET cc_start: 0.7829 (mmm) cc_final: 0.7559 (mmm) REVERT: D 128 LYS cc_start: 0.8110 (tttt) cc_final: 0.7607 (tttt) REVERT: D 130 ASP cc_start: 0.6873 (m-30) cc_final: 0.6514 (m-30) REVERT: D 133 ARG cc_start: 0.8353 (ttp-110) cc_final: 0.7967 (ttp-110) REVERT: D 153 LYS cc_start: 0.8360 (tppt) cc_final: 0.7416 (tppt) REVERT: D 155 TYR cc_start: 0.7288 (m-10) cc_final: 0.7018 (m-80) REVERT: D 167 GLN cc_start: 0.8284 (tp-100) cc_final: 0.8063 (tp-100) REVERT: D 170 HIS cc_start: 0.7973 (t-90) cc_final: 0.7755 (t-90) REVERT: D 174 LEU cc_start: 0.8141 (mt) cc_final: 0.7903 (mt) REVERT: D 192 ASP cc_start: 0.8303 (p0) cc_final: 0.7903 (p0) REVERT: D 193 LYS cc_start: 0.8442 (mttt) cc_final: 0.8098 (mttt) REVERT: D 195 CYS cc_start: 0.8134 (m) cc_final: 0.7782 (t) REVERT: D 204 ASP cc_start: 0.7578 (t0) cc_final: 0.7375 (t0) REVERT: D 220 SER cc_start: 0.7375 (m) cc_final: 0.7121 (m) REVERT: D 224 MET cc_start: 0.7677 (ptm) cc_final: 0.7409 (ptm) REVERT: D 226 LEU cc_start: 0.8388 (tt) cc_final: 0.7957 (tt) REVERT: E 96 ARG cc_start: 0.7314 (ptm160) cc_final: 0.7020 (ptm160) REVERT: E 125 TYR cc_start: 0.8020 (m-80) cc_final: 0.7139 (m-80) REVERT: E 146 MET cc_start: 0.5299 (tpt) cc_final: 0.4317 (tpt) REVERT: E 163 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7942 (mt-10) REVERT: E 168 LYS cc_start: 0.8354 (ttmm) cc_final: 0.7887 (ttmm) REVERT: E 175 LYS cc_start: 0.8773 (ptmt) cc_final: 0.8241 (ptmt) REVERT: E 180 LEU cc_start: 0.8910 (tp) cc_final: 0.8699 (tp) REVERT: E 187 MET cc_start: 0.3636 (ttt) cc_final: 0.3268 (ttt) REVERT: E 192 LYS cc_start: 0.7685 (ttpt) cc_final: 0.7439 (ttpt) REVERT: E 206 LEU cc_start: 0.6654 (tp) cc_final: 0.6318 (tp) REVERT: E 219 MET cc_start: 0.7534 (mtm) cc_final: 0.7293 (mtm) REVERT: E 236 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7455 (tm-30) REVERT: E 249 MET cc_start: 0.8142 (ppp) cc_final: 0.7938 (ppp) REVERT: E 253 LEU cc_start: 0.8723 (mt) cc_final: 0.8422 (mt) REVERT: E 256 MET cc_start: 0.7756 (ptm) cc_final: 0.7319 (ptm) REVERT: E 267 ASP cc_start: 0.7951 (p0) cc_final: 0.7634 (p0) REVERT: E 274 MET cc_start: 0.6125 (ppp) cc_final: 0.5758 (ppp) REVERT: E 316 TYR cc_start: 0.7606 (t80) cc_final: 0.7270 (t80) REVERT: E 319 ASN cc_start: 0.7970 (t0) cc_final: 0.6729 (t0) REVERT: E 320 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7675 (mm-30) REVERT: E 324 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7675 (mmtt) REVERT: E 333 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8175 (mt-10) REVERT: E 334 PHE cc_start: 0.8244 (t80) cc_final: 0.8036 (t80) REVERT: E 344 LYS cc_start: 0.8554 (tttt) cc_final: 0.8160 (mttt) REVERT: E 353 LYS cc_start: 0.8239 (mptt) cc_final: 0.7937 (mptt) REVERT: E 356 MET cc_start: 0.7063 (ppp) cc_final: 0.6571 (ppp) REVERT: E 360 PHE cc_start: 0.7842 (p90) cc_final: 0.7595 (p90) REVERT: F 88 LYS cc_start: 0.8487 (mmmt) cc_final: 0.8001 (mmmt) REVERT: F 96 ARG cc_start: 0.7379 (ptm160) cc_final: 0.6596 (ptm160) REVERT: F 125 TYR cc_start: 0.8029 (m-80) cc_final: 0.7263 (m-80) REVERT: F 175 LYS cc_start: 0.8785 (ptmt) cc_final: 0.8295 (ptmt) REVERT: F 192 LYS cc_start: 0.7359 (ttpt) cc_final: 0.7131 (ttpt) REVERT: F 206 LEU cc_start: 0.6436 (tp) cc_final: 0.6153 (tp) REVERT: F 219 MET cc_start: 0.7384 (mtp) cc_final: 0.7140 (mtp) REVERT: F 227 ARG cc_start: 0.7305 (mtm180) cc_final: 0.6903 (mtm180) REVERT: F 249 MET cc_start: 0.8076 (ppp) cc_final: 0.7848 (ppp) REVERT: F 253 LEU cc_start: 0.8723 (mt) cc_final: 0.8480 (mt) REVERT: F 256 MET cc_start: 0.7825 (ptm) cc_final: 0.7519 (ptm) REVERT: F 267 ASP cc_start: 0.7636 (p0) cc_final: 0.7243 (p0) REVERT: F 316 TYR cc_start: 0.7654 (t80) cc_final: 0.7261 (t80) REVERT: F 319 ASN cc_start: 0.7827 (t0) cc_final: 0.6445 (t0) REVERT: F 320 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7650 (mm-30) REVERT: F 333 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8328 (mt-10) outliers start: 0 outliers final: 0 residues processed: 662 average time/residue: 0.2736 time to fit residues: 246.8004 Evaluate side-chains 655 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 655 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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: 0.7980 chunk 89 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN D 11 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4207 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= 0.190 Angle : 0.695 18.020 17364 Z= 0.345 Chirality : 0.045 0.233 1918 Planarity : 0.004 0.054 2216 Dihedral : 5.296 32.381 1740 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.07 % Allowed : 0.36 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1538 helix: 0.84 (0.17), residues: 868 sheet: -2.62 (0.49), residues: 80 loop : -0.97 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 368 HIS 0.008 0.001 HIS E 358 PHE 0.025 0.002 PHE C 202 TYR 0.043 0.002 TYR D 101 ARG 0.011 0.001 ARG F 234 ********************** 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 666 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 665 time to evaluate : 1.506 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 345 GLU cc_start: 0.6268 (mp0) cc_final: 0.5717 (mp0) REVERT: A 362 THR cc_start: 0.7844 (m) cc_final: 0.7615 (m) REVERT: A 387 PHE cc_start: 0.7869 (t80) cc_final: 0.7640 (t80) REVERT: A 390 PHE cc_start: 0.7531 (t80) cc_final: 0.6941 (t80) REVERT: A 391 ARG cc_start: 0.8127 (mmt90) cc_final: 0.7608 (tpp80) REVERT: A 409 MET cc_start: 0.6057 (mtt) cc_final: 0.5623 (mtt) REVERT: A 412 MET cc_start: 0.6471 (ppp) cc_final: 0.5878 (ppp) REVERT: A 417 LEU cc_start: 0.7781 (pt) cc_final: 0.7294 (pt) REVERT: A 419 ILE cc_start: 0.6810 (mm) cc_final: 0.6324 (mm) REVERT: A 422 GLN cc_start: 0.7902 (pm20) cc_final: 0.7543 (pm20) REVERT: A 429 LEU cc_start: 0.7911 (tp) cc_final: 0.7656 (tp) REVERT: A 431 LYS cc_start: 0.7799 (mppt) cc_final: 0.7471 (mppt) REVERT: A 439 LYS cc_start: 0.8302 (mppt) cc_final: 0.7663 (mppt) REVERT: A 441 GLN cc_start: 0.6854 (mt0) cc_final: 0.6174 (mt0) REVERT: A 442 MET cc_start: 0.6904 (mpp) cc_final: 0.6548 (mpp) REVERT: A 444 GLN cc_start: 0.7706 (mt0) cc_final: 0.6704 (mt0) REVERT: A 445 LEU cc_start: 0.8298 (tp) cc_final: 0.7984 (tp) REVERT: A 456 MET cc_start: 0.7233 (tpt) cc_final: 0.6779 (tpt) REVERT: A 458 TYR cc_start: 0.8196 (t80) cc_final: 0.7782 (t80) REVERT: A 459 LEU cc_start: 0.8765 (mm) cc_final: 0.8500 (mm) REVERT: A 460 HIS cc_start: 0.7636 (m90) cc_final: 0.7299 (m-70) REVERT: A 462 LYS cc_start: 0.7874 (mttm) cc_final: 0.7545 (mttm) REVERT: A 463 ASN cc_start: 0.6526 (m-40) cc_final: 0.6227 (m-40) REVERT: A 471 SER cc_start: 0.7631 (p) cc_final: 0.7321 (p) REVERT: A 518 ARG cc_start: 0.7939 (ptp-110) cc_final: 0.7736 (ptp-110) REVERT: A 528 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7281 (mm-40) REVERT: A 534 TYR cc_start: 0.7966 (t80) cc_final: 0.7560 (t80) REVERT: A 536 ILE cc_start: 0.8090 (mm) cc_final: 0.7833 (mm) REVERT: A 541 LEU cc_start: 0.8297 (mt) cc_final: 0.7960 (mt) REVERT: A 542 MET cc_start: 0.6546 (mtp) cc_final: 0.6128 (mtp) REVERT: A 560 MET cc_start: 0.7729 (tpp) cc_final: 0.6848 (tpp) REVERT: A 572 LYS cc_start: 0.7900 (mmmm) cc_final: 0.7583 (mmmm) REVERT: A 575 LYS cc_start: 0.8014 (pptt) cc_final: 0.7769 (pptt) REVERT: A 590 LYS cc_start: 0.7664 (mmtm) cc_final: 0.7141 (mmtm) REVERT: A 592 VAL cc_start: 0.7965 (t) cc_final: 0.7430 (m) REVERT: A 601 GLN cc_start: 0.8105 (tt0) cc_final: 0.7676 (tm-30) REVERT: B 342 TRP cc_start: 0.8422 (m100) cc_final: 0.8176 (m100) REVERT: B 345 GLU cc_start: 0.6229 (mp0) cc_final: 0.5730 (mp0) REVERT: B 362 THR cc_start: 0.7637 (m) cc_final: 0.7363 (m) REVERT: B 367 LYS cc_start: 0.7745 (mmtt) cc_final: 0.6766 (mmtt) REVERT: B 369 HIS cc_start: 0.7854 (m-70) cc_final: 0.7522 (m-70) REVERT: B 383 THR cc_start: 0.8524 (p) cc_final: 0.8054 (p) REVERT: B 385 GLU cc_start: 0.8978 (pm20) cc_final: 0.8695 (pm20) REVERT: B 393 GLU cc_start: 0.7367 (tp30) cc_final: 0.6728 (tp30) REVERT: B 409 MET cc_start: 0.5735 (mtm) cc_final: 0.5363 (mtm) REVERT: B 412 MET cc_start: 0.6435 (ppp) cc_final: 0.5808 (ppp) REVERT: B 416 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7365 (p0) REVERT: B 417 LEU cc_start: 0.8030 (pt) cc_final: 0.7814 (pt) REVERT: B 419 ILE cc_start: 0.6873 (mm) cc_final: 0.6579 (mm) REVERT: B 422 GLN cc_start: 0.7813 (tt0) cc_final: 0.6972 (pt0) REVERT: B 429 LEU cc_start: 0.8074 (tp) cc_final: 0.7760 (tp) REVERT: B 439 LYS cc_start: 0.8485 (mppt) cc_final: 0.8033 (mppt) REVERT: B 441 GLN cc_start: 0.7092 (mt0) cc_final: 0.6809 (mp10) REVERT: B 442 MET cc_start: 0.6924 (mpp) cc_final: 0.6571 (mpp) REVERT: B 456 MET cc_start: 0.6819 (mmm) cc_final: 0.5952 (mmm) REVERT: B 458 TYR cc_start: 0.8186 (t80) cc_final: 0.7598 (t80) REVERT: B 459 LEU cc_start: 0.8779 (mm) cc_final: 0.8549 (mm) REVERT: B 460 HIS cc_start: 0.7470 (m170) cc_final: 0.7146 (m-70) REVERT: B 466 HIS cc_start: 0.8491 (t-90) cc_final: 0.8154 (t-90) REVERT: B 470 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7781 (mtpt) REVERT: B 471 SER cc_start: 0.7526 (p) cc_final: 0.7249 (p) REVERT: B 473 ASN cc_start: 0.7626 (m-40) cc_final: 0.7178 (m-40) REVERT: B 484 ILE cc_start: 0.7841 (mt) cc_final: 0.7126 (mt) REVERT: B 517 ILE cc_start: 0.8637 (mt) cc_final: 0.8390 (mt) REVERT: B 534 TYR cc_start: 0.7878 (t80) cc_final: 0.7540 (t80) REVERT: B 541 LEU cc_start: 0.8426 (mt) cc_final: 0.7941 (mt) REVERT: B 542 MET cc_start: 0.6731 (mtp) cc_final: 0.6468 (mtp) REVERT: B 545 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7413 (mt-10) REVERT: B 554 ARG cc_start: 0.7439 (tmm-80) cc_final: 0.7171 (tmm-80) REVERT: B 560 MET cc_start: 0.7868 (tpp) cc_final: 0.7350 (tpp) REVERT: B 567 SER cc_start: 0.8206 (t) cc_final: 0.7987 (t) REVERT: B 574 TYR cc_start: 0.7987 (m-10) cc_final: 0.7663 (m-10) REVERT: B 583 ARG cc_start: 0.8299 (ptp-170) cc_final: 0.7965 (ptp-110) REVERT: B 593 LYS cc_start: 0.7681 (ttpp) cc_final: 0.7321 (tptp) REVERT: B 603 LEU cc_start: 0.8290 (tp) cc_final: 0.8067 (tp) REVERT: B 622 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6704 (tm-30) REVERT: C 6 LYS cc_start: 0.8607 (ttpt) cc_final: 0.8145 (ttpt) REVERT: C 12 ARG cc_start: 0.8424 (ttt180) cc_final: 0.8153 (ttt180) REVERT: C 14 LYS cc_start: 0.8437 (pttm) cc_final: 0.8087 (pttm) REVERT: C 25 MET cc_start: 0.7483 (pmm) cc_final: 0.6965 (pmm) REVERT: C 29 MET cc_start: 0.8744 (mmt) cc_final: 0.8423 (mmm) REVERT: C 34 GLU cc_start: 0.7767 (pp20) cc_final: 0.7276 (pp20) REVERT: C 52 LYS cc_start: 0.8454 (tptm) cc_final: 0.8169 (tptm) REVERT: C 87 GLU cc_start: 0.8140 (pt0) cc_final: 0.7795 (pt0) REVERT: C 91 LYS cc_start: 0.8571 (tppt) cc_final: 0.7577 (tppt) REVERT: C 92 VAL cc_start: 0.8969 (m) cc_final: 0.8635 (m) REVERT: C 94 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8182 (ttpt) REVERT: C 95 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7376 (mt-10) REVERT: C 97 ARG cc_start: 0.8574 (mtm110) cc_final: 0.8188 (mtm110) REVERT: C 98 GLU cc_start: 0.6998 (tp30) cc_final: 0.6079 (tp30) REVERT: C 126 LYS cc_start: 0.8677 (tttm) cc_final: 0.8100 (tttm) REVERT: C 127 MET cc_start: 0.7620 (mmm) cc_final: 0.6826 (mmm) REVERT: C 128 LYS cc_start: 0.8130 (tttt) cc_final: 0.7628 (tttt) REVERT: C 149 GLU cc_start: 0.7978 (tp30) cc_final: 0.7513 (tp30) REVERT: C 153 LYS cc_start: 0.8592 (tppt) cc_final: 0.7789 (tppt) REVERT: C 155 TYR cc_start: 0.7228 (m-80) cc_final: 0.6876 (m-80) REVERT: C 180 PHE cc_start: 0.8331 (m-80) cc_final: 0.7580 (m-80) REVERT: C 185 TYR cc_start: 0.8207 (t80) cc_final: 0.7963 (t80) REVERT: C 195 CYS cc_start: 0.8194 (m) cc_final: 0.7652 (t) REVERT: D 10 VAL cc_start: 0.8877 (t) cc_final: 0.8659 (t) REVERT: D 14 LYS cc_start: 0.8868 (mttt) cc_final: 0.8447 (mttt) REVERT: D 25 MET cc_start: 0.7178 (pmm) cc_final: 0.6758 (pmm) REVERT: D 29 MET cc_start: 0.8606 (tpp) cc_final: 0.8167 (mmm) REVERT: D 30 LYS cc_start: 0.8045 (mtmm) cc_final: 0.7507 (mttm) REVERT: D 32 VAL cc_start: 0.8337 (t) cc_final: 0.8110 (t) REVERT: D 34 GLU cc_start: 0.7848 (pp20) cc_final: 0.7445 (pp20) REVERT: D 43 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8362 (mt-10) REVERT: D 52 LYS cc_start: 0.8446 (tptm) cc_final: 0.7931 (tptm) REVERT: D 59 ARG cc_start: 0.7871 (mtp-110) cc_final: 0.7520 (mtp180) REVERT: D 65 ILE cc_start: 0.8621 (pt) cc_final: 0.8329 (pt) REVERT: D 66 SER cc_start: 0.8005 (m) cc_final: 0.7302 (m) REVERT: D 84 MET cc_start: 0.7405 (ptp) cc_final: 0.6818 (ptp) REVERT: D 87 GLU cc_start: 0.8064 (pt0) cc_final: 0.7759 (pt0) REVERT: D 91 LYS cc_start: 0.8679 (tppt) cc_final: 0.7926 (tppt) REVERT: D 94 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8374 (ttpt) REVERT: D 97 ARG cc_start: 0.8629 (mtm110) cc_final: 0.7767 (mtm110) REVERT: D 101 TYR cc_start: 0.7657 (m-80) cc_final: 0.7449 (m-80) REVERT: D 102 ASP cc_start: 0.7438 (m-30) cc_final: 0.7137 (m-30) REVERT: D 119 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7851 (tp30) REVERT: D 127 MET cc_start: 0.7795 (mmm) cc_final: 0.7518 (mmm) REVERT: D 128 LYS cc_start: 0.8121 (tttt) cc_final: 0.7620 (tttt) REVERT: D 130 ASP cc_start: 0.6761 (m-30) cc_final: 0.6472 (m-30) REVERT: D 133 ARG cc_start: 0.8388 (ttp-110) cc_final: 0.7956 (ttp-110) REVERT: D 155 TYR cc_start: 0.7273 (m-10) cc_final: 0.7002 (m-80) REVERT: D 167 GLN cc_start: 0.8266 (tp-100) cc_final: 0.8061 (tp-100) REVERT: D 170 HIS cc_start: 0.7961 (t-90) cc_final: 0.7707 (t70) REVERT: D 174 LEU cc_start: 0.8153 (mt) cc_final: 0.7893 (mt) REVERT: D 192 ASP cc_start: 0.8238 (p0) cc_final: 0.7853 (p0) REVERT: D 193 LYS cc_start: 0.8416 (mttt) cc_final: 0.8061 (mttt) REVERT: D 195 CYS cc_start: 0.8171 (m) cc_final: 0.7755 (t) REVERT: D 220 SER cc_start: 0.7359 (m) cc_final: 0.7109 (m) REVERT: D 224 MET cc_start: 0.7707 (ptm) cc_final: 0.7400 (ptm) REVERT: D 226 LEU cc_start: 0.8381 (tt) cc_final: 0.7965 (tt) REVERT: E 125 TYR cc_start: 0.7935 (m-80) cc_final: 0.7029 (m-80) REVERT: E 144 GLU cc_start: 0.7391 (pp20) cc_final: 0.6652 (pp20) REVERT: E 146 MET cc_start: 0.5014 (tpt) cc_final: 0.4327 (tpt) REVERT: E 160 ARG cc_start: 0.7067 (mpp80) cc_final: 0.6271 (mpp80) REVERT: E 163 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7973 (mt-10) REVERT: E 168 LYS cc_start: 0.8370 (ttmm) cc_final: 0.7871 (ttmm) REVERT: E 175 LYS cc_start: 0.8766 (ptmt) cc_final: 0.8222 (ptmt) REVERT: E 180 LEU cc_start: 0.8923 (tp) cc_final: 0.8672 (tp) REVERT: E 187 MET cc_start: 0.3561 (ttt) cc_final: 0.2216 (ttt) REVERT: E 192 LYS cc_start: 0.7670 (ttpt) cc_final: 0.7424 (ttpt) REVERT: E 206 LEU cc_start: 0.6826 (tp) cc_final: 0.6508 (tp) REVERT: E 219 MET cc_start: 0.7479 (mtm) cc_final: 0.7277 (mtm) REVERT: E 230 MET cc_start: 0.7868 (tpt) cc_final: 0.5524 (tpp) REVERT: E 234 ARG cc_start: 0.8254 (ttt180) cc_final: 0.7986 (ttt180) REVERT: E 236 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7378 (tm-30) REVERT: E 253 LEU cc_start: 0.8732 (mt) cc_final: 0.8432 (mt) REVERT: E 256 MET cc_start: 0.7680 (ptm) cc_final: 0.7260 (ptm) REVERT: E 267 ASP cc_start: 0.8024 (p0) cc_final: 0.7718 (p0) REVERT: E 316 TYR cc_start: 0.7588 (t80) cc_final: 0.7269 (t80) REVERT: E 319 ASN cc_start: 0.7955 (t0) cc_final: 0.6713 (t0) REVERT: E 320 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7680 (mm-30) REVERT: E 324 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7695 (mmtt) REVERT: E 333 GLU cc_start: 0.8590 (mt-10) cc_final: 0.7614 (tm-30) REVERT: E 334 PHE cc_start: 0.8219 (t80) cc_final: 0.7716 (t80) REVERT: E 344 LYS cc_start: 0.8555 (tttt) cc_final: 0.8143 (mttt) REVERT: E 353 LYS cc_start: 0.8209 (mptt) cc_final: 0.7909 (mptt) REVERT: E 356 MET cc_start: 0.7058 (ppp) cc_final: 0.6785 (ppp) REVERT: E 360 PHE cc_start: 0.7749 (p90) cc_final: 0.6824 (p90) REVERT: F 88 LYS cc_start: 0.8482 (mmmt) cc_final: 0.7994 (mmmt) REVERT: F 96 ARG cc_start: 0.7433 (ptm160) cc_final: 0.6607 (ptm160) REVERT: F 125 TYR cc_start: 0.8013 (m-80) cc_final: 0.7226 (m-80) REVERT: F 146 MET cc_start: 0.5239 (tpt) cc_final: 0.4143 (tpt) REVERT: F 175 LYS cc_start: 0.8767 (ptmt) cc_final: 0.8285 (ptmt) REVERT: F 219 MET cc_start: 0.7367 (mtp) cc_final: 0.7107 (mtp) REVERT: F 227 ARG cc_start: 0.7264 (mtm180) cc_final: 0.6866 (mtm180) REVERT: F 236 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7484 (tm-30) REVERT: F 249 MET cc_start: 0.8046 (ppp) cc_final: 0.7833 (ppp) REVERT: F 256 MET cc_start: 0.7813 (ptm) cc_final: 0.7380 (ptm) REVERT: F 267 ASP cc_start: 0.7677 (p0) cc_final: 0.7323 (p0) REVERT: F 316 TYR cc_start: 0.7634 (t80) cc_final: 0.7267 (t80) REVERT: F 319 ASN cc_start: 0.7811 (t0) cc_final: 0.6508 (t0) REVERT: F 320 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7626 (mm-30) REVERT: F 324 LYS cc_start: 0.8049 (mmtt) cc_final: 0.7588 (mmtt) REVERT: F 333 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8329 (mt-10) outliers start: 1 outliers final: 0 residues processed: 665 average time/residue: 0.2751 time to fit residues: 249.5370 Evaluate side-chains 652 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 651 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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: 0.1980 chunk 37 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.0570 chunk 107 optimal weight: 9.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN D 117 ASN D 200 GLN ** E 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.139056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.114552 restraints weight = 27694.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.118774 restraints weight = 15797.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.121739 restraints weight = 10360.002| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12876 Z= 0.174 Angle : 0.669 14.532 17364 Z= 0.334 Chirality : 0.045 0.262 1918 Planarity : 0.004 0.054 2216 Dihedral : 5.125 32.536 1740 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1538 helix: 0.94 (0.17), residues: 870 sheet: -3.01 (0.44), residues: 92 loop : -0.98 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 368 HIS 0.011 0.001 HIS E 358 PHE 0.013 0.001 PHE F 330 TYR 0.040 0.002 TYR D 101 ARG 0.010 0.001 ARG F 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4160.10 seconds wall clock time: 74 minutes 43.59 seconds (4483.59 seconds total)