Starting phenix.real_space_refine on Sat Feb 17 05:26:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ow8_13095/02_2024/7ow8_13095_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ow8_13095/02_2024/7ow8_13095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ow8_13095/02_2024/7ow8_13095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ow8_13095/02_2024/7ow8_13095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ow8_13095/02_2024/7ow8_13095_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ow8_13095/02_2024/7ow8_13095_updated.pdb" } resolution = 3.5 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= 0.001 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8748 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 5714 2.51 5 N 1490 2.21 5 O 1694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B GLU 474": "OE1" <-> "OE2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B GLU 575": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8942 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4439 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 17, 'TRANS': 559} Chain: "B" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4439 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 17, 'TRANS': 559} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.11, per 1000 atoms: 0.57 Number of scatterers: 8942 At special positions: 0 Unit cell: (74.692, 85.212, 135.708, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 6 15.00 Mg 2 11.99 O 1694 8.00 N 1490 7.00 C 5714 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: 3.52 Conformation dependent library (CDL) restraints added in 1.8 seconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 63.4% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 11 through 21 removed outlier: 3.651A pdb=" N PHE A 15 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 49 removed outlier: 4.236A pdb=" N PHE A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Proline residue: A 47 - end of helix Processing helix chain 'A' and resid 53 through 63 removed outlier: 4.158A pdb=" N SER A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 107 removed outlier: 5.442A pdb=" N ALA A 78 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR A 90 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE A 96 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A 97 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG A 100 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TRP A 104 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 107 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 120 through 125 removed outlier: 4.089A pdb=" N SER A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 4.559A pdb=" N GLU A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 162 removed outlier: 3.749A pdb=" N MET A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 218 Proline residue: A 175 - end of helix Proline residue: A 183 - end of helix removed outlier: 4.159A pdb=" N GLU A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA A 200 " --> pdb=" O GLN A 196 " (cutoff:3.500A) Proline residue: A 211 - end of helix removed outlier: 6.095A pdb=" N ARG A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU A 215 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 276 removed outlier: 3.840A pdb=" N GLU A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix removed outlier: 3.641A pdb=" N SER A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N MET A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 314 removed outlier: 4.388A pdb=" N ILE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N MET A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 410 through 416 removed outlier: 4.281A pdb=" N HIS A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 445 through 454 removed outlier: 3.520A pdb=" N LYS A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 461 No H-bonds generated for 'chain 'A' and resid 458 through 461' Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 511 through 524 Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'A' and resid 569 through 585 removed outlier: 4.494A pdb=" N GLN A 576 " --> pdb=" O PHE A 573 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASP A 583 " --> pdb=" O MET A 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 21 removed outlier: 3.652A pdb=" N PHE B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 49 removed outlier: 4.236A pdb=" N PHE B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Proline residue: B 47 - end of helix Processing helix chain 'B' and resid 53 through 63 removed outlier: 4.158A pdb=" N SER B 58 " --> pdb=" O VAL B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 107 removed outlier: 5.441A pdb=" N ALA B 78 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B 90 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE B 96 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER B 97 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ARG B 100 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TRP B 104 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 107 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 120 through 128 removed outlier: 4.558A pdb=" N SER B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 141 through 162 removed outlier: 3.749A pdb=" N MET B 162 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 205 Proline residue: B 175 - end of helix Proline residue: B 183 - end of helix removed outlier: 4.159A pdb=" N GLU B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA B 200 " --> pdb=" O GLN B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.672A pdb=" N ILE B 213 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG B 214 " --> pdb=" O PRO B 211 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS B 217 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 218 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 276 removed outlier: 3.959A pdb=" N GLU B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Proline residue: B 252 - end of helix removed outlier: 3.640A pdb=" N SER B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 314 removed outlier: 4.388A pdb=" N ILE B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N MET B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 381 through 386 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 410 through 416 removed outlier: 4.280A pdb=" N HIS B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 Processing helix chain 'B' and resid 446 through 454 Processing helix chain 'B' and resid 458 through 461 No H-bonds generated for 'chain 'B' and resid 458 through 461' Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 511 through 524 Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'B' and resid 569 through 585 removed outlier: 4.494A pdb=" N GLN B 576 " --> pdb=" O PHE B 573 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASP B 583 " --> pdb=" O MET B 580 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 341 through 343 Processing sheet with id= B, first strand: chain 'A' and resid 553 through 558 removed outlier: 6.514A pdb=" N PHE A 548 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG A 557 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 546 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR A 530 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 372 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A 532 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 341 through 343 Processing sheet with id= D, first strand: chain 'B' and resid 553 through 558 removed outlier: 6.513A pdb=" N PHE B 548 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 557 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU B 546 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR B 530 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE B 372 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 532 " --> pdb=" O ILE B 372 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1471 1.28 - 1.42: 2086 1.42 - 1.55: 5426 1.55 - 1.68: 25 1.68 - 1.81: 70 Bond restraints: 9078 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.15e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.04e+01 bond pdb=" C ARG B 201 " pdb=" O ARG B 201 " ideal model delta sigma weight residual 1.236 1.151 0.085 1.25e-02 6.40e+03 4.62e+01 bond pdb=" C THR A 131 " pdb=" O THR A 131 " ideal model delta sigma weight residual 1.237 1.310 -0.073 1.17e-02 7.31e+03 3.91e+01 bond pdb=" CA SER A 421 " pdb=" CB SER A 421 " ideal model delta sigma weight residual 1.528 1.437 0.091 1.48e-02 4.57e+03 3.75e+01 ... (remaining 9073 not shown) Histogram of bond angle deviations from ideal: 95.52 - 103.57: 135 103.57 - 111.62: 4010 111.62 - 119.67: 4055 119.67 - 127.72: 4044 127.72 - 135.77: 58 Bond angle restraints: 12302 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 117.15 22.72 1.00e+00 1.00e+00 5.16e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 117.17 22.70 1.00e+00 1.00e+00 5.15e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 117.62 19.21 1.00e+00 1.00e+00 3.69e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 117.63 19.20 1.00e+00 1.00e+00 3.69e+02 angle pdb=" N THR A 203 " pdb=" CA THR A 203 " pdb=" C THR A 203 " ideal model delta sigma weight residual 112.90 97.66 15.24 1.31e+00 5.83e-01 1.35e+02 ... (remaining 12297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 4701 16.92 - 33.83: 607 33.83 - 50.75: 159 50.75 - 67.66: 37 67.66 - 84.58: 20 Dihedral angle restraints: 5524 sinusoidal: 2218 harmonic: 3306 Sorted by residual: dihedral pdb=" C LYS A 238 " pdb=" N LYS A 238 " pdb=" CA LYS A 238 " pdb=" CB LYS A 238 " ideal model delta harmonic sigma weight residual -122.60 -150.91 28.31 0 2.50e+00 1.60e-01 1.28e+02 dihedral pdb=" N LYS A 238 " pdb=" C LYS A 238 " pdb=" CA LYS A 238 " pdb=" CB LYS A 238 " ideal model delta harmonic sigma weight residual 122.80 146.89 -24.09 0 2.50e+00 1.60e-01 9.28e+01 dihedral pdb=" C PHE B 202 " pdb=" N PHE B 202 " pdb=" CA PHE B 202 " pdb=" CB PHE B 202 " ideal model delta harmonic sigma weight residual -122.60 -145.76 23.16 0 2.50e+00 1.60e-01 8.58e+01 ... (remaining 5521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 1435 0.218 - 0.435: 38 0.435 - 0.653: 9 0.653 - 0.870: 0 0.870 - 1.088: 2 Chirality restraints: 1484 Sorted by residual: chirality pdb=" CA LYS A 238 " pdb=" N LYS A 238 " pdb=" C LYS A 238 " pdb=" CB LYS A 238 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA PHE B 202 " pdb=" N PHE B 202 " pdb=" C PHE B 202 " pdb=" CB PHE B 202 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA LYS B 230 " pdb=" N LYS B 230 " pdb=" C LYS B 230 " pdb=" CB LYS B 230 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.80e+00 ... (remaining 1481 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 118 " 0.028 2.00e-02 2.50e+03 5.80e-02 3.37e+01 pdb=" C ASN B 118 " -0.100 2.00e-02 2.50e+03 pdb=" O ASN B 118 " 0.038 2.00e-02 2.50e+03 pdb=" N ALA B 119 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 202 " -0.028 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C PHE A 202 " 0.095 2.00e-02 2.50e+03 pdb=" O PHE A 202 " -0.034 2.00e-02 2.50e+03 pdb=" N THR A 203 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 227 " 0.027 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C GLY A 227 " -0.087 2.00e-02 2.50e+03 pdb=" O GLY A 227 " 0.031 2.00e-02 2.50e+03 pdb=" N ARG A 228 " 0.029 2.00e-02 2.50e+03 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 103 2.57 - 3.15: 7334 3.15 - 3.73: 14035 3.73 - 4.32: 19084 4.32 - 4.90: 30194 Nonbonded interactions: 70750 Sorted by model distance: nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 1.983 2.170 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 1.984 2.170 nonbonded pdb=" OE1 GLN A 422 " pdb="MG MG A 602 " model vdw 2.038 2.170 nonbonded pdb=" OE1 GLN B 422 " pdb="MG MG B 602 " model vdw 2.038 2.170 nonbonded pdb=" O2G ATP A 601 " pdb="MG MG A 602 " model vdw 2.046 2.170 ... (remaining 70745 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' } 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 4.050 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 26.780 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 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 : 0.011 0.091 9078 Z= 0.721 Angle : 1.608 22.715 12302 Z= 1.079 Chirality : 0.097 1.088 1484 Planarity : 0.010 0.078 1536 Dihedral : 17.116 84.579 3400 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.26 % Favored : 93.57 % Rotamer: Outliers : 4.22 % Allowed : 8.13 % Favored : 87.65 % Cbeta Deviations : 2.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % 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: -3.90 (0.19), residues: 1150 helix: -2.36 (0.14), residues: 750 sheet: -1.83 (0.55), residues: 66 loop : -2.81 (0.27), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 104 HIS 0.004 0.002 HIS B 561 PHE 0.032 0.003 PHE A 384 TYR 0.032 0.003 TYR B 419 ARG 0.003 0.001 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 191 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8761 (tp) cc_final: 0.8560 (tp) REVERT: A 105 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8026 (tttm) REVERT: A 129 ASN cc_start: 0.7975 (m-40) cc_final: 0.7693 (m110) REVERT: A 207 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7815 (t0) REVERT: A 231 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7338 (mtp) REVERT: A 238 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7147 (mtpt) REVERT: A 315 GLU cc_start: 0.8271 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 316 ARG cc_start: 0.7635 (mmt180) cc_final: 0.7149 (mmm160) REVERT: A 334 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8384 (mm) REVERT: A 365 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7800 (tm-30) REVERT: A 408 TYR cc_start: 0.8690 (m-80) cc_final: 0.8117 (m-80) REVERT: A 447 GLU cc_start: 0.7661 (tp30) cc_final: 0.7453 (tp30) REVERT: A 453 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7729 (tp30) REVERT: A 506 THR cc_start: 0.7604 (p) cc_final: 0.7337 (t) REVERT: A 514 GLU cc_start: 0.7897 (tt0) cc_final: 0.7607 (tt0) REVERT: A 551 LYS cc_start: 0.8871 (mttt) cc_final: 0.8274 (mptt) REVERT: B 33 LEU cc_start: 0.8783 (mp) cc_final: 0.8557 (mp) REVERT: B 80 LEU cc_start: 0.8802 (tp) cc_final: 0.8581 (tp) REVERT: B 105 LYS cc_start: 0.8297 (ttmt) cc_final: 0.8003 (tptp) REVERT: B 129 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7610 (m-40) REVERT: B 136 GLU cc_start: 0.8022 (pt0) cc_final: 0.7612 (tp30) REVERT: B 207 ASN cc_start: 0.8452 (t0) cc_final: 0.8052 (t0) REVERT: B 231 MET cc_start: 0.7615 (ttm) cc_final: 0.7311 (mtp) REVERT: B 234 SER cc_start: 0.7406 (OUTLIER) cc_final: 0.7077 (m) REVERT: B 315 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7925 (tm-30) REVERT: B 316 ARG cc_start: 0.7533 (mmt180) cc_final: 0.7145 (mmm160) REVERT: B 365 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7911 (tm-30) REVERT: B 447 GLU cc_start: 0.7606 (tp30) cc_final: 0.7142 (tp30) REVERT: B 453 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7942 (tp30) REVERT: B 514 GLU cc_start: 0.7857 (tt0) cc_final: 0.7633 (tt0) REVERT: B 551 LYS cc_start: 0.8893 (mttt) cc_final: 0.8304 (mptt) REVERT: B 572 ASP cc_start: 0.7970 (m-30) cc_final: 0.7640 (m-30) outliers start: 41 outliers final: 12 residues processed: 225 average time/residue: 0.2589 time to fit residues: 75.9427 Evaluate side-chains 165 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 257 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 0.0570 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 220 ASN A 247 GLN B 129 ASN B 220 ASN B 519 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9078 Z= 0.204 Angle : 0.642 7.223 12302 Z= 0.343 Chirality : 0.042 0.156 1484 Planarity : 0.005 0.058 1536 Dihedral : 10.120 76.533 1333 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.32 % Allowed : 12.96 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.12 (0.22), residues: 1150 helix: -0.85 (0.18), residues: 738 sheet: -1.27 (0.59), residues: 64 loop : -2.39 (0.27), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 104 HIS 0.003 0.001 HIS B 141 PHE 0.015 0.001 PHE A 573 TYR 0.015 0.002 TYR B 419 ARG 0.004 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 156 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7960 (tttm) REVERT: A 127 VAL cc_start: 0.7694 (OUTLIER) cc_final: 0.7152 (t) REVERT: A 238 LYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6786 (mtpt) REVERT: A 315 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 316 ARG cc_start: 0.7561 (mmt180) cc_final: 0.7051 (mmm160) REVERT: A 365 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 447 GLU cc_start: 0.7748 (tp30) cc_final: 0.7479 (tp30) REVERT: A 453 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7626 (tp30) REVERT: A 551 LYS cc_start: 0.8795 (mttt) cc_final: 0.8216 (mptt) REVERT: B 80 LEU cc_start: 0.8818 (tp) cc_final: 0.8611 (tp) REVERT: B 241 VAL cc_start: 0.7512 (OUTLIER) cc_final: 0.6682 (m) REVERT: B 315 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7993 (tm-30) REVERT: B 453 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7917 (tm-30) REVERT: B 454 MET cc_start: 0.8070 (ttm) cc_final: 0.7714 (ttm) REVERT: B 551 LYS cc_start: 0.8875 (mttt) cc_final: 0.8312 (mptt) REVERT: B 572 ASP cc_start: 0.7949 (m-30) cc_final: 0.7663 (m-30) outliers start: 42 outliers final: 15 residues processed: 189 average time/residue: 0.2160 time to fit residues: 55.8508 Evaluate side-chains 153 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 423 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.0470 chunk 112 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN A 333 GLN A 338 HIS B 141 HIS B 208 GLN B 338 HIS B 519 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9078 Z= 0.315 Angle : 0.653 8.255 12302 Z= 0.346 Chirality : 0.044 0.154 1484 Planarity : 0.005 0.060 1536 Dihedral : 9.941 87.824 1313 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.13 % Favored : 94.78 % Rotamer: Outliers : 3.60 % Allowed : 17.80 % Favored : 78.60 % 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: -1.46 (0.24), residues: 1150 helix: -0.36 (0.19), residues: 734 sheet: -0.92 (0.62), residues: 64 loop : -2.07 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 104 HIS 0.020 0.001 HIS A 338 PHE 0.018 0.002 PHE A 31 TYR 0.014 0.001 TYR A 419 ARG 0.004 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 127 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.7013 (t) REVERT: A 238 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6932 (mtpt) REVERT: A 243 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7115 (tm-30) REVERT: A 315 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 316 ARG cc_start: 0.7710 (mmt180) cc_final: 0.7179 (mmm160) REVERT: A 447 GLU cc_start: 0.7887 (tp30) cc_final: 0.7649 (tp30) REVERT: A 453 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 454 MET cc_start: 0.8209 (ttm) cc_final: 0.7613 (ttm) REVERT: A 551 LYS cc_start: 0.8837 (mttt) cc_final: 0.8243 (mptt) REVERT: B 105 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7963 (tttm) REVERT: B 241 VAL cc_start: 0.7590 (OUTLIER) cc_final: 0.6461 (m) REVERT: B 243 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7414 (tm-30) REVERT: B 315 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7982 (tm-30) REVERT: B 316 ARG cc_start: 0.7639 (mmt180) cc_final: 0.7228 (mmm160) REVERT: B 368 LYS cc_start: 0.8723 (mttp) cc_final: 0.8364 (mttm) REVERT: B 453 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7831 (tp30) REVERT: B 551 LYS cc_start: 0.8964 (mttt) cc_final: 0.8403 (mptt) REVERT: B 572 ASP cc_start: 0.7911 (m-30) cc_final: 0.7647 (m-30) outliers start: 35 outliers final: 23 residues processed: 168 average time/residue: 0.2173 time to fit residues: 50.1371 Evaluate side-chains 160 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 436 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 110 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN A 338 HIS B 220 ASN B 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9078 Z= 0.188 Angle : 0.572 7.576 12302 Z= 0.302 Chirality : 0.041 0.164 1484 Planarity : 0.004 0.052 1536 Dihedral : 9.271 79.641 1313 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.65 % Rotamer: Outliers : 3.91 % Allowed : 18.62 % Favored : 77.47 % 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: -0.99 (0.25), residues: 1150 helix: -0.02 (0.20), residues: 734 sheet: -0.66 (0.64), residues: 64 loop : -1.86 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 104 HIS 0.014 0.001 HIS A 338 PHE 0.026 0.001 PHE B 31 TYR 0.012 0.001 TYR B 83 ARG 0.006 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 1.037 Fit side-chains REVERT: A 105 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7989 (tttm) REVERT: A 127 VAL cc_start: 0.7599 (OUTLIER) cc_final: 0.6918 (t) REVERT: A 238 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6825 (mtpt) REVERT: A 243 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7215 (tm-30) REVERT: A 315 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8060 (tm-30) REVERT: A 316 ARG cc_start: 0.7715 (mmt180) cc_final: 0.7168 (mmm160) REVERT: A 447 GLU cc_start: 0.7897 (tp30) cc_final: 0.7649 (tp30) REVERT: A 453 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 454 MET cc_start: 0.8157 (ttm) cc_final: 0.7625 (ttm) REVERT: A 525 MET cc_start: 0.8681 (mmt) cc_final: 0.8413 (mmt) REVERT: A 551 LYS cc_start: 0.8829 (mttt) cc_final: 0.8233 (mptt) REVERT: B 105 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7993 (tptp) REVERT: B 243 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7439 (tm-30) REVERT: B 315 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7960 (tm-30) REVERT: B 316 ARG cc_start: 0.7643 (mmt180) cc_final: 0.7158 (mmm160) REVERT: B 345 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7440 (mtp85) REVERT: B 368 LYS cc_start: 0.8727 (mttp) cc_final: 0.8372 (mttm) REVERT: B 453 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7965 (tm-30) REVERT: B 454 MET cc_start: 0.8372 (ttm) cc_final: 0.8011 (ttm) REVERT: B 487 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.5938 (tt) REVERT: B 536 ARG cc_start: 0.6005 (mtp180) cc_final: 0.5285 (mtp180) REVERT: B 551 LYS cc_start: 0.8901 (mttt) cc_final: 0.8339 (mptt) REVERT: B 572 ASP cc_start: 0.7926 (m-30) cc_final: 0.7685 (m-30) outliers start: 38 outliers final: 26 residues processed: 180 average time/residue: 0.2064 time to fit residues: 51.6236 Evaluate side-chains 162 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 0.0000 chunk 94 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 220 ASN A 338 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 220 ASN B 308 GLN B 338 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9078 Z= 0.245 Angle : 0.581 7.498 12302 Z= 0.309 Chirality : 0.041 0.194 1484 Planarity : 0.004 0.052 1536 Dihedral : 9.319 84.627 1313 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.04 % Favored : 94.87 % Rotamer: Outliers : 4.42 % Allowed : 19.44 % Favored : 76.13 % 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: -0.68 (0.25), residues: 1150 helix: 0.19 (0.20), residues: 720 sheet: -0.51 (0.66), residues: 64 loop : -1.57 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 104 HIS 0.004 0.001 HIS A 338 PHE 0.022 0.002 PHE A 573 TYR 0.016 0.001 TYR B 408 ARG 0.006 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 1.063 Fit side-chains REVERT: A 105 LYS cc_start: 0.8319 (ttmt) cc_final: 0.8010 (tttm) REVERT: A 127 VAL cc_start: 0.7663 (OUTLIER) cc_final: 0.6976 (t) REVERT: A 238 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6836 (mtpt) REVERT: A 243 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7290 (tm-30) REVERT: A 299 GLN cc_start: 0.7509 (mm110) cc_final: 0.7216 (mm-40) REVERT: A 315 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 316 ARG cc_start: 0.7655 (mmt180) cc_final: 0.7162 (mmm160) REVERT: A 447 GLU cc_start: 0.7924 (tp30) cc_final: 0.7695 (tp30) REVERT: A 453 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7698 (tm-30) REVERT: A 454 MET cc_start: 0.8173 (ttm) cc_final: 0.7808 (ttt) REVERT: A 525 MET cc_start: 0.8714 (mmt) cc_final: 0.8477 (mmt) REVERT: A 551 LYS cc_start: 0.8812 (mttt) cc_final: 0.8204 (mptt) REVERT: A 572 ASP cc_start: 0.7925 (m-30) cc_final: 0.7646 (m-30) REVERT: B 33 LEU cc_start: 0.8868 (mp) cc_final: 0.8629 (mp) REVERT: B 105 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7934 (tptp) REVERT: B 243 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7509 (tm-30) REVERT: B 315 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7954 (tm-30) REVERT: B 316 ARG cc_start: 0.7693 (mmt180) cc_final: 0.7149 (mmm160) REVERT: B 368 LYS cc_start: 0.8683 (mttp) cc_final: 0.8346 (mttm) REVERT: B 453 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7994 (tm-30) REVERT: B 454 MET cc_start: 0.8447 (ttm) cc_final: 0.8120 (ttt) REVERT: B 487 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.5951 (tt) REVERT: B 536 ARG cc_start: 0.6007 (mtp180) cc_final: 0.5775 (mtt90) REVERT: B 551 LYS cc_start: 0.8911 (mttt) cc_final: 0.8339 (mptt) REVERT: B 572 ASP cc_start: 0.7934 (m-30) cc_final: 0.7687 (m-30) outliers start: 43 outliers final: 29 residues processed: 174 average time/residue: 0.2239 time to fit residues: 53.5455 Evaluate side-chains 172 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 531 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 220 ASN A 338 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 220 ASN B 338 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9078 Z= 0.289 Angle : 0.593 6.565 12302 Z= 0.314 Chirality : 0.042 0.193 1484 Planarity : 0.004 0.051 1536 Dihedral : 9.323 85.572 1312 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.96 % Favored : 94.96 % Rotamer: Outliers : 4.63 % Allowed : 20.99 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1150 helix: 0.21 (0.20), residues: 720 sheet: -0.54 (0.66), residues: 64 loop : -1.51 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 104 HIS 0.002 0.000 HIS B 141 PHE 0.020 0.001 PHE A 573 TYR 0.013 0.001 TYR B 408 ARG 0.007 0.001 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 141 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8373 (ttmt) cc_final: 0.8050 (tttm) REVERT: A 127 VAL cc_start: 0.7629 (OUTLIER) cc_final: 0.6943 (t) REVERT: A 238 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6764 (mtpt) REVERT: A 243 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 315 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 316 ARG cc_start: 0.7622 (mmt180) cc_final: 0.7263 (mmm160) REVERT: A 447 GLU cc_start: 0.7951 (tp30) cc_final: 0.7703 (tp30) REVERT: A 453 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7705 (tm-30) REVERT: A 525 MET cc_start: 0.8696 (mmt) cc_final: 0.8404 (mmt) REVERT: A 551 LYS cc_start: 0.8805 (mttt) cc_final: 0.8198 (mptt) REVERT: A 572 ASP cc_start: 0.7903 (m-30) cc_final: 0.7620 (m-30) REVERT: B 33 LEU cc_start: 0.8890 (mp) cc_final: 0.8603 (mp) REVERT: B 105 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7980 (tttm) REVERT: B 243 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7538 (tm-30) REVERT: B 315 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 316 ARG cc_start: 0.7628 (mmt180) cc_final: 0.7037 (mmm160) REVERT: B 368 LYS cc_start: 0.8689 (mttp) cc_final: 0.8350 (mttm) REVERT: B 453 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7992 (tm-30) REVERT: B 454 MET cc_start: 0.8446 (ttm) cc_final: 0.8089 (tpp) REVERT: B 487 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6001 (tt) REVERT: B 551 LYS cc_start: 0.8932 (mttt) cc_final: 0.8351 (mptt) REVERT: B 572 ASP cc_start: 0.7929 (m-30) cc_final: 0.7727 (m-30) outliers start: 45 outliers final: 36 residues processed: 172 average time/residue: 0.2195 time to fit residues: 51.8300 Evaluate side-chains 172 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 220 ASN A 338 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9078 Z= 0.222 Angle : 0.569 7.277 12302 Z= 0.300 Chirality : 0.041 0.183 1484 Planarity : 0.004 0.050 1536 Dihedral : 9.125 83.044 1311 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 4.22 % Allowed : 21.40 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.25), residues: 1150 helix: 0.31 (0.20), residues: 726 sheet: -0.46 (0.65), residues: 64 loop : -1.42 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 104 HIS 0.001 0.000 HIS B 141 PHE 0.032 0.001 PHE B 31 TYR 0.012 0.001 TYR B 83 ARG 0.006 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 1.046 Fit side-chains REVERT: A 105 LYS cc_start: 0.8349 (ttmt) cc_final: 0.8028 (tttm) REVERT: A 127 VAL cc_start: 0.7556 (OUTLIER) cc_final: 0.7022 (p) REVERT: A 238 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6610 (mtpt) REVERT: A 243 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7226 (tm-30) REVERT: A 271 MET cc_start: 0.6881 (pmm) cc_final: 0.6344 (pmm) REVERT: A 315 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 316 ARG cc_start: 0.7613 (mmt180) cc_final: 0.7064 (mmm160) REVERT: A 447 GLU cc_start: 0.7943 (tp30) cc_final: 0.7696 (tp30) REVERT: A 453 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7701 (tm-30) REVERT: A 454 MET cc_start: 0.8149 (ttm) cc_final: 0.7849 (ttt) REVERT: A 525 MET cc_start: 0.8685 (mmt) cc_final: 0.8402 (mmt) REVERT: A 551 LYS cc_start: 0.8813 (mttt) cc_final: 0.8209 (mptt) REVERT: B 33 LEU cc_start: 0.8884 (mp) cc_final: 0.8618 (mp) REVERT: B 105 LYS cc_start: 0.8251 (ttmt) cc_final: 0.7966 (tttm) REVERT: B 243 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7497 (tm-30) REVERT: B 315 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8079 (tm-30) REVERT: B 316 ARG cc_start: 0.7519 (mmt180) cc_final: 0.7086 (mmm160) REVERT: B 345 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7721 (mtp85) REVERT: B 368 LYS cc_start: 0.8674 (mttp) cc_final: 0.8312 (mttm) REVERT: B 453 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7967 (tm-30) REVERT: B 454 MET cc_start: 0.8439 (ttm) cc_final: 0.8131 (tpp) REVERT: B 487 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.5996 (tt) REVERT: B 551 LYS cc_start: 0.8921 (mttt) cc_final: 0.8357 (mptt) outliers start: 41 outliers final: 31 residues processed: 170 average time/residue: 0.2176 time to fit residues: 51.2318 Evaluate side-chains 173 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 506 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 0.0870 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 338 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 220 ASN B 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9078 Z= 0.175 Angle : 0.556 6.838 12302 Z= 0.290 Chirality : 0.040 0.182 1484 Planarity : 0.004 0.048 1536 Dihedral : 8.845 79.844 1311 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.35 % Favored : 95.57 % Rotamer: Outliers : 3.50 % Allowed : 22.22 % Favored : 74.28 % 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: -0.25 (0.25), residues: 1150 helix: 0.38 (0.20), residues: 734 sheet: -0.36 (0.66), residues: 64 loop : -1.09 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 104 HIS 0.001 0.000 HIS B 535 PHE 0.016 0.001 PHE A 573 TYR 0.008 0.001 TYR A 419 ARG 0.007 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 1.011 Fit side-chains REVERT: A 105 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8049 (tttm) REVERT: A 127 VAL cc_start: 0.7414 (OUTLIER) cc_final: 0.6845 (p) REVERT: A 238 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6586 (mtpt) REVERT: A 243 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7287 (tm-30) REVERT: A 315 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8073 (tm-30) REVERT: A 316 ARG cc_start: 0.7593 (mmt180) cc_final: 0.7070 (mmm160) REVERT: A 447 GLU cc_start: 0.7913 (tp30) cc_final: 0.7674 (tp30) REVERT: A 453 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7945 (tm-30) REVERT: A 525 MET cc_start: 0.8690 (mmt) cc_final: 0.8360 (mmt) REVERT: A 551 LYS cc_start: 0.8798 (mttt) cc_final: 0.8205 (mptt) REVERT: B 33 LEU cc_start: 0.8853 (mp) cc_final: 0.8591 (mp) REVERT: B 105 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7988 (tptp) REVERT: B 243 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7528 (tm-30) REVERT: B 315 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 316 ARG cc_start: 0.7517 (mmt180) cc_final: 0.7117 (mmm160) REVERT: B 345 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7671 (mtp85) REVERT: B 365 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7558 (tm-30) REVERT: B 368 LYS cc_start: 0.8657 (mttp) cc_final: 0.8440 (mttm) REVERT: B 453 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7959 (tm-30) REVERT: B 454 MET cc_start: 0.8425 (ttm) cc_final: 0.8096 (tpp) REVERT: B 487 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.5987 (tt) REVERT: B 512 GLN cc_start: 0.7916 (tt0) cc_final: 0.7711 (tt0) REVERT: B 551 LYS cc_start: 0.8898 (mttt) cc_final: 0.8331 (mptt) outliers start: 34 outliers final: 23 residues processed: 168 average time/residue: 0.2170 time to fit residues: 50.2051 Evaluate side-chains 161 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 0.0770 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS A 512 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 220 ASN B 338 HIS B 512 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9078 Z= 0.171 Angle : 0.561 8.796 12302 Z= 0.290 Chirality : 0.039 0.178 1484 Planarity : 0.004 0.050 1536 Dihedral : 8.778 79.980 1311 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 3.50 % Allowed : 23.05 % Favored : 73.46 % 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: -0.13 (0.26), residues: 1150 helix: 0.53 (0.20), residues: 728 sheet: -0.28 (0.66), residues: 64 loop : -1.17 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 104 HIS 0.001 0.000 HIS B 141 PHE 0.016 0.001 PHE B 573 TYR 0.008 0.001 TYR A 419 ARG 0.009 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 1.099 Fit side-chains REVERT: A 105 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8052 (tptp) REVERT: A 127 VAL cc_start: 0.7405 (OUTLIER) cc_final: 0.6852 (p) REVERT: A 188 MET cc_start: 0.8358 (mmm) cc_final: 0.7428 (tpt) REVERT: A 238 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6567 (mtpt) REVERT: A 243 GLU cc_start: 0.7655 (tm-30) cc_final: 0.6555 (tm-30) REVERT: A 315 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 316 ARG cc_start: 0.7590 (mmt180) cc_final: 0.7075 (mmm160) REVERT: A 447 GLU cc_start: 0.7916 (tp30) cc_final: 0.7703 (tp30) REVERT: A 453 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 551 LYS cc_start: 0.8796 (mttt) cc_final: 0.8208 (mptt) REVERT: B 33 LEU cc_start: 0.8870 (mp) cc_final: 0.8607 (mp) REVERT: B 105 LYS cc_start: 0.8312 (ttmt) cc_final: 0.7974 (tptp) REVERT: B 243 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7547 (tm-30) REVERT: B 315 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8061 (tm-30) REVERT: B 316 ARG cc_start: 0.7517 (mmt180) cc_final: 0.7126 (mmm160) REVERT: B 345 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7680 (mtp85) REVERT: B 365 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7532 (tm-30) REVERT: B 368 LYS cc_start: 0.8659 (mttp) cc_final: 0.8437 (mttm) REVERT: B 453 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 454 MET cc_start: 0.8409 (ttm) cc_final: 0.8080 (tpp) REVERT: B 487 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.5997 (tt) REVERT: B 525 MET cc_start: 0.8750 (mmt) cc_final: 0.7995 (mmt) REVERT: B 551 LYS cc_start: 0.8896 (mttt) cc_final: 0.8300 (mmtm) outliers start: 34 outliers final: 26 residues processed: 161 average time/residue: 0.2284 time to fit residues: 50.5781 Evaluate side-chains 166 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 96 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 338 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 9078 Z= 0.272 Angle : 0.910 59.196 12302 Z= 0.524 Chirality : 0.041 0.320 1484 Planarity : 0.005 0.109 1536 Dihedral : 8.766 80.060 1311 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 3.09 % Allowed : 23.05 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1150 helix: 0.52 (0.20), residues: 728 sheet: -0.27 (0.66), residues: 64 loop : -1.18 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 104 HIS 0.004 0.000 HIS A 141 PHE 0.016 0.002 PHE B 573 TYR 0.009 0.001 TYR A 419 ARG 0.012 0.000 ARG A 536 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8067 (tptp) REVERT: A 127 VAL cc_start: 0.7424 (OUTLIER) cc_final: 0.6861 (p) REVERT: A 238 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6569 (mtpt) REVERT: A 243 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7307 (tm-30) REVERT: A 315 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 316 ARG cc_start: 0.7594 (mmt180) cc_final: 0.7081 (mmm160) REVERT: A 447 GLU cc_start: 0.7920 (tp30) cc_final: 0.7704 (tp30) REVERT: A 453 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7926 (tm-30) REVERT: A 551 LYS cc_start: 0.8799 (mttt) cc_final: 0.8211 (mptt) REVERT: B 33 LEU cc_start: 0.8872 (mp) cc_final: 0.8610 (mp) REVERT: B 105 LYS cc_start: 0.8322 (ttmt) cc_final: 0.7980 (tptp) REVERT: B 243 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 315 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8061 (tm-30) REVERT: B 316 ARG cc_start: 0.7523 (mmt180) cc_final: 0.7133 (mmm160) REVERT: B 345 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7681 (mtp85) REVERT: B 365 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7529 (tm-30) REVERT: B 368 LYS cc_start: 0.8660 (mttp) cc_final: 0.8440 (mttm) REVERT: B 453 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 454 MET cc_start: 0.8415 (ttm) cc_final: 0.8080 (tpp) REVERT: B 487 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6014 (tt) REVERT: B 525 MET cc_start: 0.8748 (mmt) cc_final: 0.7981 (mmt) REVERT: B 551 LYS cc_start: 0.8899 (mttt) cc_final: 0.8303 (mmtm) outliers start: 30 outliers final: 27 residues processed: 158 average time/residue: 0.2221 time to fit residues: 48.1457 Evaluate side-chains 167 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.201933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.154974 restraints weight = 10264.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.153492 restraints weight = 8284.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.155754 restraints weight = 8321.142| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 9078 Z= 0.272 Angle : 0.910 59.196 12302 Z= 0.524 Chirality : 0.041 0.320 1484 Planarity : 0.005 0.109 1536 Dihedral : 8.766 80.060 1311 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 3.09 % Allowed : 23.15 % Favored : 73.77 % 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: -0.14 (0.25), residues: 1150 helix: 0.52 (0.20), residues: 728 sheet: -0.27 (0.66), residues: 64 loop : -1.18 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 104 HIS 0.004 0.000 HIS A 141 PHE 0.016 0.002 PHE B 573 TYR 0.009 0.001 TYR A 419 ARG 0.012 0.000 ARG A 536 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1908.42 seconds wall clock time: 35 minutes 32.91 seconds (2132.91 seconds total)