Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 12:56:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ow8_13095/04_2023/7ow8_13095_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ow8_13095/04_2023/7ow8_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_13095/04_2023/7ow8_13095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ow8_13095/04_2023/7ow8_13095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ow8_13095/04_2023/7ow8_13095_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ow8_13095/04_2023/7ow8_13095_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 5.04, per 1000 atoms: 0.56 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: 3.53 Conformation dependent library (CDL) restraints added in 1.4 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: 1.02 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: 2.47 Time building geometry restraints manager: 3.81 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: 4675 16.92 - 33.83: 595 33.83 - 50.75: 139 50.75 - 67.66: 37 67.66 - 84.58: 16 Dihedral angle restraints: 5462 sinusoidal: 2156 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 5459 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 4.310 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.640 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.470 ------------------------------------------------------------------------------- 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 : 16.656 84.579 3338 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 % 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 *********************** 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 : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 12 residues processed: 225 average time/residue: 0.2621 time to fit residues: 77.4148 Evaluate side-chains 151 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0839 time to fit residues: 3.3280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 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: 0.0980 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 207 ASN A 220 ASN A 247 GLN B 207 ASN B 220 ASN B 306 GLN B 519 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2096 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= 0.188 Angle : 0.649 7.072 12302 Z= 0.345 Chirality : 0.042 0.160 1484 Planarity : 0.005 0.059 1536 Dihedral : 6.613 31.230 1240 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.08 (0.22), residues: 1150 helix: -0.81 (0.18), residues: 734 sheet: -1.34 (0.59), residues: 64 loop : -2.39 (0.27), residues: 352 *********************** 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 189 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 11 residues processed: 181 average time/residue: 0.2199 time to fit residues: 54.5021 Evaluate side-chains 139 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.014 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0928 time to fit residues: 3.1685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 0.0770 chunk 112 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- 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 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN B 338 HIS B 519 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 9078 Z= 0.291 Angle : 0.647 8.413 12302 Z= 0.343 Chirality : 0.043 0.151 1484 Planarity : 0.005 0.060 1536 Dihedral : 6.179 28.685 1240 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.96 % Favored : 94.96 % Rotamer Outliers : 2.16 % 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: -1.43 (0.24), residues: 1150 helix: -0.32 (0.19), residues: 732 sheet: -1.12 (0.61), residues: 66 loop : -2.08 (0.29), residues: 352 *********************** 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 168 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.029 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 157 average time/residue: 0.2276 time to fit residues: 48.8265 Evaluate side-chains 145 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1216 time to fit residues: 4.1386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 220 ASN 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: 0.7048 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9078 Z= 0.211 Angle : 0.587 7.591 12302 Z= 0.309 Chirality : 0.041 0.156 1484 Planarity : 0.004 0.053 1536 Dihedral : 5.838 28.125 1240 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.17 % Favored : 95.74 % Rotamer Outliers : 1.65 % 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: -0.89 (0.25), residues: 1150 helix: 0.03 (0.20), residues: 724 sheet: -0.74 (0.63), residues: 64 loop : -1.66 (0.31), residues: 362 *********************** 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 161 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.091 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 157 average time/residue: 0.2211 time to fit residues: 48.1699 Evaluate side-chains 137 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0910 time to fit residues: 3.0927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 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: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN B 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 9078 Z= 0.388 Angle : 0.678 7.845 12302 Z= 0.355 Chirality : 0.045 0.191 1484 Planarity : 0.005 0.055 1536 Dihedral : 5.948 29.036 1240 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.83 % Favored : 94.09 % Rotamer Outliers : 3.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.91 (0.24), residues: 1150 helix: 0.03 (0.20), residues: 718 sheet: -1.02 (0.62), residues: 66 loop : -1.62 (0.31), residues: 366 *********************** 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 161 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 1.083 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 153 average time/residue: 0.2249 time to fit residues: 47.5379 Evaluate side-chains 144 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0855 time to fit residues: 4.4432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3106 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= 0.201 Angle : 0.599 8.175 12302 Z= 0.311 Chirality : 0.041 0.179 1484 Planarity : 0.004 0.051 1536 Dihedral : 5.712 27.246 1240 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.83 % Rotamer Outliers : 1.75 % 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: 0.27 (0.20), residues: 718 sheet: -0.86 (0.61), residues: 64 loop : -1.57 (0.31), residues: 368 *********************** 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 156 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.068 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 151 average time/residue: 0.2220 time to fit residues: 46.4965 Evaluate side-chains 133 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1013 time to fit residues: 2.3762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9078 Z= 0.287 Angle : 0.638 8.086 12302 Z= 0.330 Chirality : 0.042 0.200 1484 Planarity : 0.005 0.051 1536 Dihedral : 5.669 27.612 1240 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.30 % Favored : 94.61 % Rotamer Outliers : 1.44 % 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: -0.59 (0.25), residues: 1150 helix: 0.28 (0.20), residues: 714 sheet: -1.20 (0.61), residues: 66 loop : -1.41 (0.31), residues: 370 *********************** 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 150 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 1.014 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 142 average time/residue: 0.2196 time to fit residues: 43.3143 Evaluate side-chains 136 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0928 time to fit residues: 3.3435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 10 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 9078 Z= 0.255 Angle : 0.625 8.593 12302 Z= 0.324 Chirality : 0.041 0.175 1484 Planarity : 0.004 0.055 1536 Dihedral : 5.616 26.788 1240 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.35 % Favored : 95.57 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.25), residues: 1150 helix: 0.29 (0.20), residues: 726 sheet: -1.23 (0.61), residues: 66 loop : -1.19 (0.32), residues: 358 *********************** 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 140 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 0.916 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 137 average time/residue: 0.2176 time to fit residues: 41.3843 Evaluate side-chains 126 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0877 time to fit residues: 1.8317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 338 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 9078 Z= 0.228 Angle : 0.625 9.485 12302 Z= 0.321 Chirality : 0.041 0.154 1484 Planarity : 0.004 0.050 1536 Dihedral : 5.548 26.909 1240 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.30 % Favored : 94.61 % Rotamer Outliers : 0.21 % 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: -0.39 (0.25), residues: 1150 helix: 0.39 (0.20), residues: 720 sheet: -1.06 (0.62), residues: 64 loop : -1.26 (0.32), residues: 366 *********************** 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 128 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.013 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 127 average time/residue: 0.2268 time to fit residues: 39.7756 Evaluate side-chains 121 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9078 Z= 0.271 Angle : 0.647 9.923 12302 Z= 0.330 Chirality : 0.042 0.293 1484 Planarity : 0.004 0.049 1536 Dihedral : 5.536 26.643 1240 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1150 helix: 0.31 (0.20), residues: 730 sheet: -1.15 (0.61), residues: 64 loop : -1.09 (0.33), residues: 356 ********************** 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 132 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2238 time to fit residues: 40.9789 Evaluate side-chains 127 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 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 338 HIS ** B 207 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 = 0.4207 r_free = 0.4207 target = 0.199627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.151579 restraints weight = 10291.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.151795 restraints weight = 8637.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153506 restraints weight = 8498.648| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 9078 Z= 0.258 Angle : 0.647 9.763 12302 Z= 0.329 Chirality : 0.042 0.263 1484 Planarity : 0.004 0.050 1536 Dihedral : 5.521 27.121 1240 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.30 % Favored : 94.61 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1150 helix: 0.34 (0.20), residues: 730 sheet: -1.19 (0.61), residues: 64 loop : -1.05 (0.33), residues: 356 =============================================================================== Job complete usr+sys time: 1767.49 seconds wall clock time: 33 minutes 5.23 seconds (1985.23 seconds total)