Starting phenix.real_space_refine on Sat Apr 6 18:49:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2d_17361/04_2024/8p2d_17361_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2d_17361/04_2024/8p2d_17361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2d_17361/04_2024/8p2d_17361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2d_17361/04_2024/8p2d_17361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2d_17361/04_2024/8p2d_17361_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2d_17361/04_2024/8p2d_17361_updated.pdb" } resolution = 2.59 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 5555 2.51 5 N 1511 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8793 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4358 Classifications: {'peptide': 542} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 521} Chain breaks: 2 Chain: "B" Number of atoms: 4373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4373 Classifications: {'peptide': 545} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 524} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'DTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.92, per 1000 atoms: 0.56 Number of scatterers: 8793 At special positions: 0 Unit cell: (77.0224, 118.496, 95.6432, 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 54 16.00 P 6 15.00 Mg 2 11.99 O 1665 8.00 N 1511 7.00 C 5555 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: 3.50 Conformation dependent library (CDL) restraints added in 1.6 seconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 4 sheets defined 41.3% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 122 through 140 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 145 through 148 No H-bonds generated for 'chain 'A' and resid 145 through 148' Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 229 through 242 removed outlier: 3.600A pdb=" N GLU A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 279 through 288 removed outlier: 3.583A pdb=" N THR A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 323 through 338 removed outlier: 4.280A pdb=" N ILE A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 333 " --> pdb=" O MET A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.914A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 409 Processing helix chain 'A' and resid 443 through 449 Processing helix chain 'A' and resid 456 through 485 removed outlier: 4.115A pdb=" N ASN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 546 through 553 removed outlier: 3.530A pdb=" N LEU A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 Processing helix chain 'A' and resid 588 through 594 Processing helix chain 'A' and resid 621 through 628 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.726A pdb=" N ASP A 633 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 665 Processing helix chain 'B' and resid 122 through 141 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 145 through 151 removed outlier: 3.663A pdb=" N ALA B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 197 through 214 removed outlier: 4.165A pdb=" N VAL B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 230 through 245 removed outlier: 3.810A pdb=" N SER B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LYS B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 277 removed outlier: 3.657A pdb=" N GLU B 277 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 300 removed outlier: 3.512A pdb=" N THR B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 333 removed outlier: 3.574A pdb=" N LEU B 333 " --> pdb=" O MET B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 338 No H-bonds generated for 'chain 'B' and resid 335 through 338' Processing helix chain 'B' and resid 368 through 381 removed outlier: 3.959A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 409 Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 456 through 485 removed outlier: 3.528A pdb=" N PHE B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 465 " --> pdb=" O ASP B 461 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 545 through 569 removed outlier: 4.031A pdb=" N LEU B 552 " --> pdb=" O GLN B 548 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 554 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 Processing helix chain 'B' and resid 621 through 631 Proline residue: B 630 - end of helix Processing helix chain 'B' and resid 654 through 665 Processing sheet with id= A, first strand: chain 'A' and resid 156 through 158 removed outlier: 7.690A pdb=" N THR A 521 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE A 438 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY A 523 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N THR A 440 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLY A 525 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASN A 442 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE A 527 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 219 through 221 removed outlier: 3.747A pdb=" N ASN A 316 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 350 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYR A 317 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE A 352 " --> pdb=" O TYR A 317 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN A 385 " --> pdb=" O TRP A 353 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LYS A 355 " --> pdb=" O ASN A 385 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 387 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 156 through 158 removed outlier: 8.114A pdb=" N THR B 521 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE B 438 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY B 523 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR B 440 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLY B 525 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASN B 442 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE B 527 " --> pdb=" O ASN B 442 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 314 through 317 removed outlier: 6.543A pdb=" N ILE B 350 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N TYR B 317 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE B 352 " --> pdb=" O TYR B 317 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN B 385 " --> pdb=" O TRP B 353 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LYS B 355 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 387 " --> pdb=" O LYS B 355 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 258 hydrogen bonds defined for protein. 762 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: 1.85 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2887 1.34 - 1.46: 1546 1.46 - 1.57: 4457 1.57 - 1.69: 9 1.69 - 1.81: 90 Bond restraints: 8989 Sorted by residual: bond pdb=" C LYS B 508 " pdb=" N PRO B 509 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.08e-02 8.57e+03 1.76e+00 bond pdb=" C ILE B 221 " pdb=" O ILE B 221 " ideal model delta sigma weight residual 1.232 1.243 -0.011 1.01e-02 9.80e+03 1.29e+00 bond pdb=" C LYS A 508 " pdb=" N PRO A 509 " ideal model delta sigma weight residual 1.336 1.347 -0.011 1.08e-02 8.57e+03 9.90e-01 bond pdb=" CB PHE A 493 " pdb=" CG PHE A 493 " ideal model delta sigma weight residual 1.502 1.522 -0.020 2.30e-02 1.89e+03 7.54e-01 bond pdb=" CA SER B 304 " pdb=" C SER B 304 " ideal model delta sigma weight residual 1.528 1.516 0.011 1.33e-02 5.65e+03 7.31e-01 ... (remaining 8984 not shown) Histogram of bond angle deviations from ideal: 99.51 - 107.56: 339 107.56 - 115.61: 5421 115.61 - 123.66: 6167 123.66 - 131.71: 211 131.71 - 139.75: 16 Bond angle restraints: 12154 Sorted by residual: angle pdb=" N LEU B 536 " pdb=" CA LEU B 536 " pdb=" C LEU B 536 " ideal model delta sigma weight residual 114.56 110.46 4.10 1.27e+00 6.20e-01 1.04e+01 angle pdb=" C ASP B 605 " pdb=" CA ASP B 605 " pdb=" CB ASP B 605 " ideal model delta sigma weight residual 110.42 115.90 -5.48 1.99e+00 2.53e-01 7.59e+00 angle pdb=" N ILE B 281 " pdb=" CA ILE B 281 " pdb=" C ILE B 281 " ideal model delta sigma weight residual 112.35 108.50 3.85 1.41e+00 5.03e-01 7.45e+00 angle pdb=" N ILE B 179 " pdb=" CA ILE B 179 " pdb=" C ILE B 179 " ideal model delta sigma weight residual 113.07 109.75 3.32 1.36e+00 5.41e-01 5.96e+00 angle pdb=" C HIS A 289 " pdb=" N GLN A 290 " pdb=" CA GLN A 290 " ideal model delta sigma weight residual 121.54 126.02 -4.48 1.91e+00 2.74e-01 5.51e+00 ... (remaining 12149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.57: 5137 21.57 - 43.14: 215 43.14 - 64.70: 51 64.70 - 86.27: 6 86.27 - 107.84: 3 Dihedral angle restraints: 5412 sinusoidal: 2247 harmonic: 3165 Sorted by residual: dihedral pdb=" CA TYR B 231 " pdb=" C TYR B 231 " pdb=" N VAL B 232 " pdb=" CA VAL B 232 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA GLU A 511 " pdb=" C GLU A 511 " pdb=" N THR A 512 " pdb=" CA THR A 512 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TYR A 231 " pdb=" C TYR A 231 " pdb=" N VAL A 232 " pdb=" CA VAL A 232 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 5409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 750 0.030 - 0.060: 378 0.060 - 0.090: 111 0.090 - 0.120: 52 0.120 - 0.150: 9 Chirality restraints: 1300 Sorted by residual: chirality pdb=" CA ILE A 524 " pdb=" N ILE A 524 " pdb=" C ILE A 524 " pdb=" CB ILE A 524 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE B 524 " pdb=" N ILE B 524 " pdb=" C ILE B 524 " pdb=" CB ILE B 524 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA VAL A 613 " pdb=" N VAL A 613 " pdb=" C VAL A 613 " pdb=" CB VAL A 613 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1297 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 290 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C GLN A 290 " 0.041 2.00e-02 2.50e+03 pdb=" O GLN A 290 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 291 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 578 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.55e+00 pdb=" N PRO A 579 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 579 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 579 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 192 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 193 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " 0.016 5.00e-02 4.00e+02 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 69 2.55 - 3.14: 6922 3.14 - 3.73: 13968 3.73 - 4.31: 19619 4.31 - 4.90: 32012 Nonbonded interactions: 72590 Sorted by model distance: nonbonded pdb=" O3G DTP A 801 " pdb="MG MG B 801 " model vdw 1.968 2.170 nonbonded pdb=" O3G DTP A 802 " pdb="MG MG A 803 " model vdw 1.989 2.170 nonbonded pdb=" OE2 GLU B 293 " pdb="MG MG B 801 " model vdw 2.160 2.170 nonbonded pdb=" OD2 ASP B 591 " pdb=" OH TYR B 607 " model vdw 2.249 2.440 nonbonded pdb=" NZ LYS A 241 " pdb=" O LEU A 251 " model vdw 2.254 2.520 ... (remaining 72585 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' and (resid 120 through 674 or resid 803)) selection = (chain 'B' and (resid 120 through 302 or resid 311 through 674 or resid 801)) } 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 individual isotropic 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.820 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 25.560 Find NCS groups from input model: 0.510 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: 0.010 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 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 : 0.002 0.027 8989 Z= 0.152 Angle : 0.514 6.990 12154 Z= 0.286 Chirality : 0.042 0.150 1300 Planarity : 0.003 0.031 1569 Dihedral : 12.793 107.837 3382 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.79 % Allowed : 8.73 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.58 (0.26), residues: 1075 helix: -0.17 (0.25), residues: 487 sheet: 0.52 (0.48), residues: 111 loop : -2.42 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 501 HIS 0.002 0.001 HIS B 216 PHE 0.018 0.001 PHE B 224 TYR 0.011 0.001 TYR B 231 ARG 0.002 0.000 ARG B 419 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 173 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ASN cc_start: 0.7016 (t0) cc_final: 0.6631 (m-40) REVERT: A 595 PHE cc_start: 0.6146 (OUTLIER) cc_final: 0.5316 (m-80) REVERT: B 127 MET cc_start: 0.6589 (mmt) cc_final: 0.5050 (mpp) REVERT: B 409 TRP cc_start: 0.6544 (OUTLIER) cc_final: 0.6265 (m100) outliers start: 45 outliers final: 7 residues processed: 212 average time/residue: 1.1433 time to fit residues: 259.0866 Evaluate side-chains 157 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.0040 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 300 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN A 548 GLN A 611 ASN A 652 ASN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 154 ASN B 188 HIS B 237 GLN B 278 GLN B 297 HIS B 334 GLN B 483 GLN B 541 HIS B 609 ASN B 652 ASN B 667 ASN B 674 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8989 Z= 0.224 Angle : 0.575 6.766 12154 Z= 0.307 Chirality : 0.044 0.201 1300 Planarity : 0.004 0.032 1569 Dihedral : 10.238 108.070 1267 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 4.90 % Allowed : 14.48 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.57 (0.26), residues: 1075 helix: -0.06 (0.25), residues: 494 sheet: 0.53 (0.47), residues: 111 loop : -2.57 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 501 HIS 0.004 0.001 HIS A 541 PHE 0.025 0.002 PHE B 438 TYR 0.014 0.002 TYR B 617 ARG 0.007 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 149 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 ASN cc_start: 0.7030 (t0) cc_final: 0.6613 (m-40) REVERT: A 595 PHE cc_start: 0.6072 (OUTLIER) cc_final: 0.5257 (m-80) REVERT: B 241 LYS cc_start: 0.4454 (mmpt) cc_final: 0.3312 (mmpt) REVERT: B 513 ILE cc_start: 0.3621 (OUTLIER) cc_final: 0.3032 (pt) outliers start: 46 outliers final: 16 residues processed: 185 average time/residue: 1.1501 time to fit residues: 228.4140 Evaluate side-chains 162 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 674 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 98 optimal weight: 0.7980 chunk 106 optimal weight: 0.0050 chunk 87 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 213 ASN ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8989 Z= 0.185 Angle : 0.559 6.858 12154 Z= 0.294 Chirality : 0.044 0.206 1300 Planarity : 0.004 0.031 1569 Dihedral : 9.953 107.456 1261 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.37 % Allowed : 16.61 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.40 (0.26), residues: 1075 helix: 0.13 (0.25), residues: 488 sheet: 0.60 (0.47), residues: 111 loop : -2.51 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 501 HIS 0.003 0.001 HIS A 188 PHE 0.022 0.001 PHE B 438 TYR 0.017 0.001 TYR B 617 ARG 0.004 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 145 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 396 ASN cc_start: 0.7004 (t0) cc_final: 0.6602 (m-40) REVERT: A 421 PHE cc_start: 0.5708 (OUTLIER) cc_final: 0.5177 (t80) REVERT: A 595 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.5260 (m-80) REVERT: B 355 LYS cc_start: 0.7941 (tttp) cc_final: 0.7580 (tttt) REVERT: B 497 MET cc_start: 0.6905 (mmm) cc_final: 0.6616 (mmm) outliers start: 41 outliers final: 21 residues processed: 172 average time/residue: 1.0846 time to fit residues: 200.7796 Evaluate side-chains 166 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 674 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.6980 chunk 73 optimal weight: 0.0670 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 213 ASN B 278 GLN B 541 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8989 Z= 0.210 Angle : 0.566 6.987 12154 Z= 0.300 Chirality : 0.044 0.151 1300 Planarity : 0.004 0.030 1569 Dihedral : 9.942 104.920 1261 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 5.01 % Allowed : 17.68 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.33 (0.26), residues: 1075 helix: 0.28 (0.25), residues: 477 sheet: 0.55 (0.46), residues: 111 loop : -2.51 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 501 HIS 0.003 0.001 HIS A 541 PHE 0.020 0.002 PHE B 438 TYR 0.020 0.002 TYR A 164 ARG 0.002 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 151 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 ASN cc_start: 0.7037 (t0) cc_final: 0.6616 (m-40) REVERT: A 595 PHE cc_start: 0.6046 (OUTLIER) cc_final: 0.5295 (m-80) REVERT: B 241 LYS cc_start: 0.4341 (OUTLIER) cc_final: 0.4058 (mmmt) REVERT: B 497 MET cc_start: 0.6934 (mmm) cc_final: 0.6733 (mmm) outliers start: 47 outliers final: 19 residues processed: 183 average time/residue: 1.1612 time to fit residues: 227.5740 Evaluate side-chains 169 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8989 Z= 0.217 Angle : 0.573 7.221 12154 Z= 0.304 Chirality : 0.044 0.202 1300 Planarity : 0.004 0.031 1569 Dihedral : 9.913 101.244 1261 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 5.22 % Allowed : 18.74 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.36 (0.26), residues: 1075 helix: 0.23 (0.25), residues: 484 sheet: 0.51 (0.46), residues: 111 loop : -2.52 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 501 HIS 0.005 0.001 HIS B 541 PHE 0.017 0.002 PHE B 438 TYR 0.027 0.002 TYR A 164 ARG 0.006 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 155 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 ASN cc_start: 0.7050 (t0) cc_final: 0.6634 (m-40) REVERT: A 595 PHE cc_start: 0.6068 (OUTLIER) cc_final: 0.5354 (m-80) REVERT: B 277 GLU cc_start: 0.5457 (OUTLIER) cc_final: 0.5165 (mm-30) outliers start: 49 outliers final: 26 residues processed: 188 average time/residue: 1.1588 time to fit residues: 233.0653 Evaluate side-chains 177 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 663 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.0670 chunk 104 optimal weight: 0.0040 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 overall best weight: 0.3530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 278 GLN B 334 GLN B 342 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8989 Z= 0.167 Angle : 0.553 7.533 12154 Z= 0.291 Chirality : 0.043 0.155 1300 Planarity : 0.003 0.032 1569 Dihedral : 9.514 88.005 1261 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 4.69 % Allowed : 20.55 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.18 (0.26), residues: 1075 helix: 0.37 (0.25), residues: 485 sheet: 0.50 (0.46), residues: 112 loop : -2.40 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 501 HIS 0.004 0.001 HIS B 541 PHE 0.015 0.001 PHE B 438 TYR 0.020 0.001 TYR B 617 ARG 0.006 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 147 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 ASN cc_start: 0.7027 (t0) cc_final: 0.6618 (m-40) REVERT: A 433 ARG cc_start: 0.6923 (mtm-85) cc_final: 0.6721 (mtp-110) REVERT: A 595 PHE cc_start: 0.6032 (OUTLIER) cc_final: 0.5276 (m-80) REVERT: B 153 HIS cc_start: 0.6625 (m90) cc_final: 0.6414 (m90) REVERT: B 355 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7586 (tttt) outliers start: 44 outliers final: 20 residues processed: 175 average time/residue: 1.1948 time to fit residues: 224.3793 Evaluate side-chains 165 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 355 LYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.0010 chunk 11 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN B 334 GLN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8989 Z= 0.160 Angle : 0.552 8.328 12154 Z= 0.288 Chirality : 0.044 0.270 1300 Planarity : 0.003 0.049 1569 Dihedral : 8.827 87.563 1259 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.15 % Allowed : 21.94 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.07 (0.26), residues: 1075 helix: 0.46 (0.25), residues: 491 sheet: 0.54 (0.47), residues: 112 loop : -2.37 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 409 HIS 0.004 0.001 HIS B 541 PHE 0.016 0.001 PHE B 438 TYR 0.020 0.001 TYR B 617 ARG 0.012 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.5665 (OUTLIER) cc_final: 0.5221 (mtm) REVERT: A 387 LEU cc_start: 0.6540 (tp) cc_final: 0.6332 (tp) REVERT: A 396 ASN cc_start: 0.7008 (t0) cc_final: 0.6608 (m-40) REVERT: A 433 ARG cc_start: 0.6803 (mtm-85) cc_final: 0.6596 (mtp-110) REVERT: A 595 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.5325 (m-80) outliers start: 39 outliers final: 21 residues processed: 169 average time/residue: 1.1774 time to fit residues: 213.0438 Evaluate side-chains 161 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 0.0980 chunk 99 optimal weight: 0.5980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 334 GLN B 674 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8989 Z= 0.164 Angle : 0.558 7.846 12154 Z= 0.291 Chirality : 0.043 0.185 1300 Planarity : 0.004 0.048 1569 Dihedral : 8.373 82.092 1259 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.09 % Allowed : 23.86 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.01 (0.26), residues: 1075 helix: 0.52 (0.25), residues: 485 sheet: 0.49 (0.47), residues: 112 loop : -2.29 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 501 HIS 0.007 0.001 HIS A 153 PHE 0.014 0.001 PHE B 224 TYR 0.019 0.001 TYR B 617 ARG 0.015 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.6578 (tp) cc_final: 0.6367 (tp) REVERT: A 396 ASN cc_start: 0.7032 (t0) cc_final: 0.6649 (m-40) REVERT: A 595 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.5098 (m-80) outliers start: 29 outliers final: 19 residues processed: 162 average time/residue: 1.1540 time to fit residues: 200.0758 Evaluate side-chains 161 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 674 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.0030 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.0470 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 91 optimal weight: 0.0870 chunk 96 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 overall best weight: 0.2666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 278 GLN B 485 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8989 Z= 0.159 Angle : 0.571 9.423 12154 Z= 0.294 Chirality : 0.043 0.153 1300 Planarity : 0.004 0.051 1569 Dihedral : 8.000 74.143 1259 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.98 % Allowed : 24.17 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.93 (0.26), residues: 1075 helix: 0.71 (0.25), residues: 477 sheet: 0.59 (0.47), residues: 112 loop : -2.37 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 501 HIS 0.006 0.001 HIS A 153 PHE 0.018 0.001 PHE B 484 TYR 0.018 0.001 TYR B 164 ARG 0.012 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 236 TYR cc_start: 0.5273 (OUTLIER) cc_final: 0.4810 (t80) REVERT: A 396 ASN cc_start: 0.6951 (t0) cc_final: 0.6660 (m-40) REVERT: A 595 PHE cc_start: 0.6060 (OUTLIER) cc_final: 0.5077 (m-80) REVERT: B 242 ASN cc_start: 0.5320 (m-40) cc_final: 0.5101 (m-40) outliers start: 28 outliers final: 18 residues processed: 166 average time/residue: 1.1283 time to fit residues: 200.9834 Evaluate side-chains 159 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 639 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.0030 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B 298 ASN B 674 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 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 0.053 8989 Z= 0.263 Angle : 0.648 9.497 12154 Z= 0.340 Chirality : 0.047 0.167 1300 Planarity : 0.004 0.050 1569 Dihedral : 8.463 83.344 1259 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.19 % Allowed : 23.96 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.20 (0.26), residues: 1075 helix: 0.36 (0.25), residues: 481 sheet: 0.48 (0.47), residues: 112 loop : -2.40 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 501 HIS 0.006 0.001 HIS B 279 PHE 0.029 0.002 PHE B 484 TYR 0.020 0.002 TYR B 164 ARG 0.012 0.001 ARG B 330 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 ASN cc_start: 0.6979 (t0) cc_final: 0.6668 (m-40) REVERT: A 595 PHE cc_start: 0.6055 (OUTLIER) cc_final: 0.5305 (m-80) outliers start: 30 outliers final: 20 residues processed: 171 average time/residue: 1.1589 time to fit residues: 212.7503 Evaluate side-chains 165 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 595 PHE Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 639 HIS Chi-restraints excluded: chain B residue 674 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 75 optimal weight: 0.0070 overall best weight: 0.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.196367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.186197 restraints weight = 12133.756| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 1.60 r_work: 0.4364 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4250 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8989 Z= 0.179 Angle : 0.626 11.339 12154 Z= 0.320 Chirality : 0.044 0.190 1300 Planarity : 0.004 0.045 1569 Dihedral : 8.149 76.405 1259 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.45 % Allowed : 24.81 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.11 (0.26), residues: 1075 helix: 0.40 (0.25), residues: 484 sheet: 0.43 (0.46), residues: 115 loop : -2.31 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 501 HIS 0.005 0.001 HIS A 153 PHE 0.024 0.001 PHE B 438 TYR 0.016 0.001 TYR A 231 ARG 0.011 0.000 ARG B 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4049.54 seconds wall clock time: 73 minutes 16.71 seconds (4396.71 seconds total)