Starting phenix.real_space_refine on Tue Nov 14 13:27:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2d_17361/11_2023/8p2d_17361_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2d_17361/11_2023/8p2d_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_17361/11_2023/8p2d_17361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2d_17361/11_2023/8p2d_17361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2d_17361/11_2023/8p2d_17361_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2d_17361/11_2023/8p2d_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-1.21rc1-5144/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: 4.76, per 1000 atoms: 0.54 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: 3.18 Conformation dependent library (CDL) restraints added in 1.5 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: 1.82 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: 2.14 Time building geometry restraints manager: 3.51 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: 5106 21.57 - 43.14: 205 43.14 - 64.70: 43 64.70 - 86.27: 2 86.27 - 107.84: 2 Dihedral angle restraints: 5358 sinusoidal: 2193 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 5355 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: 1.340 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: 5.730 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.350 Find NCS groups from input model: 0.560 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:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.510 ------------------------------------------------------------------------------- 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 : 12.076 107.837 3328 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 *********************** 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 : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 7 residues processed: 212 average time/residue: 1.0871 time to fit residues: 246.9342 Evaluate side-chains 155 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.2168 time to fit residues: 1.6227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 45 optimal weight: 0.0040 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 0.0170 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 overall best weight: 0.4230 ------------------------------------------------------------------------------- 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 483 GLN A 548 GLN A 611 ASN A 652 ASN A 674 ASN B 153 HIS B 154 ASN B 188 HIS B 237 GLN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6151 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8989 Z= 0.172 Angle : 0.545 7.843 12154 Z= 0.289 Chirality : 0.043 0.163 1300 Planarity : 0.004 0.033 1569 Dihedral : 6.288 106.877 1193 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.69 % Allowed : 14.59 % Favored : 80.72 % 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: -1.46 (0.26), residues: 1075 helix: 0.03 (0.25), residues: 495 sheet: 0.52 (0.47), residues: 112 loop : -2.52 (0.26), residues: 468 *********************** 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 191 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 147 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 16 residues processed: 180 average time/residue: 1.0982 time to fit residues: 212.3763 Evaluate side-chains 156 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 6 average time/residue: 0.4280 time to fit residues: 4.3204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 674 ASN B 153 HIS B 213 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8989 Z= 0.207 Angle : 0.572 7.408 12154 Z= 0.300 Chirality : 0.044 0.213 1300 Planarity : 0.004 0.030 1569 Dihedral : 6.418 108.616 1193 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 4.79 % Allowed : 16.29 % Favored : 78.91 % 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: -1.44 (0.26), residues: 1075 helix: 0.18 (0.25), residues: 487 sheet: 0.47 (0.46), residues: 111 loop : -2.60 (0.26), residues: 477 *********************** 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 192 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 147 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 21 residues processed: 174 average time/residue: 1.0534 time to fit residues: 197.6507 Evaluate side-chains 162 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 7 average time/residue: 0.2883 time to fit residues: 3.9337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 0.0670 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 153 HIS B 213 ASN ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8989 Z= 0.189 Angle : 0.556 7.118 12154 Z= 0.292 Chirality : 0.043 0.150 1300 Planarity : 0.003 0.031 1569 Dihedral : 6.414 108.732 1193 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.69 % Allowed : 18.42 % Favored : 76.89 % 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: -1.29 (0.26), residues: 1075 helix: 0.34 (0.25), residues: 486 sheet: 0.48 (0.46), residues: 111 loop : -2.55 (0.26), residues: 478 *********************** 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 188 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 144 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 21 residues processed: 173 average time/residue: 1.0844 time to fit residues: 201.9178 Evaluate side-chains 161 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 4 average time/residue: 0.1668 time to fit residues: 2.3381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 385 ASN A 492 GLN ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 278 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 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 : 0.005 0.046 8989 Z= 0.324 Angle : 0.649 7.334 12154 Z= 0.346 Chirality : 0.047 0.161 1300 Planarity : 0.004 0.041 1569 Dihedral : 7.012 116.286 1193 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 4.58 % Allowed : 19.49 % Favored : 75.93 % 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: -1.64 (0.25), residues: 1075 helix: 0.04 (0.24), residues: 479 sheet: 0.35 (0.46), residues: 111 loop : -2.70 (0.25), residues: 485 *********************** 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 193 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 150 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 24 residues processed: 181 average time/residue: 1.0922 time to fit residues: 212.7213 Evaluate side-chains 170 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 7 average time/residue: 0.3155 time to fit residues: 4.1167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.2980 chunk 94 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 86 optimal weight: 0.3980 chunk 48 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 153 HIS B 334 GLN B 338 GLN B 342 ASN ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8989 Z= 0.182 Angle : 0.572 9.474 12154 Z= 0.301 Chirality : 0.043 0.162 1300 Planarity : 0.003 0.030 1569 Dihedral : 6.630 111.542 1193 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.94 % Allowed : 21.41 % Favored : 74.65 % 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: -1.27 (0.26), residues: 1075 helix: 0.34 (0.25), residues: 481 sheet: 0.37 (0.46), residues: 112 loop : -2.46 (0.26), residues: 482 *********************** 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 186 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 149 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 22 residues processed: 178 average time/residue: 1.1156 time to fit residues: 215.6336 Evaluate side-chains 164 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 4 average time/residue: 0.1818 time to fit residues: 2.5104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 B 153 HIS B 334 GLN ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8989 Z= 0.203 Angle : 0.585 8.843 12154 Z= 0.305 Chirality : 0.044 0.157 1300 Planarity : 0.004 0.030 1569 Dihedral : 6.680 113.217 1193 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.05 % Allowed : 22.26 % Favored : 73.70 % 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: -1.24 (0.26), residues: 1075 helix: 0.34 (0.25), residues: 484 sheet: 0.37 (0.46), residues: 112 loop : -2.43 (0.26), residues: 479 *********************** 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 176 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 138 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 25 residues processed: 167 average time/residue: 1.1415 time to fit residues: 204.7948 Evaluate side-chains 162 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 6 average time/residue: 0.5239 time to fit residues: 5.0062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 0.0980 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.0570 chunk 99 optimal weight: 0.7980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS A 298 ASN B 300 ASN B 334 GLN ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8989 Z= 0.165 Angle : 0.577 8.533 12154 Z= 0.295 Chirality : 0.044 0.300 1300 Planarity : 0.003 0.032 1569 Dihedral : 6.342 104.699 1193 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.30 % Allowed : 23.54 % Favored : 73.16 % 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: 0.55 (0.25), residues: 485 sheet: 0.46 (0.46), residues: 112 loop : -2.33 (0.27), residues: 478 *********************** 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 172 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 21 residues processed: 167 average time/residue: 1.0447 time to fit residues: 188.3306 Evaluate side-chains 159 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 0.825 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 4 average time/residue: 0.5051 time to fit residues: 3.7889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.0370 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 B 153 HIS B 334 GLN ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.2667 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= 0.209 Angle : 0.601 9.674 12154 Z= 0.311 Chirality : 0.045 0.199 1300 Planarity : 0.004 0.033 1569 Dihedral : 6.488 106.633 1193 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.77 % Allowed : 24.39 % 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: -1.09 (0.26), residues: 1075 helix: 0.44 (0.25), residues: 483 sheet: 0.49 (0.47), residues: 112 loop : -2.32 (0.27), residues: 480 *********************** 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 162 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 20 residues processed: 157 average time/residue: 1.1208 time to fit residues: 188.8082 Evaluate side-chains 155 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 4 average time/residue: 0.3977 time to fit residues: 3.1722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 0.0060 chunk 71 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 0.0670 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 overall best weight: 0.4334 ------------------------------------------------------------------------------- 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 B 153 HIS B 334 GLN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8989 Z= 0.191 Angle : 0.600 9.327 12154 Z= 0.308 Chirality : 0.044 0.159 1300 Planarity : 0.004 0.033 1569 Dihedral : 6.508 107.674 1193 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.24 % Allowed : 25.03 % 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: -1.05 (0.26), residues: 1075 helix: 0.46 (0.25), residues: 485 sheet: 0.53 (0.46), residues: 112 loop : -2.30 (0.27), residues: 478 ********************** 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 154 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 17 residues processed: 152 average time/residue: 1.1523 time to fit residues: 188.0540 Evaluate side-chains 150 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 2 average time/residue: 0.1814 time to fit residues: 2.0461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0570 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 0.0030 chunk 75 optimal weight: 0.1980 overall best weight: 0.2708 ------------------------------------------------------------------------------- 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** B 334 GLN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.197124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.186943 restraints weight = 12013.724| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 1.53 r_work: 0.4367 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4258 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8989 Z= 0.169 Angle : 0.594 10.842 12154 Z= 0.301 Chirality : 0.044 0.214 1300 Planarity : 0.003 0.033 1569 Dihedral : 6.296 102.107 1193 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.34 % Allowed : 25.24 % Favored : 72.42 % 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: -0.98 (0.26), residues: 1075 helix: 0.53 (0.25), residues: 486 sheet: 0.55 (0.46), residues: 112 loop : -2.29 (0.27), residues: 477 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3874.92 seconds wall clock time: 69 minutes 16.94 seconds (4156.94 seconds total)