Starting phenix.real_space_refine (version: dev) on Sun Feb 19 19:15:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0w_10361/02_2023/6t0w_10361.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0w_10361/02_2023/6t0w_10361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0w_10361/02_2023/6t0w_10361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0w_10361/02_2023/6t0w_10361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0w_10361/02_2023/6t0w_10361.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0w_10361/02_2023/6t0w_10361.pdb" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 Process input model Symmetric amino acids flipped Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10556 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4161 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 21, 'TRANS': 499} Chain: "B" Number of atoms: 5174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5174 Classifications: {'peptide': 661} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 627} Chain breaks: 1 Chain: "C" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "V" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 533 Classifications: {'RNA': 25} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 9} Link IDs: {'rna2p': 6, 'rna3p': 18} Chain breaks: 2 Time building chain proxies: 6.55, per 1000 atoms: 0.62 Number of scatterers: 10556 At special positions: 0 Unit cell: (104.009, 101.908, 113.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 25 15.00 O 2047 8.00 N 1806 7.00 C 6599 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: 4.10 Conformation dependent library (CDL) restraints added in 1.4 seconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 11 sheets defined 47.4% alpha, 12.0% beta 6 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.804A pdb=" N MET A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 4.213A pdb=" N ARG A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.564A pdb=" N ILE A 269 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 270' Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.684A pdb=" N ARG A 317 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 318' Processing helix chain 'A' and resid 332 through 347 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.631A pdb=" N THR A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 447 removed outlier: 3.845A pdb=" N ASN A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 472 removed outlier: 3.942A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.566A pdb=" N TRP A 533 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 Processing helix chain 'A' and resid 574 through 592 removed outlier: 3.921A pdb=" N LEU A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 628 through 646 Processing helix chain 'A' and resid 648 through 670 removed outlier: 4.594A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 687 removed outlier: 3.598A pdb=" N MET A 682 " --> pdb=" O ASP A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 715 removed outlier: 3.687A pdb=" N LYS A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.185A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.608A pdb=" N THR B 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 115 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.805A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.840A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.610A pdb=" N LEU B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.528A pdb=" N LEU B 373 " --> pdb=" O CYS B 370 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE B 374 " --> pdb=" O PRO B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.507A pdb=" N TYR B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 415 through 426 Processing helix chain 'B' and resid 454 through 471 removed outlier: 3.746A pdb=" N LEU B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'B' and resid 539 through 558 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.924A pdb=" N GLY B 587 " --> pdb=" O GLY B 584 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 588 " --> pdb=" O ARG B 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 584 through 588' Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 606 through 612 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.655A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 128 removed outlier: 3.602A pdb=" N PHE C 121 " --> pdb=" O TYR C 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 256 removed outlier: 3.550A pdb=" N GLY B 304 " --> pdb=" O PHE B 446 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B 446 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 294 removed outlier: 7.325A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 555 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG A 540 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N CYS A 557 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VAL A 538 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 538 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 294 removed outlier: 5.290A pdb=" N ASP A 494 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 485 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU A 496 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASN A 483 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 498 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 477 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 476 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.966A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 625 through 627 removed outlier: 7.066A pdb=" N VAL A 625 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN B 2 " --> pdb=" O THR A 619 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.564A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 184 Processing sheet with id=AA9, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.938A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB2, first strand: chain 'B' and resid 641 through 642 removed outlier: 4.101A pdb=" N ALA B 642 " --> pdb=" O MET B 654 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B 654 " --> pdb=" O ALA B 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 455 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2394 1.33 - 1.45: 2340 1.45 - 1.57: 5907 1.57 - 1.69: 47 1.69 - 1.81: 133 Bond restraints: 10821 Sorted by residual: bond pdb=" N ASP B 445 " pdb=" CA ASP B 445 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.21e-02 6.83e+03 8.55e+00 bond pdb=" N LYS A 300 " pdb=" CA LYS A 300 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.16e-02 7.43e+03 6.84e+00 bond pdb=" N PHE B 446 " pdb=" CA PHE B 446 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.75e+00 bond pdb=" N ASP B 444 " pdb=" CA ASP B 444 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.27e-02 6.20e+03 6.49e+00 bond pdb=" N LYS A 301 " pdb=" CA LYS A 301 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.41e-02 5.03e+03 6.28e+00 ... (remaining 10816 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.83: 371 105.83 - 112.91: 5724 112.91 - 119.99: 3950 119.99 - 127.07: 4501 127.07 - 134.15: 169 Bond angle restraints: 14715 Sorted by residual: angle pdb=" N LYS B 393 " pdb=" CA LYS B 393 " pdb=" C LYS B 393 " ideal model delta sigma weight residual 109.81 119.58 -9.77 2.21e+00 2.05e-01 1.95e+01 angle pdb=" N ILE B 339 " pdb=" CA ILE B 339 " pdb=" C ILE B 339 " ideal model delta sigma weight residual 112.12 108.89 3.23 8.40e-01 1.42e+00 1.48e+01 angle pdb=" CA TRP B 437 " pdb=" CB TRP B 437 " pdb=" CG TRP B 437 " ideal model delta sigma weight residual 113.60 120.80 -7.20 1.90e+00 2.77e-01 1.44e+01 angle pdb=" C ILE B 427 " pdb=" N LYS B 428 " pdb=" CA LYS B 428 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" N GLY A 542 " pdb=" CA GLY A 542 " pdb=" C GLY A 542 " ideal model delta sigma weight residual 110.58 115.27 -4.69 1.35e+00 5.49e-01 1.21e+01 ... (remaining 14710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 5828 17.31 - 34.61: 524 34.61 - 51.92: 114 51.92 - 69.22: 40 69.22 - 86.53: 10 Dihedral angle restraints: 6516 sinusoidal: 2859 harmonic: 3657 Sorted by residual: dihedral pdb=" CA MET B 409 " pdb=" C MET B 409 " pdb=" N MET B 410 " pdb=" CA MET B 410 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA MET B 408 " pdb=" C MET B 408 " pdb=" N MET B 409 " pdb=" CA MET B 409 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA THR B 303 " pdb=" C THR B 303 " pdb=" N GLY B 304 " pdb=" CA GLY B 304 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1100 0.050 - 0.101: 450 0.101 - 0.151: 78 0.151 - 0.201: 7 0.201 - 0.252: 2 Chirality restraints: 1637 Sorted by residual: chirality pdb=" CB VAL A 485 " pdb=" CA VAL A 485 " pdb=" CG1 VAL A 485 " pdb=" CG2 VAL A 485 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB VAL A 277 " pdb=" CA VAL A 277 " pdb=" CG1 VAL A 277 " pdb=" CG2 VAL A 277 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA LYS B 393 " pdb=" N LYS B 393 " pdb=" C LYS B 393 " pdb=" CB LYS B 393 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 1634 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " 0.034 2.00e-02 2.50e+03 1.53e-02 6.40e+00 pdb=" N9 A V 4 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A V 4 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A V 4 " 0.006 2.00e-02 2.50e+03 pdb=" C5 A V 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A V 4 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A V 4 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A V 4 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 137 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO B 138 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 314 " 0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO B 315 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 315 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 315 " 0.031 5.00e-02 4.00e+02 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2449 2.78 - 3.31: 8765 3.31 - 3.84: 17233 3.84 - 4.37: 20970 4.37 - 4.90: 36206 Nonbonded interactions: 85623 Sorted by model distance: nonbonded pdb=" OD2 ASP B 521 " pdb=" OH TYR B 558 " model vdw 2.251 2.440 nonbonded pdb=" O ILE B 18 " pdb=" OG1 THR B 21 " model vdw 2.283 2.440 nonbonded pdb=" O LEU A 211 " pdb=" OG SER A 215 " model vdw 2.286 2.440 nonbonded pdb=" O SER B 291 " pdb=" OG SER B 291 " model vdw 2.305 2.440 nonbonded pdb=" O ALA A 362 " pdb=" OG1 THR A 366 " model vdw 2.311 2.440 ... (remaining 85618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 25 5.49 5 S 79 5.16 5 C 6599 2.51 5 N 1806 2.21 5 O 2047 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.270 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: 2.060 Check model and map are aligned: 0.160 Process input model: 31.970 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.008 0.072 10821 Z= 0.515 Angle : 0.803 9.768 14715 Z= 0.459 Chirality : 0.052 0.252 1637 Planarity : 0.007 0.063 1796 Dihedral : 14.458 86.528 4164 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer Outliers : 6.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -3.70 (0.18), residues: 1260 helix: -2.29 (0.16), residues: 548 sheet: -1.83 (0.37), residues: 151 loop : -2.71 (0.22), residues: 561 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 171 time to evaluate : 1.095 Fit side-chains revert: symmetry clash outliers start: 69 outliers final: 31 residues processed: 233 average time/residue: 0.2246 time to fit residues: 72.3805 Evaluate side-chains 158 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.0917 time to fit residues: 6.7538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN A 666 GLN B 47 HIS B 70 ASN B 99 HIS B 104 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN B 548 GLN ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN C 68 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 10821 Z= 0.253 Angle : 0.547 7.872 14715 Z= 0.290 Chirality : 0.041 0.178 1637 Planarity : 0.005 0.045 1796 Dihedral : 7.436 71.733 1656 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.41 % Favored : 96.51 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.86 (0.21), residues: 1260 helix: -0.19 (0.21), residues: 547 sheet: -1.66 (0.38), residues: 154 loop : -2.16 (0.23), residues: 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.114 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 147 average time/residue: 0.2349 time to fit residues: 49.6505 Evaluate side-chains 134 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 1.242 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1845 time to fit residues: 3.9109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 314 ASN ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 10821 Z= 0.354 Angle : 0.580 7.985 14715 Z= 0.303 Chirality : 0.043 0.172 1637 Planarity : 0.005 0.043 1796 Dihedral : 7.442 72.586 1656 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.21 % Favored : 95.71 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.26 (0.22), residues: 1260 helix: 0.45 (0.22), residues: 547 sheet: -1.50 (0.39), residues: 148 loop : -1.95 (0.23), residues: 565 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 1.277 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 140 average time/residue: 0.2369 time to fit residues: 48.0396 Evaluate side-chains 130 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1050 time to fit residues: 3.7937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 123 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 33 optimal weight: 0.0980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 10821 Z= 0.175 Angle : 0.483 7.303 14715 Z= 0.256 Chirality : 0.039 0.158 1637 Planarity : 0.004 0.041 1796 Dihedral : 7.179 72.161 1656 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.78 % Favored : 97.14 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.74 (0.23), residues: 1260 helix: 0.99 (0.22), residues: 548 sheet: -1.37 (0.39), residues: 144 loop : -1.78 (0.24), residues: 568 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.228 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 135 average time/residue: 0.2406 time to fit residues: 46.6470 Evaluate side-chains 125 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.332 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1109 time to fit residues: 2.8438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 10821 Z= 0.327 Angle : 0.552 7.600 14715 Z= 0.286 Chirality : 0.043 0.167 1637 Planarity : 0.004 0.039 1796 Dihedral : 7.298 72.220 1656 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.03 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.67 (0.23), residues: 1260 helix: 1.03 (0.22), residues: 548 sheet: -1.25 (0.40), residues: 144 loop : -1.74 (0.24), residues: 568 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.130 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 125 average time/residue: 0.2314 time to fit residues: 41.3692 Evaluate side-chains 123 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1765 time to fit residues: 3.4233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 10821 Z= 0.228 Angle : 0.508 8.947 14715 Z= 0.264 Chirality : 0.040 0.164 1637 Planarity : 0.004 0.039 1796 Dihedral : 7.183 72.065 1656 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.86 % Favored : 97.06 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.42 (0.23), residues: 1260 helix: 1.23 (0.22), residues: 549 sheet: -1.13 (0.40), residues: 144 loop : -1.59 (0.24), residues: 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 1.237 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 122 average time/residue: 0.2715 time to fit residues: 46.9295 Evaluate side-chains 117 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1085 time to fit residues: 2.3197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 10821 Z= 0.233 Angle : 0.500 7.294 14715 Z= 0.262 Chirality : 0.040 0.152 1637 Planarity : 0.004 0.038 1796 Dihedral : 7.172 71.630 1656 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.32 (0.23), residues: 1260 helix: 1.31 (0.22), residues: 549 sheet: -1.03 (0.40), residues: 144 loop : -1.54 (0.25), residues: 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.324 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 124 average time/residue: 0.2558 time to fit residues: 45.1497 Evaluate side-chains 118 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.344 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1120 time to fit residues: 2.0543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.004 0.035 10821 Z= 0.251 Angle : 0.523 11.113 14715 Z= 0.269 Chirality : 0.041 0.152 1637 Planarity : 0.004 0.038 1796 Dihedral : 7.183 71.568 1656 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.23), residues: 1260 helix: 1.33 (0.22), residues: 549 sheet: -0.92 (0.39), residues: 153 loop : -1.56 (0.25), residues: 558 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 1.321 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 122 average time/residue: 0.2553 time to fit residues: 44.5448 Evaluate side-chains 117 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.359 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1578 time to fit residues: 2.7081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10821 Z= 0.201 Angle : 0.501 11.425 14715 Z= 0.259 Chirality : 0.040 0.162 1637 Planarity : 0.004 0.038 1796 Dihedral : 7.120 71.131 1656 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.23 (0.23), residues: 1260 helix: 1.38 (0.22), residues: 551 sheet: -0.67 (0.41), residues: 141 loop : -1.60 (0.24), residues: 568 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 1.143 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 122 average time/residue: 0.2647 time to fit residues: 46.1200 Evaluate side-chains 117 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 1.281 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1104 time to fit residues: 2.1823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 78 optimal weight: 0.2980 chunk 62 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 10821 Z= 0.274 Angle : 0.541 12.327 14715 Z= 0.278 Chirality : 0.042 0.159 1637 Planarity : 0.004 0.037 1796 Dihedral : 7.194 71.239 1656 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.31 (0.23), residues: 1260 helix: 1.29 (0.22), residues: 552 sheet: -0.69 (0.41), residues: 141 loop : -1.63 (0.24), residues: 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.229 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 117 average time/residue: 0.2641 time to fit residues: 44.2178 Evaluate side-chains 114 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1356 time to fit residues: 1.9637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.0870 chunk 93 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 18 optimal weight: 6.9990 chunk 89 optimal weight: 0.0170 chunk 5 optimal weight: 4.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.154060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.123628 restraints weight = 12993.664| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.71 r_work: 0.3138 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 10821 Z= 0.118 Angle : 0.470 12.473 14715 Z= 0.243 Chirality : 0.039 0.209 1637 Planarity : 0.003 0.038 1796 Dihedral : 6.969 70.903 1656 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1260 helix: 1.63 (0.23), residues: 549 sheet: -0.61 (0.43), residues: 132 loop : -1.35 (0.25), residues: 579 =============================================================================== Job complete usr+sys time: 2125.79 seconds wall clock time: 39 minutes 50.09 seconds (2390.09 seconds total)