Starting phenix.real_space_refine on Mon Apr 8 21:30:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnp_17782/04_2024/8pnp_17782_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnp_17782/04_2024/8pnp_17782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnp_17782/04_2024/8pnp_17782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnp_17782/04_2024/8pnp_17782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnp_17782/04_2024/8pnp_17782_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pnp_17782/04_2024/8pnp_17782_updated.pdb" } resolution = 2.49 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 88 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 103 5.16 5 C 8978 2.51 5 N 2494 2.21 5 O 2854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14460 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5748 Classifications: {'peptide': 708} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 5850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5850 Classifications: {'peptide': 735} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 702} Chain breaks: 1 Chain: "C" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2024 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "V" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 616 Classifications: {'RNA': 29} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna2p': 7, 'rna3p': 21} Chain breaks: 1 Chain: "G" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 179 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 6, 'TRANS': 16} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "V" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 8.46, per 1000 atoms: 0.59 Number of scatterers: 14460 At special positions: 0 Unit cell: (94.08, 102.48, 144.48, 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 103 16.00 P 31 15.00 O 2854 8.00 N 2494 7.00 C 8978 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: 6.44 Conformation dependent library (CDL) restraints added in 3.0 seconds 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 16 sheets defined 46.6% alpha, 10.6% beta 5 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 7.00 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.712A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 49 Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 165 through 185 Processing helix chain 'A' and resid 210 through 217 removed outlier: 3.532A pdb=" N GLN A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 303 through 313 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.763A pdb=" N GLU A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 434 through 451 Processing helix chain 'A' and resid 454 through 475 Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 534 through 537 Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 581 through 600 removed outlier: 3.640A pdb=" N SER A 594 " --> pdb=" O GLN A 591 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU A 597 " --> pdb=" O SER A 594 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 598 " --> pdb=" O MET A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 633 through 649 Processing helix chain 'A' and resid 653 through 673 removed outlier: 4.002A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 4.032A pdb=" N CYS A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 714 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 15 through 21 removed outlier: 5.690A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.537A pdb=" N GLN B 115 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 157 through 160 removed outlier: 3.905A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 160' Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.639A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 246 through 265 removed outlier: 4.710A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 293 removed outlier: 3.582A pdb=" N ASN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 293 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 331 through 346 removed outlier: 4.447A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 370 through 375 removed outlier: 4.159A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 375 " --> pdb=" O MET B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 383 through 395 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.519A pdb=" N THR B 417 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 456 through 473 Processing helix chain 'B' and resid 506 through 511 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 519 through 536 Processing helix chain 'B' and resid 541 through 559 Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' Processing helix chain 'B' and resid 591 through 593 No H-bonds generated for 'chain 'B' and resid 591 through 593' Processing helix chain 'B' and resid 608 through 611 No H-bonds generated for 'chain 'B' and resid 608 through 611' 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 618 through 624 Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 673 through 676 Processing helix chain 'B' and resid 678 through 699 removed outlier: 4.085A pdb=" N GLY B 681 " --> pdb=" O SER B 678 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 684 " --> pdb=" O GLY B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 3.818A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 714 through 732 Processing helix chain 'B' and resid 737 through 755 removed outlier: 3.696A pdb=" N ARG B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 25 through 31 removed outlier: 4.142A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 removed outlier: 4.052A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 111 through 114 No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 116 through 126 Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 180 through 192 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 226 through 229 No H-bonds generated for 'chain 'C' and resid 226 through 229' Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing sheet with id= A, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.881A pdb=" N HIS A 144 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N GLY A 121 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N HIS A 146 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N THR A 123 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 148 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.762A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 502 through 506 removed outlier: 6.475A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU A 544 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 619 through 623 removed outlier: 6.725A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= F, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= G, first strand: chain 'B' and resid 178 through 183 Processing sheet with id= H, first strand: chain 'B' and resid 224 through 228 Processing sheet with id= I, first strand: chain 'B' and resid 483 through 486 removed outlier: 3.682A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE B 447 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 348 through 350 Processing sheet with id= K, first strand: chain 'B' and resid 355 through 359 Processing sheet with id= L, first strand: chain 'B' and resid 489 through 492 Processing sheet with id= M, first strand: chain 'B' and resid 642 through 645 Processing sheet with id= N, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= O, first strand: chain 'C' and resid 133 through 135 Processing sheet with id= P, first strand: chain 'C' and resid 141 through 145 586 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 4.86 Time building geometry restraints manager: 6.72 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: 4412 1.33 - 1.46: 2337 1.46 - 1.58: 7783 1.58 - 1.70: 64 1.70 - 1.82: 177 Bond restraints: 14773 Sorted by residual: bond pdb=" N TYR G 1 " pdb=" CA TYR G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" CB GLU C 158 " pdb=" CG GLU C 158 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.29e-01 bond pdb=" CD LYS A 361 " pdb=" CE LYS A 361 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.10e-01 ... (remaining 14768 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.62: 421 105.62 - 112.73: 7827 112.73 - 119.84: 4973 119.84 - 126.95: 6613 126.95 - 134.05: 237 Bond angle restraints: 20071 Sorted by residual: angle pdb=" CB MET C 1 " pdb=" CG MET C 1 " pdb=" SD MET C 1 " ideal model delta sigma weight residual 112.70 121.49 -8.79 3.00e+00 1.11e-01 8.59e+00 angle pdb=" CG LYS A 361 " pdb=" CD LYS A 361 " pdb=" CE LYS A 361 " ideal model delta sigma weight residual 111.30 117.88 -6.58 2.30e+00 1.89e-01 8.19e+00 angle pdb=" C2' A V 4 " pdb=" C1' A V 4 " pdb=" N9 A V 4 " ideal model delta sigma weight residual 112.00 115.46 -3.46 1.50e+00 4.44e-01 5.33e+00 angle pdb=" CB MET B 744 " pdb=" CG MET B 744 " pdb=" SD MET B 744 " ideal model delta sigma weight residual 112.70 119.51 -6.81 3.00e+00 1.11e-01 5.16e+00 angle pdb=" CA GLU C 158 " pdb=" CB GLU C 158 " pdb=" CG GLU C 158 " ideal model delta sigma weight residual 114.10 118.58 -4.48 2.00e+00 2.50e-01 5.01e+00 ... (remaining 20066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7700 17.77 - 35.54: 945 35.54 - 53.32: 300 53.32 - 71.09: 113 71.09 - 88.86: 30 Dihedral angle restraints: 9088 sinusoidal: 4079 harmonic: 5009 Sorted by residual: dihedral pdb=" CA ASP C 161 " pdb=" CB ASP C 161 " pdb=" CG ASP C 161 " pdb=" OD1 ASP C 161 " ideal model delta sinusoidal sigma weight residual -30.00 -88.13 58.13 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA VAL A 517 " pdb=" C VAL A 517 " pdb=" N VAL A 518 " pdb=" CA VAL A 518 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU B 78 " pdb=" CG GLU B 78 " pdb=" CD GLU B 78 " pdb=" OE1 GLU B 78 " ideal model delta sinusoidal sigma weight residual 0.00 -88.86 88.86 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 9085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1744 0.041 - 0.081: 358 0.081 - 0.122: 100 0.122 - 0.163: 11 0.163 - 0.204: 1 Chirality restraints: 2214 Sorted by residual: chirality pdb=" CB VAL B 719 " pdb=" CA VAL B 719 " pdb=" CG1 VAL B 719 " pdb=" CG2 VAL B 719 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA VAL B 368 " pdb=" N VAL B 368 " pdb=" C VAL B 368 " pdb=" CB VAL B 368 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 2211 not shown) Planarity restraints: 2479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.028 2.00e-02 2.50e+03 1.27e-02 4.41e+00 pdb=" N9 A V 4 " 0.029 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 495 " 0.173 9.50e-02 1.11e+02 7.77e-02 4.27e+00 pdb=" NE ARG A 495 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 495 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 495 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 495 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 587 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C GLN A 587 " -0.030 2.00e-02 2.50e+03 pdb=" O GLN A 587 " 0.011 2.00e-02 2.50e+03 pdb=" N SER A 588 " 0.010 2.00e-02 2.50e+03 ... (remaining 2476 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 159 2.60 - 3.17: 12444 3.17 - 3.75: 23549 3.75 - 4.32: 34092 4.32 - 4.90: 54404 Nonbonded interactions: 124648 Sorted by model distance: nonbonded pdb=" OD2 ASP B 522 " pdb=" OH TYR B 559 " model vdw 2.019 2.440 nonbonded pdb=" OP1 A V 6 " pdb=" O HOH V 101 " model vdw 2.085 2.440 nonbonded pdb=" OE1 GLU A 524 " pdb=" O HOH A 801 " model vdw 2.097 2.440 nonbonded pdb=" OE1 GLU A 610 " pdb=" ND2 ASN A 614 " model vdw 2.137 2.520 nonbonded pdb=" O MET C 11 " pdb=" NH1 ARG C 17 " model vdw 2.160 2.520 ... (remaining 124643 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 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 10.070 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 47.130 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 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 : 0.003 0.035 14773 Z= 0.177 Angle : 0.497 8.794 20071 Z= 0.255 Chirality : 0.037 0.204 2214 Planarity : 0.004 0.078 2479 Dihedral : 18.516 88.860 5844 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.70 % Rotamer: Outliers : 1.24 % Allowed : 22.64 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.87 (0.21), residues: 1697 helix: 1.64 (0.19), residues: 807 sheet: -0.13 (0.38), residues: 190 loop : -0.42 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 88 HIS 0.002 0.001 HIS A 128 PHE 0.010 0.001 PHE B 551 TYR 0.016 0.001 TYR A 305 ARG 0.013 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 189 time to evaluate : 1.736 Fit side-chains revert: symmetry clash REVERT: A 116 ARG cc_start: 0.6162 (ppt90) cc_final: 0.5523 (ppt90) REVERT: A 222 ASN cc_start: 0.8401 (p0) cc_final: 0.8171 (p0) REVERT: B 135 ARG cc_start: 0.8199 (ptp-110) cc_final: 0.7947 (ptt90) REVERT: B 653 LYS cc_start: 0.8365 (mtmm) cc_final: 0.7958 (mmtm) REVERT: C 146 ASP cc_start: 0.7066 (p0) cc_final: 0.6617 (p0) outliers start: 19 outliers final: 15 residues processed: 203 average time/residue: 1.6253 time to fit residues: 357.7458 Evaluate side-chains 200 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.0970 chunk 155 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 466 ASN A 513 ASN A 556 GLN A 670 GLN B 485 ASN C 82 ASN C 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.0543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14773 Z= 0.170 Angle : 0.485 7.285 20071 Z= 0.252 Chirality : 0.038 0.160 2214 Planarity : 0.004 0.043 2479 Dihedral : 10.715 73.782 2343 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.00 % Favored : 97.94 % Rotamer: Outliers : 2.23 % Allowed : 20.88 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1697 helix: 1.63 (0.19), residues: 804 sheet: 0.32 (0.41), residues: 168 loop : -0.49 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 188 HIS 0.003 0.001 HIS A 510 PHE 0.009 0.001 PHE A 520 TYR 0.014 0.001 TYR B 555 ARG 0.007 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 1.746 Fit side-chains revert: symmetry clash REVERT: A 222 ASN cc_start: 0.8377 (p0) cc_final: 0.8118 (p0) REVERT: A 495 ARG cc_start: 0.8176 (ptp-110) cc_final: 0.7972 (ptm160) REVERT: B 75 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7992 (mm-30) REVERT: B 331 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7519 (tm-30) outliers start: 34 outliers final: 10 residues processed: 215 average time/residue: 1.6666 time to fit residues: 386.7283 Evaluate side-chains 198 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 0.1980 chunk 105 optimal weight: 0.3980 chunk 42 optimal weight: 0.0770 chunk 155 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 513 ASN A 556 GLN C 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14773 Z= 0.142 Angle : 0.460 7.974 20071 Z= 0.238 Chirality : 0.037 0.155 2214 Planarity : 0.004 0.046 2479 Dihedral : 10.435 73.832 2324 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.89 % Favored : 98.06 % Rotamer: Outliers : 2.29 % Allowed : 20.62 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.94 (0.21), residues: 1697 helix: 1.68 (0.19), residues: 803 sheet: 0.24 (0.40), residues: 178 loop : -0.45 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.003 0.001 HIS A 128 PHE 0.009 0.001 PHE B 333 TYR 0.017 0.001 TYR A 305 ARG 0.004 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 191 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.8377 (p0) cc_final: 0.8070 (p0) REVERT: B 75 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7992 (mm-30) REVERT: B 331 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: B 642 ASN cc_start: 0.8550 (t0) cc_final: 0.8335 (t0) REVERT: C 6 GLU cc_start: 0.7858 (tp30) cc_final: 0.7489 (mt-10) REVERT: C 64 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8478 (mmm) outliers start: 35 outliers final: 13 residues processed: 214 average time/residue: 1.6607 time to fit residues: 383.7160 Evaluate side-chains 201 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 0.0970 chunk 116 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 513 ASN A 556 GLN C 82 ASN C 102 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14773 Z= 0.186 Angle : 0.478 7.370 20071 Z= 0.248 Chirality : 0.038 0.158 2214 Planarity : 0.004 0.047 2479 Dihedral : 10.449 73.711 2324 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.70 % Rotamer: Outliers : 2.09 % Allowed : 21.99 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.88 (0.20), residues: 1697 helix: 1.61 (0.19), residues: 805 sheet: 0.41 (0.41), residues: 166 loop : -0.51 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.003 0.001 HIS A 128 PHE 0.010 0.001 PHE A 411 TYR 0.019 0.001 TYR A 305 ARG 0.007 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ASN cc_start: 0.8365 (p0) cc_final: 0.8040 (p0) REVERT: A 495 ARG cc_start: 0.8152 (ptp-110) cc_final: 0.7941 (ptm160) REVERT: B 75 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7994 (mm-30) REVERT: B 331 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: B 642 ASN cc_start: 0.8575 (t0) cc_final: 0.8354 (t0) REVERT: C 90 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8058 (mmt) REVERT: C 158 GLU cc_start: 0.5782 (mp0) cc_final: 0.5462 (mp0) outliers start: 32 outliers final: 17 residues processed: 203 average time/residue: 1.7071 time to fit residues: 374.2052 Evaluate side-chains 199 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 556 GLN C 13 GLN C 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14773 Z= 0.268 Angle : 0.521 8.116 20071 Z= 0.271 Chirality : 0.041 0.172 2214 Planarity : 0.004 0.047 2479 Dihedral : 10.575 73.590 2324 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.41 % Rotamer: Outliers : 2.55 % Allowed : 21.66 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.75 (0.20), residues: 1697 helix: 1.50 (0.19), residues: 805 sheet: 0.15 (0.40), residues: 177 loop : -0.52 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 438 HIS 0.004 0.001 HIS A 128 PHE 0.014 0.001 PHE B 551 TYR 0.022 0.002 TYR A 305 ARG 0.006 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 1.719 Fit side-chains revert: symmetry clash REVERT: A 136 ASN cc_start: 0.5821 (OUTLIER) cc_final: 0.4339 (m110) REVERT: A 222 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8025 (p0) REVERT: B 75 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7979 (mm-30) REVERT: B 331 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: B 684 GLU cc_start: 0.7175 (mp0) cc_final: 0.6752 (mp0) REVERT: C 90 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8065 (mmt) REVERT: C 146 ASP cc_start: 0.7133 (p0) cc_final: 0.6562 (p0) REVERT: C 158 GLU cc_start: 0.5757 (mp0) cc_final: 0.5445 (mp0) outliers start: 39 outliers final: 20 residues processed: 213 average time/residue: 1.6585 time to fit residues: 381.4496 Evaluate side-chains 208 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 165 optimal weight: 0.0170 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 556 GLN C 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14773 Z= 0.160 Angle : 0.484 9.705 20071 Z= 0.249 Chirality : 0.038 0.164 2214 Planarity : 0.004 0.051 2479 Dihedral : 10.477 73.592 2324 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.06 % Favored : 97.88 % Rotamer: Outliers : 2.49 % Allowed : 22.05 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.82 (0.20), residues: 1697 helix: 1.56 (0.19), residues: 804 sheet: 0.21 (0.39), residues: 184 loop : -0.50 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.003 0.001 HIS A 128 PHE 0.009 0.001 PHE A 520 TYR 0.020 0.001 TYR A 305 ARG 0.012 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 188 time to evaluate : 1.858 Fit side-chains revert: symmetry clash REVERT: A 495 ARG cc_start: 0.8152 (ptp-110) cc_final: 0.7900 (ptm160) REVERT: B 75 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7971 (mm-30) REVERT: B 177 GLU cc_start: 0.7725 (pm20) cc_final: 0.7480 (pm20) REVERT: B 331 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: B 642 ASN cc_start: 0.8554 (t0) cc_final: 0.8333 (t0) REVERT: B 684 GLU cc_start: 0.7111 (mp0) cc_final: 0.6702 (mp0) REVERT: C 6 GLU cc_start: 0.7822 (tp30) cc_final: 0.7593 (mt-10) REVERT: C 90 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8042 (mmt) REVERT: C 146 ASP cc_start: 0.7095 (p0) cc_final: 0.6506 (p0) REVERT: C 158 GLU cc_start: 0.5714 (mp0) cc_final: 0.5438 (mp0) outliers start: 38 outliers final: 21 residues processed: 210 average time/residue: 1.6327 time to fit residues: 370.8278 Evaluate side-chains 207 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 183 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 76 optimal weight: 0.0000 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN A 388 ASN A 556 GLN C 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14773 Z= 0.174 Angle : 0.490 11.354 20071 Z= 0.251 Chirality : 0.038 0.160 2214 Planarity : 0.004 0.050 2479 Dihedral : 10.445 73.589 2324 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.47 % Favored : 97.47 % Rotamer: Outliers : 2.68 % Allowed : 21.53 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.83 (0.20), residues: 1697 helix: 1.57 (0.19), residues: 804 sheet: 0.31 (0.40), residues: 174 loop : -0.53 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.003 0.001 HIS A 128 PHE 0.009 0.001 PHE A 520 TYR 0.020 0.001 TYR A 305 ARG 0.008 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 186 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: A 136 ASN cc_start: 0.5872 (OUTLIER) cc_final: 0.4347 (m110) REVERT: A 495 ARG cc_start: 0.8145 (ptp-110) cc_final: 0.7928 (ptm160) REVERT: B 56 THR cc_start: 0.9033 (m) cc_final: 0.8827 (p) REVERT: B 75 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7974 (mm-30) REVERT: B 177 GLU cc_start: 0.7704 (pm20) cc_final: 0.7468 (pm20) REVERT: B 331 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: B 642 ASN cc_start: 0.8555 (t0) cc_final: 0.8345 (t0) REVERT: B 684 GLU cc_start: 0.7129 (mp0) cc_final: 0.6727 (mp0) REVERT: C 6 GLU cc_start: 0.7839 (tp30) cc_final: 0.7610 (mt-10) REVERT: C 22 LYS cc_start: 0.8618 (tttm) cc_final: 0.8357 (tttp) REVERT: C 90 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8047 (mmt) REVERT: C 146 ASP cc_start: 0.7091 (p0) cc_final: 0.6511 (p0) REVERT: C 158 GLU cc_start: 0.5804 (mp0) cc_final: 0.5535 (mp0) outliers start: 41 outliers final: 23 residues processed: 214 average time/residue: 1.6579 time to fit residues: 384.8670 Evaluate side-chains 210 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 104 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN A 388 ASN C 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14773 Z= 0.220 Angle : 0.519 11.967 20071 Z= 0.266 Chirality : 0.039 0.167 2214 Planarity : 0.004 0.049 2479 Dihedral : 10.505 73.479 2324 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.41 % Rotamer: Outliers : 2.49 % Allowed : 21.92 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.72 (0.20), residues: 1697 helix: 1.49 (0.19), residues: 804 sheet: 0.05 (0.39), residues: 185 loop : -0.54 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.003 0.001 HIS A 128 PHE 0.012 0.001 PHE B 551 TYR 0.027 0.001 TYR A 305 ARG 0.007 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 1.553 Fit side-chains revert: symmetry clash REVERT: A 136 ASN cc_start: 0.5914 (OUTLIER) cc_final: 0.4344 (m110) REVERT: A 495 ARG cc_start: 0.8161 (ptp-110) cc_final: 0.7948 (ptm160) REVERT: B 75 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7991 (mm-30) REVERT: B 331 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: B 642 ASN cc_start: 0.8581 (t0) cc_final: 0.8371 (t0) REVERT: B 684 GLU cc_start: 0.7173 (mp0) cc_final: 0.6773 (mp0) REVERT: C 6 GLU cc_start: 0.7833 (tp30) cc_final: 0.7605 (mt-10) REVERT: C 90 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8049 (mmt) REVERT: C 146 ASP cc_start: 0.7044 (p0) cc_final: 0.6493 (p0) REVERT: C 158 GLU cc_start: 0.5800 (mp0) cc_final: 0.5534 (mp0) outliers start: 38 outliers final: 23 residues processed: 209 average time/residue: 1.6625 time to fit residues: 374.8807 Evaluate side-chains 209 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 182 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 144 optimal weight: 0.3980 chunk 153 optimal weight: 0.0470 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 120 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN A 388 ASN C 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14773 Z= 0.142 Angle : 0.488 12.480 20071 Z= 0.249 Chirality : 0.037 0.170 2214 Planarity : 0.004 0.049 2479 Dihedral : 10.397 73.521 2324 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.82 % Rotamer: Outliers : 1.96 % Allowed : 22.58 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.82 (0.20), residues: 1697 helix: 1.54 (0.19), residues: 808 sheet: 0.32 (0.40), residues: 174 loop : -0.52 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 188 HIS 0.003 0.001 HIS A 510 PHE 0.012 0.001 PHE B 333 TYR 0.013 0.001 TYR B 555 ARG 0.007 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 1.745 Fit side-chains revert: symmetry clash REVERT: A 136 ASN cc_start: 0.5906 (OUTLIER) cc_final: 0.4333 (m110) REVERT: A 182 MET cc_start: 0.3894 (ppp) cc_final: 0.3592 (pmt) REVERT: A 495 ARG cc_start: 0.8146 (ptp-110) cc_final: 0.7945 (ptm160) REVERT: B 75 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7962 (mm-30) REVERT: B 331 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: B 684 GLU cc_start: 0.7161 (mp0) cc_final: 0.6768 (mp0) REVERT: C 22 LYS cc_start: 0.8571 (tttm) cc_final: 0.8328 (tttp) REVERT: C 90 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8043 (mmt) REVERT: C 117 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8448 (p) REVERT: C 146 ASP cc_start: 0.6933 (p0) cc_final: 0.6387 (p0) REVERT: C 158 GLU cc_start: 0.5798 (mp0) cc_final: 0.5577 (mp0) outliers start: 30 outliers final: 16 residues processed: 204 average time/residue: 1.7149 time to fit residues: 377.0679 Evaluate side-chains 203 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 21 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 135 optimal weight: 0.0040 chunk 14 optimal weight: 7.9990 chunk 104 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN A 388 ASN C 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14773 Z= 0.229 Angle : 0.537 12.738 20071 Z= 0.274 Chirality : 0.039 0.167 2214 Planarity : 0.004 0.051 2479 Dihedral : 10.482 73.420 2324 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Rotamer: Outliers : 1.83 % Allowed : 22.71 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.75 (0.20), residues: 1697 helix: 1.48 (0.19), residues: 804 sheet: 0.09 (0.39), residues: 185 loop : -0.48 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 88 HIS 0.003 0.001 HIS A 128 PHE 0.012 0.001 PHE B 551 TYR 0.030 0.002 TYR A 305 ARG 0.009 0.000 ARG A 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 1.676 Fit side-chains revert: symmetry clash REVERT: A 136 ASN cc_start: 0.5929 (OUTLIER) cc_final: 0.4349 (m110) REVERT: A 182 MET cc_start: 0.3921 (ppp) cc_final: 0.3547 (pmt) REVERT: A 222 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7946 (p0) REVERT: B 75 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7988 (mm-30) REVERT: B 331 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: B 684 GLU cc_start: 0.7185 (mp0) cc_final: 0.6779 (mp0) REVERT: C 6 GLU cc_start: 0.7884 (tp30) cc_final: 0.7559 (mt-10) REVERT: C 22 LYS cc_start: 0.8644 (tttm) cc_final: 0.8379 (tttp) REVERT: C 90 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8046 (mmt) REVERT: C 146 ASP cc_start: 0.6883 (p0) cc_final: 0.6393 (p0) REVERT: C 158 GLU cc_start: 0.5784 (mp0) cc_final: 0.5525 (mp0) outliers start: 28 outliers final: 16 residues processed: 201 average time/residue: 1.7549 time to fit residues: 380.4291 Evaluate side-chains 201 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 180 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 429 LYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 3.9990 chunk 41 optimal weight: 0.0370 chunk 125 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN A 388 ASN C 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.134024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098213 restraints weight = 17458.867| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.94 r_work: 0.2936 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14773 Z= 0.177 Angle : 0.522 12.799 20071 Z= 0.265 Chirality : 0.038 0.162 2214 Planarity : 0.004 0.054 2479 Dihedral : 10.447 73.420 2324 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.70 % Allowed : 22.77 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 0.80 (0.20), residues: 1697 helix: 1.49 (0.19), residues: 805 sheet: 0.36 (0.40), residues: 174 loop : -0.48 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 88 HIS 0.002 0.001 HIS A 128 PHE 0.010 0.001 PHE A 520 TYR 0.028 0.001 TYR A 305 ARG 0.012 0.000 ARG A 495 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6446.63 seconds wall clock time: 116 minutes 1.44 seconds (6961.44 seconds total)