Starting phenix.real_space_refine on Sat Mar 23 03:11:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3l_18872/03_2024/8r3l_18872_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3l_18872/03_2024/8r3l_18872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3l_18872/03_2024/8r3l_18872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3l_18872/03_2024/8r3l_18872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3l_18872/03_2024/8r3l_18872_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3l_18872/03_2024/8r3l_18872_trim_updated.pdb" } resolution = 3.25 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 33 5.49 5 S 126 5.16 5 C 11144 2.51 5 N 3117 2.21 5 O 3458 1.98 5 H 17547 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A GLU 597": "OE1" <-> "OE2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B GLU 656": "OE1" <-> "OE2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "B GLU 751": "OE1" <-> "OE2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35425 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 11437 Classifications: {'peptide': 708} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 11774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 11774 Classifications: {'peptide': 740} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 707} Chain breaks: 1 Chain: "C" Number of atoms: 10917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 10917 Classifications: {'peptide': 677} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 649} Chain: "R" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 438 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 1, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 10} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "V" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 527 Classifications: {'RNA': 16} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 12} Chain: "G" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 332 Classifications: {'peptide': 24} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 16} Time building chain proxies: 12.50, per 1000 atoms: 0.35 Number of scatterers: 35425 At special positions: 0 Unit cell: (105, 128.52, 144.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 126 16.00 P 33 15.00 O 3458 8.00 N 3117 7.00 C 11144 6.00 H 17547 1.00 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: 30.18 Conformation dependent library (CDL) restraints added in 3.7 seconds 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 20 sheets defined 42.8% alpha, 11.0% beta 5 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 20.22 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.760A 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 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 312 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.737A 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 578 Processing helix chain 'A' and resid 581 through 600 removed outlier: 3.937A pdb=" N SER A 594 " --> pdb=" O GLN A 591 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 597 " --> pdb=" O SER A 594 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 598 " --> pdb=" O MET A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 633 through 649 Processing helix chain 'A' and resid 653 through 673 removed outlier: 4.123A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 4.002A pdb=" N CYS A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 713 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 14 through 21 removed outlier: 3.653A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.525A 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: 3.506A pdb=" N GLN B 115 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 3.786A 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 163 through 174 Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 246 through 265 removed outlier: 4.191A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 331 through 345 removed outlier: 4.545A 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 374 removed outlier: 4.102A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) 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: 3.968A 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 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 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: 4.287A pdb=" N GLY B 681 " --> pdb=" O SER B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 732 Processing helix chain 'B' and resid 737 through 755 removed outlier: 3.666A 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: 3.719A pdb=" N ALA C 29 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 removed outlier: 3.986A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 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 127 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 193 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 226 through 235 removed outlier: 4.154A pdb=" N VAL C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N HIS C 233 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 276 through 284 Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 391 through 404 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 430 through 440 Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 515 through 517 No H-bonds generated for 'chain 'C' and resid 515 through 517' Processing helix chain 'C' and resid 542 through 555 Processing helix chain 'C' and resid 557 through 566 Processing helix chain 'C' and resid 568 through 572 Processing helix chain 'C' and resid 578 through 581 No H-bonds generated for 'chain 'C' and resid 578 through 581' Processing helix chain 'C' and resid 586 through 605 removed outlier: 4.348A pdb=" N GLY C 590 " --> pdb=" O LYS C 586 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 595 " --> pdb=" O GLN C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 623 Proline residue: C 620 - end of helix removed outlier: 4.412A pdb=" N ALA C 623 " --> pdb=" O LEU C 619 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.665A pdb=" N HIS A 144 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N GLY A 121 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS A 146 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N THR A 123 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.318A 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 292 removed outlier: 6.743A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 502 through 506 removed outlier: 6.679A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU A 544 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.194A 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: 6.741A 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 179 through 185 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 484 through 486 Processing sheet with id= J, first strand: chain 'B' and resid 347 through 350 removed outlier: 4.098A pdb=" N LYS B 347 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 354 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 646 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 Processing sheet with id= Q, first strand: chain 'C' and resid 323 through 325 removed outlier: 6.930A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA C 377 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 339 through 345 Processing sheet with id= S, first strand: chain 'C' and resid 635 through 640 Processing sheet with id= T, first strand: chain 'C' and resid 657 through 659 707 hydrogen bonds defined for protein. 1902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 14.93 Time building geometry restraints manager: 31.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17515 1.03 - 1.23: 227 1.23 - 1.43: 7436 1.43 - 1.62: 10442 1.62 - 1.82: 220 Bond restraints: 35840 Sorted by residual: bond pdb=" N TYR G 3 " pdb=" H1 TYR G 3 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N MET A 1 " pdb=" H MET A 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" CA ILE C 147 " pdb=" CB ILE C 147 " ideal model delta sigma weight residual 1.528 1.543 -0.015 1.34e-02 5.57e+03 1.24e+00 bond pdb=" C SER B 444 " pdb=" O SER B 444 " ideal model delta sigma weight residual 1.243 1.235 0.009 9.50e-03 1.11e+04 8.18e-01 ... (remaining 35835 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.49: 671 106.49 - 113.37: 42110 113.37 - 120.25: 11762 120.25 - 127.13: 9974 127.13 - 134.01: 246 Bond angle restraints: 64763 Sorted by residual: angle pdb=" C SER B 444 " pdb=" CA SER B 444 " pdb=" CB SER B 444 " ideal model delta sigma weight residual 117.23 111.21 6.02 1.36e+00 5.41e-01 1.96e+01 angle pdb=" CB MET A 86 " pdb=" CG MET A 86 " pdb=" SD MET A 86 " ideal model delta sigma weight residual 112.70 121.87 -9.17 3.00e+00 1.11e-01 9.34e+00 angle pdb=" CA SER B 444 " pdb=" C SER B 444 " pdb=" N ASP B 445 " ideal model delta sigma weight residual 119.98 117.57 2.41 8.50e-01 1.38e+00 8.02e+00 angle pdb=" CG MET A 86 " pdb=" SD MET A 86 " pdb=" CE MET A 86 " ideal model delta sigma weight residual 100.90 105.89 -4.99 2.20e+00 2.07e-01 5.15e+00 angle pdb=" CB MET C 206 " pdb=" CG MET C 206 " pdb=" SD MET C 206 " ideal model delta sigma weight residual 112.70 118.94 -6.24 3.00e+00 1.11e-01 4.33e+00 ... (remaining 64758 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14787 17.94 - 35.88: 1422 35.88 - 53.82: 487 53.82 - 71.76: 129 71.76 - 89.70: 35 Dihedral angle restraints: 16860 sinusoidal: 9597 harmonic: 7263 Sorted by residual: dihedral pdb=" CA PHE A 612 " pdb=" C PHE A 612 " pdb=" N GLU A 613 " pdb=" CA GLU A 613 " ideal model delta harmonic sigma weight residual 180.00 152.52 27.48 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ASP A 386 " pdb=" CB ASP A 386 " pdb=" CG ASP A 386 " pdb=" OD1 ASP A 386 " ideal model delta sinusoidal sigma weight residual -30.00 -89.55 59.55 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CB GLU A 252 " pdb=" CG GLU A 252 " pdb=" CD GLU A 252 " pdb=" OE1 GLU A 252 " ideal model delta sinusoidal sigma weight residual 0.00 -89.70 89.70 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 16857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2393 0.052 - 0.104: 291 0.104 - 0.155: 71 0.155 - 0.207: 0 0.207 - 0.259: 1 Chirality restraints: 2756 Sorted by residual: chirality pdb=" P U R 18 " pdb=" OP1 U R 18 " pdb=" OP2 U R 18 " pdb=" O5' U R 18 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE A 354 " pdb=" N ILE A 354 " pdb=" C ILE A 354 " pdb=" CB ILE A 354 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE C 647 " pdb=" N ILE C 647 " pdb=" C ILE C 647 " pdb=" CB ILE C 647 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 2753 not shown) Planarity restraints: 5157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 571 " 0.214 9.50e-02 1.11e+02 7.16e-02 6.37e+00 pdb=" NE ARG B 571 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 571 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 571 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 571 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 571 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B 571 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 571 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG B 571 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 148 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO C 149 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.022 2.00e-02 2.50e+03 9.09e-03 2.68e+00 pdb=" N9 A V 4 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" H8 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" H2 A V 4 " 0.001 2.00e-02 2.50e+03 ... (remaining 5154 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 1170 2.14 - 2.75: 65463 2.75 - 3.37: 102742 3.37 - 3.98: 132315 3.98 - 4.60: 207990 Nonbonded interactions: 509680 Sorted by model distance: nonbonded pdb=" OE1 GLU A 610 " pdb=" H GLU A 610 " model vdw 1.519 1.850 nonbonded pdb=" OE1 GLU A 243 " pdb=" H GLU A 243 " model vdw 1.521 1.850 nonbonded pdb=" OE1 GLU A 206 " pdb=" H GLU A 206 " model vdw 1.582 1.850 nonbonded pdb=" OD1 ASN C 148 " pdb=" H LYS C 214 " model vdw 1.587 1.850 nonbonded pdb=" O MET B 409 " pdb=" H22 G R 16 " model vdw 1.592 1.850 ... (remaining 509675 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.510 Extract box with map and model: 14.640 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 126.030 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.120 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18293 Z= 0.164 Angle : 0.475 9.170 24830 Z= 0.250 Chirality : 0.038 0.259 2756 Planarity : 0.003 0.095 3092 Dihedral : 17.480 89.696 7198 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.21 % Allowed : 17.91 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.70 (0.19), residues: 2131 helix: 1.60 (0.17), residues: 956 sheet: 0.23 (0.31), residues: 271 loop : -0.66 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 557 HIS 0.003 0.001 HIS A 41 PHE 0.021 0.001 PHE A 612 TYR 0.011 0.001 TYR G 17 ARG 0.015 0.000 ARG B 571 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 194 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 483 MET cc_start: 0.4067 (mmt) cc_final: 0.3699 (mmm) REVERT: C 493 ARG cc_start: 0.5071 (mmt-90) cc_final: 0.4690 (mtm-85) outliers start: 4 outliers final: 3 residues processed: 198 average time/residue: 0.7528 time to fit residues: 220.7497 Evaluate side-chains 190 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain C residue 537 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN B 641 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18293 Z= 0.272 Angle : 0.493 4.946 24830 Z= 0.258 Chirality : 0.039 0.156 2756 Planarity : 0.004 0.035 3092 Dihedral : 10.172 74.750 2829 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.57 % Allowed : 17.12 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.49 (0.18), residues: 2131 helix: 1.46 (0.17), residues: 960 sheet: 0.12 (0.31), residues: 271 loop : -0.82 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 98 HIS 0.007 0.001 HIS C 233 PHE 0.026 0.001 PHE A 612 TYR 0.015 0.001 TYR G 17 ARG 0.004 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 192 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8340 (pp) REVERT: B 707 ARG cc_start: 0.7479 (mtm110) cc_final: 0.7166 (mtt180) REVERT: C 493 ARG cc_start: 0.4984 (mmt-90) cc_final: 0.4614 (mtm-85) REVERT: C 522 GLN cc_start: 0.6251 (mt0) cc_final: 0.5547 (mp10) outliers start: 30 outliers final: 18 residues processed: 214 average time/residue: 0.7401 time to fit residues: 239.0484 Evaluate side-chains 204 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain G residue 4 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN B 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18293 Z= 0.260 Angle : 0.484 4.613 24830 Z= 0.254 Chirality : 0.039 0.165 2756 Planarity : 0.004 0.040 3092 Dihedral : 10.115 74.467 2823 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.20 % Allowed : 17.02 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.34 (0.18), residues: 2131 helix: 1.33 (0.17), residues: 959 sheet: -0.01 (0.31), residues: 271 loop : -0.89 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 78 HIS 0.004 0.001 HIS C 27 PHE 0.030 0.001 PHE A 612 TYR 0.016 0.001 TYR G 17 ARG 0.004 0.000 ARG B 571 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 186 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8330 (pp) REVERT: A 677 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: C 522 GLN cc_start: 0.6435 (mt0) cc_final: 0.5675 (mp10) outliers start: 42 outliers final: 26 residues processed: 217 average time/residue: 0.7363 time to fit residues: 236.5973 Evaluate side-chains 211 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 186 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN C 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18293 Z= 0.263 Angle : 0.485 4.606 24830 Z= 0.255 Chirality : 0.039 0.170 2756 Planarity : 0.004 0.035 3092 Dihedral : 10.148 73.434 2823 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.20 % Allowed : 17.91 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.22 (0.18), residues: 2131 helix: 1.28 (0.17), residues: 959 sheet: -0.04 (0.32), residues: 251 loop : -1.00 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 78 HIS 0.004 0.001 HIS C 27 PHE 0.032 0.001 PHE A 612 TYR 0.017 0.001 TYR G 17 ARG 0.003 0.000 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 188 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.2571 (OUTLIER) cc_final: 0.2013 (mtt-85) REVERT: A 292 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8339 (pp) REVERT: C 458 MET cc_start: 0.2271 (OUTLIER) cc_final: 0.2004 (tpp) REVERT: C 493 ARG cc_start: 0.5141 (mmt-90) cc_final: 0.4616 (mtm-85) REVERT: C 522 GLN cc_start: 0.6479 (mt0) cc_final: 0.5677 (mp10) REVERT: C 575 MET cc_start: 0.5761 (tmm) cc_final: 0.4823 (tmm) outliers start: 42 outliers final: 31 residues processed: 218 average time/residue: 0.7624 time to fit residues: 245.6559 Evaluate side-chains 216 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 182 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 611 ASP Chi-restraints excluded: chain G residue 4 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 186 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 537 ASN B 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18293 Z= 0.345 Angle : 0.528 4.766 24830 Z= 0.280 Chirality : 0.040 0.191 2756 Planarity : 0.004 0.039 3092 Dihedral : 10.252 73.700 2823 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.09 % Allowed : 17.70 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2131 helix: 1.01 (0.17), residues: 958 sheet: -0.09 (0.32), residues: 246 loop : -1.18 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 78 HIS 0.005 0.001 HIS C 27 PHE 0.037 0.001 PHE A 612 TYR 0.019 0.002 TYR G 17 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 183 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.2642 (OUTLIER) cc_final: 0.2002 (mtt-85) REVERT: A 292 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8320 (pp) REVERT: A 524 GLU cc_start: 0.8282 (mp0) cc_final: 0.7915 (mp0) REVERT: A 677 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: B 522 ASP cc_start: 0.8420 (m-30) cc_final: 0.8120 (m-30) REVERT: C 10 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7804 (tp) REVERT: C 13 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7111 (mp10) REVERT: C 522 GLN cc_start: 0.6752 (mt0) cc_final: 0.6147 (tp40) REVERT: C 575 MET cc_start: 0.5981 (tmm) cc_final: 0.5526 (tmm) outliers start: 59 outliers final: 45 residues processed: 231 average time/residue: 0.7521 time to fit residues: 254.7758 Evaluate side-chains 229 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 179 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 611 ASP Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 208 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS B 306 ASN B 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18293 Z= 0.220 Angle : 0.478 4.686 24830 Z= 0.251 Chirality : 0.038 0.172 2756 Planarity : 0.004 0.038 3092 Dihedral : 10.196 73.586 2823 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.51 % Allowed : 19.01 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.07 (0.18), residues: 2131 helix: 1.19 (0.17), residues: 958 sheet: -0.03 (0.32), residues: 246 loop : -1.15 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 577 HIS 0.004 0.001 HIS A 74 PHE 0.033 0.001 PHE A 612 TYR 0.016 0.001 TYR G 17 ARG 0.003 0.000 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 181 time to evaluate : 3.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.2507 (OUTLIER) cc_final: 0.2104 (mtp180) REVERT: A 292 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8327 (pp) REVERT: A 677 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: B 707 ARG cc_start: 0.7427 (mtm110) cc_final: 0.7130 (mtt180) REVERT: C 10 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7855 (tp) REVERT: C 13 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7179 (mp10) REVERT: C 493 ARG cc_start: 0.5142 (mmt-90) cc_final: 0.4687 (mtm-85) REVERT: C 522 GLN cc_start: 0.6771 (mt0) cc_final: 0.6135 (tp40) outliers start: 48 outliers final: 38 residues processed: 219 average time/residue: 0.7201 time to fit residues: 237.2798 Evaluate side-chains 223 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 180 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18293 Z= 0.296 Angle : 0.511 6.810 24830 Z= 0.269 Chirality : 0.039 0.187 2756 Planarity : 0.004 0.037 3092 Dihedral : 10.264 73.493 2823 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.83 % Allowed : 18.85 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.11 (0.18), residues: 2131 helix: 1.06 (0.17), residues: 958 sheet: -0.14 (0.32), residues: 246 loop : -1.25 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 537 HIS 0.003 0.001 HIS B 47 PHE 0.037 0.001 PHE A 612 TYR 0.018 0.001 TYR G 17 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 187 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.2527 (OUTLIER) cc_final: 0.2051 (mtp180) REVERT: A 292 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8346 (pp) REVERT: A 677 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: B 522 ASP cc_start: 0.8430 (m-30) cc_final: 0.8132 (m-30) REVERT: C 10 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7955 (tp) REVERT: C 13 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7310 (mp10) REVERT: C 318 ARG cc_start: 0.7447 (mtt180) cc_final: 0.6567 (ptt180) REVERT: C 522 GLN cc_start: 0.6864 (mt0) cc_final: 0.6135 (tp40) outliers start: 54 outliers final: 44 residues processed: 229 average time/residue: 0.7190 time to fit residues: 242.5871 Evaluate side-chains 234 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 185 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 0.1980 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 131 optimal weight: 0.0870 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 162 optimal weight: 0.6980 chunk 188 optimal weight: 5.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18293 Z= 0.133 Angle : 0.456 6.183 24830 Z= 0.236 Chirality : 0.037 0.149 2756 Planarity : 0.003 0.037 3092 Dihedral : 10.097 73.568 2823 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.73 % Allowed : 19.95 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.30 (0.18), residues: 2131 helix: 1.41 (0.17), residues: 959 sheet: 0.06 (0.33), residues: 247 loop : -1.06 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 557 HIS 0.003 0.000 HIS A 74 PHE 0.026 0.001 PHE A 612 TYR 0.013 0.001 TYR G 17 ARG 0.002 0.000 ARG A 443 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 191 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.2490 (OUTLIER) cc_final: 0.2092 (mtp180) REVERT: A 524 GLU cc_start: 0.8303 (mp0) cc_final: 0.8034 (mp0) REVERT: B 148 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7415 (mp0) REVERT: B 707 ARG cc_start: 0.7403 (mtm110) cc_final: 0.7110 (mtt180) REVERT: B 744 MET cc_start: 0.4887 (tpp) cc_final: 0.4661 (mmt) REVERT: C 493 ARG cc_start: 0.5041 (mmt-90) cc_final: 0.4614 (mtm-85) REVERT: C 522 GLN cc_start: 0.6810 (mt0) cc_final: 0.6059 (tp40) outliers start: 33 outliers final: 25 residues processed: 216 average time/residue: 0.7466 time to fit residues: 236.4297 Evaluate side-chains 214 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18293 Z= 0.248 Angle : 0.483 6.491 24830 Z= 0.251 Chirality : 0.039 0.168 2756 Planarity : 0.004 0.043 3092 Dihedral : 10.124 73.442 2823 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.73 % Allowed : 20.00 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.21 (0.18), residues: 2131 helix: 1.35 (0.17), residues: 958 sheet: 0.02 (0.33), residues: 247 loop : -1.12 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 580 HIS 0.003 0.001 HIS B 47 PHE 0.031 0.001 PHE A 612 TYR 0.015 0.001 TYR G 17 ARG 0.003 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.2548 (OUTLIER) cc_final: 0.2087 (mtp180) REVERT: B 707 ARG cc_start: 0.7433 (mtm110) cc_final: 0.7108 (mtt180) REVERT: B 744 MET cc_start: 0.4908 (tpp) cc_final: 0.4703 (mmt) REVERT: C 318 ARG cc_start: 0.7443 (mtt180) cc_final: 0.6581 (ptt180) REVERT: C 522 GLN cc_start: 0.6889 (mt0) cc_final: 0.6172 (tp40) outliers start: 33 outliers final: 32 residues processed: 211 average time/residue: 0.7804 time to fit residues: 242.7148 Evaluate side-chains 218 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 611 ASP Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 214 optimal weight: 0.3980 chunk 197 optimal weight: 0.3980 chunk 170 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18293 Z= 0.146 Angle : 0.455 6.745 24830 Z= 0.234 Chirality : 0.037 0.148 2756 Planarity : 0.003 0.044 3092 Dihedral : 10.025 73.504 2823 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.47 % Allowed : 20.31 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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 (0.18), residues: 2131 helix: 1.50 (0.17), residues: 960 sheet: 0.13 (0.33), residues: 247 loop : -1.00 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 557 HIS 0.002 0.000 HIS A 74 PHE 0.026 0.001 PHE A 612 TYR 0.012 0.001 TYR G 17 ARG 0.002 0.000 ARG A 496 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.2493 (OUTLIER) cc_final: 0.2085 (mtp180) REVERT: B 707 ARG cc_start: 0.7413 (mtm110) cc_final: 0.7114 (mtt180) REVERT: B 744 MET cc_start: 0.4891 (tpp) cc_final: 0.4687 (mmt) REVERT: C 318 ARG cc_start: 0.7448 (mtt180) cc_final: 0.6565 (ptt180) REVERT: C 522 GLN cc_start: 0.6892 (mt0) cc_final: 0.6194 (tp40) outliers start: 28 outliers final: 25 residues processed: 211 average time/residue: 0.7607 time to fit residues: 235.2908 Evaluate side-chains 210 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 680 ARG Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 6.9990 chunk 52 optimal weight: 0.2980 chunk 157 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.138571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.101087 restraints weight = 88687.841| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.21 r_work: 0.3199 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18293 Z= 0.145 Angle : 0.449 7.130 24830 Z= 0.231 Chirality : 0.037 0.143 2756 Planarity : 0.003 0.039 3092 Dihedral : 9.959 73.441 2823 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.36 % Allowed : 20.42 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.51 (0.18), residues: 2131 helix: 1.58 (0.17), residues: 961 sheet: 0.21 (0.33), residues: 247 loop : -0.96 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 577 HIS 0.002 0.000 HIS A 52 PHE 0.025 0.001 PHE A 612 TYR 0.011 0.001 TYR G 17 ARG 0.003 0.000 ARG A 496 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7678.70 seconds wall clock time: 140 minutes 29.64 seconds (8429.64 seconds total)