Starting phenix.real_space_refine on Wed Mar 4 18:36:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6szu_10354/03_2026/6szu_10354.cif Found real_map, /net/cci-nas-00/data/ceres_data/6szu_10354/03_2026/6szu_10354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6szu_10354/03_2026/6szu_10354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6szu_10354/03_2026/6szu_10354.map" model { file = "/net/cci-nas-00/data/ceres_data/6szu_10354/03_2026/6szu_10354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6szu_10354/03_2026/6szu_10354.cif" } resolution = 2.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.006 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 56 5.49 5 Mg 6 5.21 5 S 92 5.16 5 C 9213 2.51 5 N 2605 2.21 5 O 3273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15245 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 705, 5750 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 25, 'TRANS': 679} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 705, 5750 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 25, 'TRANS': 679} Chain breaks: 2 bond proxies already assigned to first conformer: 5860 Chain: "B" Number of atoms: 5964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5964 Classifications: {'peptide': 745} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 716} Chain breaks: 1 Chain: "C" Number of atoms: 2022 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 249, 2012 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 249, 2012 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} bond proxies already assigned to first conformer: 2040 Chain: "V" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 929 Classifications: {'RNA': 44} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 12, 'rna3p_pyr': 15} Link IDs: {'rna2p': 17, 'rna3p': 26} Chain: "M" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' MG': 2, 'M4H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 2, 'POP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "B" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Classifications: {'water': 136} Link IDs: {None: 135} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "V" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "M" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 491 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 491 " occ=0.50 residue: pdb=" N AHIS C 27 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 27 " occ=0.50 Time building chain proxies: 4.61, per 1000 atoms: 0.30 Number of scatterers: 15245 At special positions: 0 Unit cell: (97.524, 119.467, 117.841, 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 92 16.00 P 56 15.00 Mg 6 11.99 O 3273 8.00 N 2605 7.00 C 9213 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 - 3.00 Amino acid : True - 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: 1.14 Conformation dependent library (CDL) restraints added in 911.6 milliseconds 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 15 sheets defined 51.9% alpha, 13.8% beta 12 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 31 through 50 removed outlier: 3.752A pdb=" N SER A 49 " --> pdb=" O CYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 164 through 183 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.688A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.519A pdb=" N SER A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 446 removed outlier: 3.646A pdb=" N PHE A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 471 Processing helix chain 'A' and resid 524 through 533 removed outlier: 3.588A pdb=" N ASN A 527 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE A 529 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N HIS A 530 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU A 533 " --> pdb=" O HIS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 578 through 599 removed outlier: 3.655A pdb=" N GLN A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 609 Processing helix chain 'A' and resid 627 through 645 Processing helix chain 'A' and resid 647 through 669 removed outlier: 3.970A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 687 Processing helix chain 'A' and resid 692 through 712 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.578A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.785A pdb=" N GLN B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.574A pdb=" N GLY B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 264 removed outlier: 4.038A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 412 through 427 removed outlier: 4.068A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.668A pdb=" N MET B 507 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 614 through 616 No H-bonds generated for 'chain 'B' and resid 614 through 616' Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 679 through 697 removed outlier: 5.400A pdb=" N ASP B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU B 686 " --> pdb=" O ILE B 682 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B 687 " --> pdb=" O LEU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 0 through 12 removed outlier: 3.671A pdb=" N ILE C 4 " --> pdb=" O GLY C 0 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 24 through 33 removed outlier: 3.818A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.976A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 removed outlier: 3.725A pdb=" N LYS A 73 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.489A pdb=" N PHE A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.266A pdb=" N TYR A 496 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 552 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU A 544 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS A 554 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP A 542 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL A 556 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 537 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLY A 541 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS A 319 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N MET A 543 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N TRP A 317 " --> pdb=" O MET A 543 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.310A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 374 removed outlier: 4.406A pdb=" N GLN B 367 " --> pdb=" O MET A 374 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 622 through 626 removed outlier: 6.326A pdb=" N GLY A 626 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 127 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 192 removed outlier: 8.323A pdb=" N ASN B 678 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG B 203 " --> pdb=" O ASN B 678 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.781A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB4, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.525A pdb=" N THR B 667 " --> pdb=" O SER C 58 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.794A pdb=" N GLN C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.419A pdb=" N ARG C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 712 hydrogen bonds defined for protein. 1978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 3.07 Time building geometry restraints manager: 1.55 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: 3139 1.33 - 1.45: 3674 1.45 - 1.57: 8260 1.57 - 1.69: 108 1.69 - 1.81: 160 Bond restraints: 15341 Sorted by residual: bond pdb=" O POP B 803 " pdb=" P2 POP B 803 " ideal model delta sigma weight residual 1.661 1.594 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O POP B 803 " pdb=" P1 POP B 803 " ideal model delta sigma weight residual 1.660 1.600 0.060 2.00e-02 2.50e+03 9.01e+00 bond pdb=" C19 M4H A 801 " pdb=" C20 M4H A 801 " ideal model delta sigma weight residual 1.414 1.464 -0.050 2.00e-02 2.50e+03 6.18e+00 bond pdb=" C1 M4H A 801 " pdb=" C6 M4H A 801 " ideal model delta sigma weight residual 1.437 1.481 -0.044 2.00e-02 2.50e+03 4.75e+00 bond pdb=" C13 M4H A 801 " pdb=" N18 M4H A 801 " ideal model delta sigma weight residual 1.459 1.498 -0.039 2.00e-02 2.50e+03 3.84e+00 ... (remaining 15336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 20661 2.72 - 5.44: 262 5.44 - 8.16: 22 8.16 - 10.88: 2 10.88 - 13.60: 2 Bond angle restraints: 20949 Sorted by residual: angle pdb=" N ILE A 79 " pdb=" CA ILE A 79 " pdb=" C ILE A 79 " ideal model delta sigma weight residual 112.96 107.05 5.91 1.00e+00 1.00e+00 3.50e+01 angle pdb=" N18 M4H A 801 " pdb=" C19 M4H A 801 " pdb=" N26 M4H A 801 " ideal model delta sigma weight residual 125.81 139.41 -13.60 3.00e+00 1.11e-01 2.06e+01 angle pdb=" P1 POP B 803 " pdb=" O POP B 803 " pdb=" P2 POP B 803 " ideal model delta sigma weight residual 139.66 127.09 12.57 3.00e+00 1.11e-01 1.76e+01 angle pdb=" O4' A V 7 " pdb=" C1' A V 7 " pdb=" N9 A V 7 " ideal model delta sigma weight residual 108.20 113.95 -5.75 1.50e+00 4.44e-01 1.47e+01 angle pdb=" C ASN B 628 " pdb=" N ASN B 629 " pdb=" CA ASN B 629 " ideal model delta sigma weight residual 121.80 131.07 -9.27 2.44e+00 1.68e-01 1.44e+01 ... (remaining 20944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.80: 8402 18.80 - 37.59: 703 37.59 - 56.39: 216 56.39 - 75.18: 107 75.18 - 93.98: 16 Dihedral angle restraints: 9444 sinusoidal: 4474 harmonic: 4970 Sorted by residual: dihedral pdb=" CA VAL A 512 " pdb=" C VAL A 512 " pdb=" N VAL A 513 " pdb=" CA VAL A 513 " ideal model delta harmonic sigma weight residual 180.00 155.85 24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ILE A 481 " pdb=" C ILE A 481 " pdb=" N THR A 482 " pdb=" CA THR A 482 " ideal model delta harmonic sigma weight residual 180.00 156.20 23.80 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ASN B 134 " pdb=" C ASN B 134 " pdb=" N ARG B 135 " pdb=" CA ARG B 135 " ideal model delta harmonic sigma weight residual -180.00 -157.02 -22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 9441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1712 0.057 - 0.113: 531 0.113 - 0.170: 76 0.170 - 0.226: 5 0.226 - 0.283: 1 Chirality restraints: 2325 Sorted by residual: chirality pdb=" C1' A V 7 " pdb=" O4' A V 7 " pdb=" C2' A V 7 " pdb=" N9 A V 7 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.28 2.00e-01 2.50e+01 2.00e+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 2.24 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB ILE B 392 " pdb=" CA ILE B 392 " pdb=" CG1 ILE B 392 " pdb=" CG2 ILE B 392 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2322 not shown) Planarity restraints: 2493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.046 2.00e-02 2.50e+03 1.99e-02 1.09e+01 pdb=" N9 A V 7 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A V 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.012 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.010 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.010 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 10 " 0.047 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO A 11 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 11 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 11 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 557 " -0.036 2.00e-02 2.50e+03 1.92e-02 7.41e+00 pdb=" CG TYR B 557 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 557 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 557 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 557 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 557 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 557 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 557 " -0.014 2.00e-02 2.50e+03 ... (remaining 2490 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 277 2.59 - 3.17: 11883 3.17 - 3.75: 26600 3.75 - 4.32: 38998 4.32 - 4.90: 59175 Nonbonded interactions: 136933 Sorted by model distance: nonbonded pdb=" OD2 ASP A 108 " pdb="MG MG A 803 " model vdw 2.013 2.170 nonbonded pdb=" O11 M4H A 801 " pdb="MG MG A 803 " model vdw 2.026 2.170 nonbonded pdb=" OD1 ASP A 108 " pdb="MG MG A 802 " model vdw 2.027 2.170 nonbonded pdb=" O8 M4H A 801 " pdb="MG MG A 802 " model vdw 2.039 2.170 nonbonded pdb=" O10 M4H A 801 " pdb="MG MG A 803 " model vdw 2.090 2.170 ... (remaining 136928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.50 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 17.490 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 15341 Z= 0.333 Angle : 0.832 13.604 20949 Z= 0.461 Chirality : 0.052 0.283 2325 Planarity : 0.006 0.072 2493 Dihedral : 17.009 93.978 6228 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.21 % Favored : 95.67 % Rotamer: Outliers : 5.28 % Allowed : 7.53 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.17), residues: 1693 helix: -1.43 (0.14), residues: 815 sheet: -0.78 (0.35), residues: 173 loop : -1.30 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 316 TYR 0.036 0.003 TYR B 557 PHE 0.024 0.003 PHE A 515 TRP 0.025 0.004 TRP B 438 HIS 0.006 0.002 HIS B 605 Details of bonding type rmsd covalent geometry : bond 0.00758 (15341) covalent geometry : angle 0.83222 (20949) hydrogen bonds : bond 0.16519 ( 739) hydrogen bonds : angle 6.28265 ( 2040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 240 time to evaluate : 0.591 Fit side-chains REVERT: A 21 MET cc_start: 0.7606 (mtp) cc_final: 0.7108 (mtm) REVERT: A 26 GLU cc_start: 0.5885 (OUTLIER) cc_final: 0.5596 (pm20) REVERT: A 78 ILE cc_start: 0.8813 (mt) cc_final: 0.8587 (mt) REVERT: A 141 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6379 (mm-30) REVERT: A 187 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.5849 (pp) REVERT: A 201 LEU cc_start: 0.4900 (OUTLIER) cc_final: 0.4542 (tt) REVERT: A 272 GLU cc_start: 0.7678 (tp30) cc_final: 0.7449 (mm-30) REVERT: A 346 LYS cc_start: 0.7987 (tttt) cc_final: 0.7684 (tppp) REVERT: A 578 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7942 (ptm160) REVERT: A 618 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: B 120 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7622 (p0) REVERT: B 367 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8097 (tp40) REVERT: B 638 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6310 (mm-30) REVERT: B 672 ARG cc_start: 0.7345 (mtm180) cc_final: 0.7113 (ptp-170) REVERT: B 680 ARG cc_start: 0.7391 (mtt90) cc_final: 0.6903 (mtt90) REVERT: B 731 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7305 (mm-30) REVERT: C 192 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7072 (mt-10) REVERT: C 214 ARG cc_start: 0.7808 (mmt180) cc_final: 0.7339 (mmt-90) REVERT: C 217 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8703 (t80) outliers start: 80 outliers final: 32 residues processed: 303 average time/residue: 0.8901 time to fit residues: 289.2384 Evaluate side-chains 250 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 578 ARG Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 736 SER Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 85 ASN A 254 ASN B 134 ASN B 137 GLN B 202 GLN B 313 GLN B 372 ASN B 633 HIS C 75 ASN C 127 HIS C 233 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.147095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.113830 restraints weight = 25153.656| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.54 r_work: 0.2964 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15341 Z= 0.132 Angle : 0.540 6.667 20949 Z= 0.294 Chirality : 0.040 0.207 2325 Planarity : 0.004 0.055 2493 Dihedral : 15.217 88.832 2824 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.24 % Allowed : 12.68 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 1693 helix: 0.51 (0.18), residues: 812 sheet: -0.27 (0.38), residues: 167 loop : -0.87 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.032 0.002 TYR B 557 PHE 0.015 0.001 PHE A 35 TRP 0.017 0.002 TRP A 363 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00273 (15341) covalent geometry : angle 0.53962 (20949) hydrogen bonds : bond 0.05103 ( 739) hydrogen bonds : angle 4.66026 ( 2040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.591 Fit side-chains REVERT: A 14 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7342 (mt) REVERT: A 21 MET cc_start: 0.7935 (mtp) cc_final: 0.7700 (mtm) REVERT: A 26 GLU cc_start: 0.5590 (OUTLIER) cc_final: 0.5146 (pm20) REVERT: A 171 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6445 (mp) REVERT: A 187 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5813 (pp) REVERT: A 191 PHE cc_start: 0.4671 (OUTLIER) cc_final: 0.4126 (t80) REVERT: A 201 LEU cc_start: 0.4744 (OUTLIER) cc_final: 0.4403 (tt) REVERT: A 272 GLU cc_start: 0.8266 (tp30) cc_final: 0.7898 (mm-30) REVERT: A 346 LYS cc_start: 0.8142 (tttt) cc_final: 0.7436 (tppp) REVERT: A 347 GLU cc_start: 0.7553 (pt0) cc_final: 0.7287 (mt-10) REVERT: A 378 ASP cc_start: 0.7973 (m-30) cc_final: 0.7104 (m-30) REVERT: A 670 ASN cc_start: 0.8713 (m-40) cc_final: 0.8432 (t0) REVERT: B 1 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8020 (tmm) REVERT: B 120 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8274 (p0) REVERT: B 152 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8144 (mttt) REVERT: B 362 MET cc_start: 0.8507 (mmm) cc_final: 0.8057 (mmp) REVERT: B 367 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8381 (tp40) REVERT: B 371 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7287 (pt0) REVERT: B 414 MET cc_start: 0.9070 (mmt) cc_final: 0.8824 (mpp) REVERT: B 638 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6175 (mm-30) REVERT: B 672 ARG cc_start: 0.7668 (mtm180) cc_final: 0.7321 (ptp-170) REVERT: B 679 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8245 (pt0) REVERT: B 680 ARG cc_start: 0.7754 (mtt90) cc_final: 0.7454 (mtt180) REVERT: B 707 ARG cc_start: 0.7935 (ttt-90) cc_final: 0.7731 (ttp80) REVERT: B 718 MET cc_start: 0.9319 (mtm) cc_final: 0.9111 (mtp) REVERT: B 729 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: C 70 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8446 (mmmm) REVERT: C 192 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7409 (mt-10) REVERT: C 214 ARG cc_start: 0.8084 (mmt180) cc_final: 0.7720 (mmt-90) REVERT: C 216 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8016 (tpp-160) REVERT: C 217 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8724 (t80) outliers start: 49 outliers final: 15 residues processed: 258 average time/residue: 0.8609 time to fit residues: 238.9882 Evaluate side-chains 238 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 104 optimal weight: 7.9990 chunk 13 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 239 ASN B 413 ASN B 633 HIS C 127 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.149071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.114385 restraints weight = 30367.190| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.67 r_work: 0.3014 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15341 Z= 0.105 Angle : 0.483 6.893 20949 Z= 0.263 Chirality : 0.039 0.205 2325 Planarity : 0.004 0.047 2493 Dihedral : 14.557 88.225 2788 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.10 % Allowed : 14.00 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.20), residues: 1693 helix: 1.20 (0.18), residues: 811 sheet: 0.07 (0.40), residues: 160 loop : -0.67 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 135 TYR 0.027 0.001 TYR B 557 PHE 0.012 0.001 PHE B 333 TRP 0.014 0.001 TRP A 363 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00213 (15341) covalent geometry : angle 0.48329 (20949) hydrogen bonds : bond 0.04304 ( 739) hydrogen bonds : angle 4.40578 ( 2040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 14 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7368 (mt) REVERT: A 21 MET cc_start: 0.7903 (mtp) cc_final: 0.7682 (mtm) REVERT: A 26 GLU cc_start: 0.5536 (OUTLIER) cc_final: 0.5083 (pm20) REVERT: A 171 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6486 (mp) REVERT: A 187 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5793 (pp) REVERT: A 191 PHE cc_start: 0.4609 (OUTLIER) cc_final: 0.4050 (t80) REVERT: A 201 LEU cc_start: 0.4856 (OUTLIER) cc_final: 0.4524 (tt) REVERT: A 272 GLU cc_start: 0.8130 (tp30) cc_final: 0.7781 (mm-30) REVERT: A 346 LYS cc_start: 0.8137 (tttt) cc_final: 0.7456 (tppp) REVERT: A 347 GLU cc_start: 0.7406 (pt0) cc_final: 0.7181 (mt-10) REVERT: A 374 MET cc_start: 0.8598 (mtp) cc_final: 0.8355 (tpp) REVERT: A 670 ASN cc_start: 0.8707 (m-40) cc_final: 0.8453 (t0) REVERT: B 1 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7945 (tmm) REVERT: B 120 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8252 (p0) REVERT: B 135 ARG cc_start: 0.8522 (ttt90) cc_final: 0.8316 (ttt90) REVERT: B 152 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8126 (mttt) REVERT: B 362 MET cc_start: 0.8506 (mmm) cc_final: 0.8047 (mmp) REVERT: B 371 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7381 (pt0) REVERT: B 414 MET cc_start: 0.9063 (mmt) cc_final: 0.8855 (mpp) REVERT: B 638 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6304 (mm-30) REVERT: B 672 ARG cc_start: 0.7653 (mtm180) cc_final: 0.7310 (ptp-170) REVERT: B 679 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: B 680 ARG cc_start: 0.7741 (mtt90) cc_final: 0.7466 (mtt180) REVERT: B 707 ARG cc_start: 0.7951 (ttt-90) cc_final: 0.7725 (ttp80) REVERT: B 729 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7502 (m-30) REVERT: B 742 GLU cc_start: 0.7066 (tt0) cc_final: 0.6658 (tp30) REVERT: C 70 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8446 (mmmm) REVERT: C 157 ARG cc_start: 0.6793 (mpp-170) cc_final: 0.6355 (mmt-90) REVERT: C 214 ARG cc_start: 0.8075 (mmt180) cc_final: 0.7688 (mmt-90) REVERT: C 217 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8721 (t80) outliers start: 47 outliers final: 15 residues processed: 259 average time/residue: 0.8807 time to fit residues: 245.6704 Evaluate side-chains 241 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 151 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 239 ASN B 633 HIS C 27 HIS A C 127 HIS C 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.144103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.109900 restraints weight = 29185.301| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.79 r_work: 0.2909 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15341 Z= 0.245 Angle : 0.622 6.632 20949 Z= 0.335 Chirality : 0.046 0.232 2325 Planarity : 0.005 0.046 2493 Dihedral : 14.546 90.069 2769 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.76 % Allowed : 13.74 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.20), residues: 1693 helix: 1.10 (0.18), residues: 814 sheet: -0.13 (0.37), residues: 178 loop : -0.57 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 560 TYR 0.036 0.002 TYR B 557 PHE 0.022 0.002 PHE A 702 TRP 0.018 0.003 TRP C 98 HIS 0.005 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00553 (15341) covalent geometry : angle 0.62233 (20949) hydrogen bonds : bond 0.05966 ( 739) hydrogen bonds : angle 4.62009 ( 2040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 211 time to evaluate : 0.618 Fit side-chains REVERT: A 14 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7317 (mt) REVERT: A 26 GLU cc_start: 0.5637 (OUTLIER) cc_final: 0.5235 (pm20) REVERT: A 38 ILE cc_start: 0.7157 (mt) cc_final: 0.6952 (mt) REVERT: A 96 ASN cc_start: 0.8610 (m110) cc_final: 0.8289 (m110) REVERT: A 171 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6539 (mp) REVERT: A 187 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5803 (pp) REVERT: A 191 PHE cc_start: 0.4457 (OUTLIER) cc_final: 0.3876 (t80) REVERT: A 272 GLU cc_start: 0.8210 (tp30) cc_final: 0.7835 (mm-30) REVERT: A 346 LYS cc_start: 0.8169 (tttt) cc_final: 0.7513 (tppp) REVERT: A 347 GLU cc_start: 0.7626 (pt0) cc_final: 0.7399 (mt-10) REVERT: A 378 ASP cc_start: 0.7886 (m-30) cc_final: 0.7182 (m-30) REVERT: A 670 ASN cc_start: 0.8798 (m-40) cc_final: 0.8509 (t0) REVERT: B 120 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8181 (p0) REVERT: B 152 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8219 (mttt) REVERT: B 171 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9078 (mp) REVERT: B 211 LYS cc_start: 0.8437 (mttt) cc_final: 0.7845 (mtmm) REVERT: B 367 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8420 (tp40) REVERT: B 638 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6306 (mm-30) REVERT: B 672 ARG cc_start: 0.7759 (mtm180) cc_final: 0.7417 (ptp-170) REVERT: B 679 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8277 (pt0) REVERT: B 680 ARG cc_start: 0.7777 (mtt90) cc_final: 0.7491 (mtt180) REVERT: C 62 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7650 (ptm-80) REVERT: C 214 ARG cc_start: 0.8156 (mmt180) cc_final: 0.7771 (mmt-90) outliers start: 57 outliers final: 26 residues processed: 253 average time/residue: 0.8430 time to fit residues: 230.2267 Evaluate side-chains 248 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 239 ASN C 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.147490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.112118 restraints weight = 29565.224| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.73 r_work: 0.2964 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15341 Z= 0.126 Angle : 0.510 6.671 20949 Z= 0.276 Chirality : 0.040 0.235 2325 Planarity : 0.004 0.042 2493 Dihedral : 14.273 88.738 2765 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.58 % Allowed : 15.46 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.20), residues: 1693 helix: 1.40 (0.19), residues: 812 sheet: 0.08 (0.39), residues: 161 loop : -0.50 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.027 0.001 TYR B 557 PHE 0.013 0.001 PHE A 211 TRP 0.015 0.002 TRP C 49 HIS 0.005 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00267 (15341) covalent geometry : angle 0.50978 (20949) hydrogen bonds : bond 0.04572 ( 739) hydrogen bonds : angle 4.39274 ( 2040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 0.580 Fit side-chains REVERT: A 1 MET cc_start: 0.2695 (OUTLIER) cc_final: 0.1733 (tpt) REVERT: A 14 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7296 (mt) REVERT: A 38 ILE cc_start: 0.6981 (mt) cc_final: 0.6714 (mt) REVERT: A 96 ASN cc_start: 0.8499 (m110) cc_final: 0.8207 (m110) REVERT: A 187 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5827 (pp) REVERT: A 272 GLU cc_start: 0.8253 (tp30) cc_final: 0.7939 (mm-30) REVERT: A 346 LYS cc_start: 0.8153 (tttt) cc_final: 0.7487 (tppp) REVERT: A 347 GLU cc_start: 0.7445 (pt0) cc_final: 0.7224 (mt-10) REVERT: A 519 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8540 (mt-10) REVERT: A 608 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.6580 (mpt180) REVERT: A 670 ASN cc_start: 0.8766 (m-40) cc_final: 0.8492 (t0) REVERT: B 120 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8230 (p0) REVERT: B 135 ARG cc_start: 0.8602 (ttt90) cc_final: 0.8350 (ttt90) REVERT: B 152 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8176 (mttt) REVERT: B 247 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8398 (mt0) REVERT: B 362 MET cc_start: 0.8547 (mmm) cc_final: 0.8209 (mmp) REVERT: B 371 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7315 (pt0) REVERT: B 638 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6241 (mm-30) REVERT: B 672 ARG cc_start: 0.7756 (mtm180) cc_final: 0.7402 (ptp-170) REVERT: B 679 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: B 680 ARG cc_start: 0.7731 (mtt90) cc_final: 0.7490 (mtt180) REVERT: B 707 ARG cc_start: 0.8033 (ttt-90) cc_final: 0.7781 (ttp80) REVERT: B 729 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: C 157 ARG cc_start: 0.6900 (mpp-170) cc_final: 0.6443 (mmt-90) REVERT: C 214 ARG cc_start: 0.8135 (mmt180) cc_final: 0.7740 (mmt-90) outliers start: 39 outliers final: 18 residues processed: 245 average time/residue: 0.8502 time to fit residues: 224.4742 Evaluate side-chains 238 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 147 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 38 optimal weight: 0.0870 chunk 167 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 239 ASN C 127 HIS C 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.146575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.111785 restraints weight = 28443.861| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.62 r_work: 0.2976 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15341 Z= 0.152 Angle : 0.533 8.056 20949 Z= 0.288 Chirality : 0.041 0.208 2325 Planarity : 0.004 0.041 2493 Dihedral : 14.146 88.829 2760 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.77 % Allowed : 15.32 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1693 helix: 1.40 (0.18), residues: 814 sheet: -0.06 (0.38), residues: 166 loop : -0.42 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 135 TYR 0.029 0.002 TYR B 557 PHE 0.015 0.001 PHE A 211 TRP 0.013 0.002 TRP C 49 HIS 0.004 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00333 (15341) covalent geometry : angle 0.53277 (20949) hydrogen bonds : bond 0.04860 ( 739) hydrogen bonds : angle 4.40793 ( 2040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.553 Fit side-chains REVERT: A 1 MET cc_start: 0.2608 (OUTLIER) cc_final: 0.1672 (tpt) REVERT: A 14 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7314 (mt) REVERT: A 38 ILE cc_start: 0.7002 (mt) cc_final: 0.6753 (mt) REVERT: A 96 ASN cc_start: 0.8464 (m110) cc_final: 0.8196 (m110) REVERT: A 171 ILE cc_start: 0.6879 (OUTLIER) cc_final: 0.6425 (mp) REVERT: A 187 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.5816 (pp) REVERT: A 272 GLU cc_start: 0.8184 (tp30) cc_final: 0.7837 (mm-30) REVERT: A 346 LYS cc_start: 0.8145 (tttt) cc_final: 0.7502 (tppp) REVERT: A 347 GLU cc_start: 0.7502 (pt0) cc_final: 0.7270 (mt-10) REVERT: A 608 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.6551 (mpt180) REVERT: A 656 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8408 (mm-30) REVERT: A 670 ASN cc_start: 0.8734 (m-40) cc_final: 0.8458 (t0) REVERT: B 120 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8218 (p0) REVERT: B 135 ARG cc_start: 0.8636 (ttt90) cc_final: 0.8341 (ttt90) REVERT: B 152 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8162 (mttt) REVERT: B 247 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8413 (mt0) REVERT: B 362 MET cc_start: 0.8534 (mmm) cc_final: 0.8200 (mmp) REVERT: B 638 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6259 (mm-30) REVERT: B 672 ARG cc_start: 0.7801 (mtm180) cc_final: 0.7413 (ptp-170) REVERT: B 679 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8236 (pt0) REVERT: B 680 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7480 (mtt180) REVERT: B 707 ARG cc_start: 0.8011 (ttt-90) cc_final: 0.7766 (ttp80) REVERT: B 729 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: B 742 GLU cc_start: 0.7135 (tt0) cc_final: 0.6649 (tp30) REVERT: C 213 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8377 (ttt180) REVERT: C 214 ARG cc_start: 0.8130 (mmt180) cc_final: 0.7721 (mmt-90) outliers start: 42 outliers final: 23 residues processed: 242 average time/residue: 0.8140 time to fit residues: 213.1256 Evaluate side-chains 244 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 239 ASN C 127 HIS C 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.145973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.112218 restraints weight = 23615.567| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.60 r_work: 0.2980 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15341 Z= 0.175 Angle : 0.554 7.706 20949 Z= 0.299 Chirality : 0.042 0.211 2325 Planarity : 0.004 0.039 2493 Dihedral : 14.172 88.956 2760 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.91 % Allowed : 15.65 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.20), residues: 1693 helix: 1.38 (0.19), residues: 814 sheet: -0.17 (0.37), residues: 176 loop : -0.38 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 560 TYR 0.031 0.002 TYR B 557 PHE 0.017 0.002 PHE A 211 TRP 0.014 0.002 TRP C 98 HIS 0.004 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00389 (15341) covalent geometry : angle 0.55397 (20949) hydrogen bonds : bond 0.05108 ( 739) hydrogen bonds : angle 4.44515 ( 2040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.562 Fit side-chains REVERT: A 1 MET cc_start: 0.2453 (OUTLIER) cc_final: 0.1491 (tpt) REVERT: A 14 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7275 (mt) REVERT: A 21 MET cc_start: 0.7881 (mtp) cc_final: 0.7639 (mtm) REVERT: A 38 ILE cc_start: 0.6963 (mt) cc_final: 0.6747 (mt) REVERT: A 96 ASN cc_start: 0.8445 (m110) cc_final: 0.8211 (m110) REVERT: A 171 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6447 (mp) REVERT: A 187 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5780 (pp) REVERT: A 272 GLU cc_start: 0.8183 (tp30) cc_final: 0.7818 (mm-30) REVERT: A 346 LYS cc_start: 0.8175 (tttt) cc_final: 0.7510 (tppp) REVERT: A 347 GLU cc_start: 0.7530 (pt0) cc_final: 0.7291 (mt-10) REVERT: A 608 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.6554 (mpt180) REVERT: A 656 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8432 (mm-30) REVERT: A 670 ASN cc_start: 0.8722 (m-40) cc_final: 0.8441 (t0) REVERT: B 120 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8090 (p0) REVERT: B 152 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8149 (mttt) REVERT: B 211 LYS cc_start: 0.8401 (mttt) cc_final: 0.7969 (mtmm) REVERT: B 247 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8415 (mt0) REVERT: B 362 MET cc_start: 0.8480 (mmm) cc_final: 0.8142 (mmp) REVERT: B 367 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8266 (tp40) REVERT: B 638 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6229 (mm-30) REVERT: B 672 ARG cc_start: 0.7794 (mtm180) cc_final: 0.7404 (ptp-170) REVERT: B 679 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8205 (pt0) REVERT: B 680 ARG cc_start: 0.7694 (mtt90) cc_final: 0.7450 (mtt180) REVERT: C 197 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8237 (mmpt) REVERT: C 213 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8358 (ttt180) REVERT: C 214 ARG cc_start: 0.8127 (mmt180) cc_final: 0.7716 (mmt-90) outliers start: 44 outliers final: 25 residues processed: 244 average time/residue: 0.7950 time to fit residues: 209.4244 Evaluate side-chains 246 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 608 ARG Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 77 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 140 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 chunk 130 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 26 optimal weight: 40.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 239 ASN C 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.150090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.115456 restraints weight = 30042.413| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.67 r_work: 0.2987 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15341 Z= 0.109 Angle : 0.483 7.141 20949 Z= 0.262 Chirality : 0.039 0.206 2325 Planarity : 0.003 0.039 2493 Dihedral : 14.008 88.141 2758 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.31 % Allowed : 16.45 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.20), residues: 1693 helix: 1.60 (0.19), residues: 813 sheet: 0.19 (0.40), residues: 160 loop : -0.36 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.024 0.001 TYR B 557 PHE 0.012 0.001 PHE B 333 TRP 0.017 0.001 TRP C 49 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00228 (15341) covalent geometry : angle 0.48347 (20949) hydrogen bonds : bond 0.04070 ( 739) hydrogen bonds : angle 4.27931 ( 2040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.2510 (OUTLIER) cc_final: 0.1554 (tpt) REVERT: A 14 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7324 (mt) REVERT: A 21 MET cc_start: 0.7905 (mtp) cc_final: 0.7650 (mtm) REVERT: A 38 ILE cc_start: 0.6982 (mt) cc_final: 0.6765 (mt) REVERT: A 171 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6435 (mp) REVERT: A 187 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5805 (pp) REVERT: A 272 GLU cc_start: 0.8170 (tp30) cc_final: 0.7862 (mm-30) REVERT: A 346 LYS cc_start: 0.8156 (tttt) cc_final: 0.7447 (tppp) REVERT: A 519 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8487 (mt-10) REVERT: A 656 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8559 (mm-30) REVERT: A 670 ASN cc_start: 0.8711 (m-40) cc_final: 0.8463 (t0) REVERT: B 120 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8310 (p0) REVERT: B 135 ARG cc_start: 0.8489 (ttt90) cc_final: 0.8222 (ttt90) REVERT: B 152 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8164 (mttt) REVERT: B 211 LYS cc_start: 0.8446 (mttt) cc_final: 0.7987 (mtmm) REVERT: B 247 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8392 (mt0) REVERT: B 362 MET cc_start: 0.8575 (mmm) cc_final: 0.8209 (mmp) REVERT: B 371 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7360 (pt0) REVERT: B 638 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6299 (mm-30) REVERT: B 672 ARG cc_start: 0.7809 (mtm180) cc_final: 0.7425 (ptp-170) REVERT: B 679 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8213 (pt0) REVERT: B 680 ARG cc_start: 0.7749 (mtt90) cc_final: 0.7529 (mtt180) REVERT: B 697 GLU cc_start: 0.8396 (tp30) cc_final: 0.8099 (tp30) REVERT: B 707 ARG cc_start: 0.8014 (ttt-90) cc_final: 0.7769 (ttp80) REVERT: B 742 GLU cc_start: 0.7104 (tt0) cc_final: 0.6701 (tp30) REVERT: C 81 THR cc_start: 0.7733 (m) cc_final: 0.7039 (p) REVERT: C 157 ARG cc_start: 0.6875 (mpp-170) cc_final: 0.6440 (mmt-90) REVERT: C 197 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8275 (mmpt) REVERT: C 213 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8333 (ttt180) REVERT: C 214 ARG cc_start: 0.8158 (mmt180) cc_final: 0.7697 (mmt-90) outliers start: 35 outliers final: 16 residues processed: 254 average time/residue: 0.8264 time to fit residues: 226.9666 Evaluate side-chains 245 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 64 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 147 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 113 optimal weight: 0.4980 chunk 158 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 239 ASN C 42 ASN C 127 HIS C 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.147966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.114667 restraints weight = 23220.529| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.55 r_work: 0.2995 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15341 Z= 0.143 Angle : 0.518 7.154 20949 Z= 0.280 Chirality : 0.041 0.203 2325 Planarity : 0.004 0.039 2493 Dihedral : 14.026 88.613 2758 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.44 % Allowed : 16.84 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.20), residues: 1693 helix: 1.55 (0.19), residues: 814 sheet: 0.04 (0.39), residues: 167 loop : -0.28 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 610 TYR 0.028 0.002 TYR B 557 PHE 0.015 0.001 PHE A 211 TRP 0.014 0.002 TRP C 49 HIS 0.004 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00312 (15341) covalent geometry : angle 0.51796 (20949) hydrogen bonds : bond 0.04657 ( 739) hydrogen bonds : angle 4.34545 ( 2040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.2470 (OUTLIER) cc_final: 0.1441 (tpt) REVERT: A 14 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7265 (mt) REVERT: A 21 MET cc_start: 0.7862 (mtp) cc_final: 0.7610 (mtm) REVERT: A 171 ILE cc_start: 0.6889 (OUTLIER) cc_final: 0.6452 (mp) REVERT: A 187 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5774 (pp) REVERT: A 272 GLU cc_start: 0.8076 (tp30) cc_final: 0.7760 (mm-30) REVERT: A 346 LYS cc_start: 0.8130 (tttt) cc_final: 0.7464 (tppp) REVERT: A 670 ASN cc_start: 0.8680 (m-40) cc_final: 0.8396 (t0) REVERT: B 120 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8234 (p0) REVERT: B 152 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8126 (mttt) REVERT: B 211 LYS cc_start: 0.8416 (mttt) cc_final: 0.7973 (mtmm) REVERT: B 247 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8397 (mt0) REVERT: B 362 MET cc_start: 0.8525 (mmm) cc_final: 0.8152 (mmp) REVERT: B 638 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6288 (mm-30) REVERT: B 672 ARG cc_start: 0.7773 (mtm180) cc_final: 0.7377 (ptp-170) REVERT: B 679 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8159 (pt0) REVERT: B 680 ARG cc_start: 0.7705 (mtt90) cc_final: 0.7489 (mtt180) REVERT: B 697 GLU cc_start: 0.8323 (tp30) cc_final: 0.7994 (tp30) REVERT: B 707 ARG cc_start: 0.7934 (ttt-90) cc_final: 0.7712 (ttp80) REVERT: C 81 THR cc_start: 0.7716 (m) cc_final: 0.6997 (p) REVERT: C 197 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8215 (mmpt) REVERT: C 213 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8328 (ttt180) REVERT: C 214 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7691 (mmt-90) outliers start: 37 outliers final: 19 residues processed: 246 average time/residue: 0.8117 time to fit residues: 215.3230 Evaluate side-chains 243 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 201 ILE 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: 173 random chunks: chunk 91 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 239 ASN C 42 ASN C 127 HIS C 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.150135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.116545 restraints weight = 27520.539| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.68 r_work: 0.2989 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15341 Z= 0.106 Angle : 0.482 6.817 20949 Z= 0.261 Chirality : 0.039 0.204 2325 Planarity : 0.003 0.038 2493 Dihedral : 13.934 88.132 2757 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.11 % Allowed : 16.97 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1693 helix: 1.68 (0.19), residues: 813 sheet: 0.21 (0.40), residues: 160 loop : -0.28 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 572 TYR 0.024 0.001 TYR B 557 PHE 0.012 0.001 PHE B 333 TRP 0.016 0.001 TRP C 49 HIS 0.003 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00220 (15341) covalent geometry : angle 0.48195 (20949) hydrogen bonds : bond 0.04008 ( 739) hydrogen bonds : angle 4.24679 ( 2040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.2413 (OUTLIER) cc_final: 0.1478 (tpt) REVERT: A 21 MET cc_start: 0.7881 (mtp) cc_final: 0.7600 (mtm) REVERT: A 171 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6401 (mp) REVERT: A 187 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5828 (pp) REVERT: A 272 GLU cc_start: 0.8149 (tp30) cc_final: 0.7787 (mm-30) REVERT: A 346 LYS cc_start: 0.8105 (tttt) cc_final: 0.7399 (tppp) REVERT: A 519 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8488 (mt-10) REVERT: A 670 ASN cc_start: 0.8702 (m-40) cc_final: 0.8453 (t0) REVERT: B 152 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8149 (mttt) REVERT: B 211 LYS cc_start: 0.8455 (mttt) cc_final: 0.7999 (mtmm) REVERT: B 247 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8381 (mt0) REVERT: B 362 MET cc_start: 0.8542 (mmm) cc_final: 0.8170 (mmp) REVERT: B 371 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7323 (pt0) REVERT: B 638 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6221 (mm-30) REVERT: B 672 ARG cc_start: 0.7791 (mtm180) cc_final: 0.7401 (ptp-170) REVERT: B 679 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8198 (pt0) REVERT: B 680 ARG cc_start: 0.7741 (mtt90) cc_final: 0.7528 (mtt180) REVERT: B 697 GLU cc_start: 0.8405 (tp30) cc_final: 0.8054 (tp30) REVERT: B 729 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7567 (m-30) REVERT: B 742 GLU cc_start: 0.7063 (tt0) cc_final: 0.6633 (tp30) REVERT: C 81 THR cc_start: 0.7549 (m) cc_final: 0.6776 (p) REVERT: C 157 ARG cc_start: 0.6866 (mpp-170) cc_final: 0.6402 (mmt-90) REVERT: C 197 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8262 (mmpt) REVERT: C 213 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8309 (ttt180) REVERT: C 214 ARG cc_start: 0.8124 (mmt180) cc_final: 0.7656 (mmt-90) outliers start: 32 outliers final: 17 residues processed: 249 average time/residue: 0.8180 time to fit residues: 220.2727 Evaluate side-chains 250 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 679 GLN Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 201 ILE 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: 173 random chunks: chunk 69 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 239 ASN C 42 ASN C 127 HIS C 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.146985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.112095 restraints weight = 27986.285| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.62 r_work: 0.2967 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15341 Z= 0.179 Angle : 0.555 7.179 20949 Z= 0.300 Chirality : 0.042 0.209 2325 Planarity : 0.004 0.039 2493 Dihedral : 14.036 89.169 2755 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.18 % Allowed : 16.91 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1693 helix: 1.43 (0.18), residues: 821 sheet: -0.07 (0.37), residues: 179 loop : -0.32 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 560 TYR 0.032 0.002 TYR B 557 PHE 0.017 0.002 PHE A 211 TRP 0.014 0.002 TRP C 98 HIS 0.004 0.001 HIS C 127 Details of bonding type rmsd covalent geometry : bond 0.00399 (15341) covalent geometry : angle 0.55544 (20949) hydrogen bonds : bond 0.05091 ( 739) hydrogen bonds : angle 4.41480 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7338.44 seconds wall clock time: 125 minutes 29.76 seconds (7529.76 seconds total)