Starting phenix.real_space_refine on Wed Feb 21 16:59:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9m_14574/02_2024/7z9m_14574_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9m_14574/02_2024/7z9m_14574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9m_14574/02_2024/7z9m_14574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9m_14574/02_2024/7z9m_14574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9m_14574/02_2024/7z9m_14574_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z9m_14574/02_2024/7z9m_14574_trim_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 64 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 9821 2.51 5 N 2840 2.21 5 O 3181 1.98 5 H 15359 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31325 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8207 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6405 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "C" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8207 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 6405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6405 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "E" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 450 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "F" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 448 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 561 Classifications: {'DNA': 18} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 568 Classifications: {'DNA': 18} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IL1': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 13.05, per 1000 atoms: 0.42 Number of scatterers: 31325 At special positions: 0 Unit cell: (128.14, 139.32, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 P 64 15.00 Mg 2 11.99 O 3181 8.00 N 2840 7.00 C 9821 6.00 H 15359 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.38 Conformation dependent library (CDL) restraints added in 3.1 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 21 sheets defined 44.2% alpha, 9.1% beta 7 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 17.25 Creating SS restraints... Processing helix chain 'A' and resid 13 through 29 Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 82 through 93 removed outlier: 3.597A pdb=" N MET A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 removed outlier: 3.560A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 347 through 388 removed outlier: 3.562A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.852A pdb=" N ALA A 421 " --> pdb=" O GLY A 418 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA A 422 " --> pdb=" O ASN A 419 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 423 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 424 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU A 425 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 463 through 466 Processing helix chain 'A' and resid 468 through 493 removed outlier: 3.581A pdb=" N LEU A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 513 Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 458 through 463 removed outlier: 3.746A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 458 through 463' Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 501 through 517 Processing helix chain 'B' and resid 519 through 524 Processing helix chain 'B' and resid 548 through 561 removed outlier: 3.604A pdb=" N MET B 552 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 561 " --> pdb=" O ILE B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 596 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 626 through 638 removed outlier: 3.855A pdb=" N VAL B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 683 Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.675A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 733 removed outlier: 5.017A pdb=" N GLY B 733 " --> pdb=" O GLU B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 744 No H-bonds generated for 'chain 'B' and resid 742 through 744' Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 770 through 781 Processing helix chain 'B' and resid 785 through 794 Processing helix chain 'B' and resid 797 through 800 No H-bonds generated for 'chain 'B' and resid 797 through 800' Processing helix chain 'C' and resid 13 through 31 Processing helix chain 'C' and resid 43 through 54 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.624A pdb=" N MET C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 227 through 235 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 313 through 323 removed outlier: 3.571A pdb=" N TYR C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 399 removed outlier: 3.539A pdb=" N ILE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Proline residue: C 392 - end of helix removed outlier: 3.889A pdb=" N HIS C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 Processing helix chain 'C' and resid 418 through 426 removed outlier: 3.813A pdb=" N ALA C 421 " --> pdb=" O GLY C 418 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA C 422 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 459 Processing helix chain 'C' and resid 463 through 466 Processing helix chain 'C' and resid 468 through 492 removed outlier: 3.738A pdb=" N LEU C 474 " --> pdb=" O GLU C 470 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 475 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP C 483 " --> pdb=" O LYS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 513 Processing helix chain 'D' and resid 426 through 434 removed outlier: 3.728A pdb=" N GLN D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 466 through 474 Processing helix chain 'D' and resid 501 through 517 Processing helix chain 'D' and resid 519 through 524 Processing helix chain 'D' and resid 550 through 560 Processing helix chain 'D' and resid 578 through 597 removed outlier: 4.005A pdb=" N MET D 597 " --> pdb=" O MET D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 610 removed outlier: 3.525A pdb=" N LEU D 609 " --> pdb=" O MET D 605 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 620 No H-bonds generated for 'chain 'D' and resid 617 through 620' Processing helix chain 'D' and resid 626 through 639 Processing helix chain 'D' and resid 679 through 683 Processing helix chain 'D' and resid 685 through 696 removed outlier: 3.884A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 730 Processing helix chain 'D' and resid 742 through 744 No H-bonds generated for 'chain 'D' and resid 742 through 744' Processing helix chain 'D' and resid 747 through 754 Processing helix chain 'D' and resid 770 through 781 Processing helix chain 'D' and resid 785 through 794 Processing sheet with id= A, first strand: chain 'A' and resid 103 through 106 Processing sheet with id= B, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= C, first strand: chain 'A' and resid 171 through 174 Processing sheet with id= D, first strand: chain 'A' and resid 222 through 224 removed outlier: 6.551A pdb=" N GLU A 520 " --> pdb=" O ILE A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 237 through 243 Processing sheet with id= F, first strand: chain 'A' and resid 245 through 250 removed outlier: 3.821A pdb=" N GLU A 263 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLU A 247 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL A 261 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU A 249 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE A 259 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 307 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 335 through 337 Processing sheet with id= H, first strand: chain 'B' and resid 419 through 421 removed outlier: 6.853A pdb=" N SER B 492 " --> pdb=" O LEU B 420 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 528 through 530 Processing sheet with id= J, first strand: chain 'B' and resid 542 through 546 removed outlier: 4.010A pdb=" N GLN B 542 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 646 through 648 Processing sheet with id= L, first strand: chain 'B' and resid 651 through 653 Processing sheet with id= M, first strand: chain 'C' and resid 103 through 106 Processing sheet with id= N, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= O, first strand: chain 'C' and resid 171 through 174 Processing sheet with id= P, first strand: chain 'C' and resid 520 through 522 removed outlier: 4.082A pdb=" N TYR C 241 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 245 through 249 removed outlier: 3.907A pdb=" N GLU C 263 " --> pdb=" O ARG C 245 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLU C 247 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL C 261 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU C 249 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE C 259 " --> pdb=" O GLU C 249 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 419 through 421 removed outlier: 6.938A pdb=" N SER D 492 " --> pdb=" O LEU D 420 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 528 through 530 Processing sheet with id= T, first strand: chain 'D' and resid 542 through 546 removed outlier: 4.055A pdb=" N GLN D 542 " --> pdb=" O LYS D 539 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 646 through 652 592 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 11.96 Time building geometry restraints manager: 23.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15351 1.03 - 1.23: 35 1.23 - 1.42: 6727 1.42 - 1.61: 9490 1.61 - 1.81: 109 Bond restraints: 31712 Sorted by residual: bond pdb=" OH PTR C 122 " pdb=" P PTR C 122 " ideal model delta sigma weight residual 1.769 1.610 0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" OH PTR A 122 " pdb=" P PTR A 122 " ideal model delta sigma weight residual 1.769 1.613 0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C ALA A 412 " pdb=" N ASN A 413 " ideal model delta sigma weight residual 1.327 1.392 -0.065 1.71e-02 3.42e+03 1.45e+01 bond pdb=" C7 IL1 A 901 " pdb=" O3 IL1 A 901 " ideal model delta sigma weight residual 1.247 1.308 -0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" O1P PTR C 122 " pdb=" P PTR C 122 " ideal model delta sigma weight residual 1.522 1.476 0.046 2.00e-02 2.50e+03 5.29e+00 ... (remaining 31707 not shown) Histogram of bond angle deviations from ideal: 100.04 - 115.71: 41118 115.71 - 131.39: 16285 131.39 - 147.06: 38 147.06 - 162.74: 0 162.74 - 178.41: 1 Bond angle restraints: 57442 Sorted by residual: angle pdb=" OH PTR C 122 " pdb=" P PTR C 122 " pdb=" O2P PTR C 122 " ideal model delta sigma weight residual 99.92 111.24 -11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" OH PTR A 122 " pdb=" P PTR A 122 " pdb=" O2P PTR A 122 " ideal model delta sigma weight residual 99.92 109.57 -9.65 3.00e+00 1.11e-01 1.03e+01 angle pdb=" O3' DG E 7 " pdb=" C3' DG E 7 " pdb=" C2' DG E 7 " ideal model delta sigma weight residual 111.50 116.08 -4.58 1.50e+00 4.44e-01 9.33e+00 angle pdb=" O3' DA F 7 " pdb=" C3' DA F 7 " pdb=" C2' DA F 7 " ideal model delta sigma weight residual 111.50 115.81 -4.31 1.50e+00 4.44e-01 8.27e+00 angle pdb=" C ASP B 414 " pdb=" N PRO B 415 " pdb=" CA PRO B 415 " ideal model delta sigma weight residual 121.65 119.04 2.61 1.01e+00 9.80e-01 6.67e+00 ... (remaining 57437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.29: 13803 27.29 - 54.57: 579 54.57 - 81.86: 99 81.86 - 109.15: 5 109.15 - 136.44: 2 Dihedral angle restraints: 14488 sinusoidal: 8514 harmonic: 5974 Sorted by residual: dihedral pdb=" CA ARG A 32 " pdb=" C ARG A 32 " pdb=" N ALA A 33 " pdb=" CA ALA A 33 " ideal model delta harmonic sigma weight residual -180.00 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ASP A 297 " pdb=" C ASP A 297 " pdb=" N LYS A 298 " pdb=" CA LYS A 298 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ARG C 32 " pdb=" C ARG C 32 " pdb=" N ALA C 33 " pdb=" CA ALA C 33 " ideal model delta harmonic sigma weight residual 180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 14485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1699 0.036 - 0.071: 597 0.071 - 0.106: 122 0.106 - 0.142: 79 0.142 - 0.177: 6 Chirality restraints: 2503 Sorted by residual: chirality pdb=" CA ILE A 163 " pdb=" N ILE A 163 " pdb=" C ILE A 163 " pdb=" CB ILE A 163 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA ILE A 155 " pdb=" N ILE A 155 " pdb=" C ILE A 155 " pdb=" CB ILE A 155 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 2500 not shown) Planarity restraints: 4515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 IL1 A 901 " -0.246 2.00e-02 2.50e+03 1.23e-01 3.41e+02 pdb=" C29 IL1 A 901 " 0.023 2.00e-02 2.50e+03 pdb=" C30 IL1 A 901 " 0.073 2.00e-02 2.50e+03 pdb=" C31 IL1 A 901 " 0.105 2.00e-02 2.50e+03 pdb=" C32 IL1 A 901 " 0.092 2.00e-02 2.50e+03 pdb=" C33 IL1 A 901 " -0.050 2.00e-02 2.50e+03 pdb=" C34 IL1 A 901 " 0.105 2.00e-02 2.50e+03 pdb=" C35 IL1 A 901 " 0.075 2.00e-02 2.50e+03 pdb=" N8 IL1 A 901 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 IL1 A 901 " -0.123 2.00e-02 2.50e+03 1.02e-01 1.30e+02 pdb=" C23 IL1 A 901 " 0.033 2.00e-02 2.50e+03 pdb=" C24 IL1 A 901 " -0.093 2.00e-02 2.50e+03 pdb=" N6 IL1 A 901 " 0.163 2.00e-02 2.50e+03 pdb=" O6 IL1 A 901 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C IL1 A 901 " 0.016 2.00e-02 2.50e+03 5.98e-02 8.93e+01 pdb=" O IL1 A 901 " 0.076 2.00e-02 2.50e+03 pdb=" C1 IL1 A 901 " -0.011 2.00e-02 2.50e+03 pdb=" C10 IL1 A 901 " -0.048 2.00e-02 2.50e+03 pdb=" C11 IL1 A 901 " -0.027 2.00e-02 2.50e+03 pdb=" C12 IL1 A 901 " 0.011 2.00e-02 2.50e+03 pdb=" C2 IL1 A 901 " 0.009 2.00e-02 2.50e+03 pdb=" C38 IL1 A 901 " 0.004 2.00e-02 2.50e+03 pdb=" N1 IL1 A 901 " 0.099 2.00e-02 2.50e+03 pdb=" O8 IL1 A 901 " -0.128 2.00e-02 2.50e+03 ... (remaining 4512 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 4986 2.30 - 2.87: 69413 2.87 - 3.45: 71438 3.45 - 4.02: 98860 4.02 - 4.60: 154540 Nonbonded interactions: 399237 Sorted by model distance: nonbonded pdb=" O GLN D 749 " pdb=" HG1 THR D 753 " model vdw 1.722 1.850 nonbonded pdb="HD21 ASN B 569 " pdb=" O LEU B 700 " model vdw 1.725 1.850 nonbonded pdb="HH22 ARG B 516 " pdb=" OD1 ASP B 774 " model vdw 1.727 1.850 nonbonded pdb=" OD1 ASP B 622 " pdb=" HG1 THR B 653 " model vdw 1.730 1.850 nonbonded pdb="MG MG D 901 " pdb=" O HOH D1003 " model vdw 1.731 2.050 ... (remaining 399232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 524) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 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: 0.450 Extract box with map and model: 15.070 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 105.820 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.004 0.159 16353 Z= 0.284 Angle : 0.628 11.324 22381 Z= 0.338 Chirality : 0.041 0.177 2503 Planarity : 0.005 0.123 2710 Dihedral : 14.138 136.435 6420 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.26 % Allowed : 3.03 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.20), residues: 1824 helix: 2.34 (0.18), residues: 831 sheet: -0.21 (0.40), residues: 180 loop : -1.71 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 647 HIS 0.004 0.001 HIS B 669 PHE 0.009 0.001 PHE D 777 TYR 0.013 0.001 TYR C 266 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7865 (mmm) cc_final: 0.7600 (mmt) REVERT: A 491 ILE cc_start: 0.7944 (mt) cc_final: 0.7627 (mt) REVERT: B 483 TYR cc_start: 0.7855 (t80) cc_final: 0.7603 (t80) REVERT: B 548 ASP cc_start: 0.8060 (t0) cc_final: 0.7822 (m-30) REVERT: B 581 GLU cc_start: 0.8429 (tt0) cc_final: 0.8090 (tm-30) REVERT: B 642 GLN cc_start: 0.6727 (pm20) cc_final: 0.6436 (mm-40) REVERT: D 593 MET cc_start: 0.7049 (mtt) cc_final: 0.6755 (mtt) outliers start: 4 outliers final: 2 residues processed: 228 average time/residue: 0.8332 time to fit residues: 256.6412 Evaluate side-chains 112 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 631 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16353 Z= 0.261 Angle : 0.527 5.909 22381 Z= 0.292 Chirality : 0.041 0.148 2503 Planarity : 0.004 0.046 2710 Dihedral : 16.265 142.910 2772 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.97 % Allowed : 6.39 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.20), residues: 1824 helix: 2.37 (0.18), residues: 836 sheet: -0.09 (0.40), residues: 176 loop : -1.81 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 647 HIS 0.005 0.001 HIS A 262 PHE 0.022 0.001 PHE B 719 TYR 0.013 0.001 TYR C 266 ARG 0.003 0.000 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7892 (mmm) cc_final: 0.7609 (mmt) REVERT: A 286 VAL cc_start: 0.8379 (t) cc_final: 0.8160 (p) REVERT: B 483 TYR cc_start: 0.7806 (t80) cc_final: 0.7558 (t80) REVERT: B 581 GLU cc_start: 0.8374 (tt0) cc_final: 0.8096 (tm-30) REVERT: D 712 ARG cc_start: 0.5408 (mmm-85) cc_final: 0.5191 (tpp-160) outliers start: 15 outliers final: 11 residues processed: 129 average time/residue: 0.6880 time to fit residues: 128.4526 Evaluate side-chains 117 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 595 ASN Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS C 346 ASN D 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16353 Z= 0.270 Angle : 0.521 6.858 22381 Z= 0.288 Chirality : 0.041 0.151 2503 Planarity : 0.004 0.042 2710 Dihedral : 16.236 140.717 2772 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.84 % Allowed : 7.48 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.20), residues: 1824 helix: 2.33 (0.18), residues: 830 sheet: -0.14 (0.39), residues: 180 loop : -1.86 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 436 HIS 0.004 0.001 HIS C 78 PHE 0.008 0.001 PHE D 706 TYR 0.013 0.001 TYR C 266 ARG 0.005 0.000 ARG B 713 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7940 (mmm) cc_final: 0.7661 (mmt) REVERT: A 286 VAL cc_start: 0.8440 (t) cc_final: 0.8187 (p) REVERT: B 483 TYR cc_start: 0.7812 (t80) cc_final: 0.7600 (t80) REVERT: B 581 GLU cc_start: 0.8377 (tt0) cc_final: 0.8110 (tm-30) REVERT: D 712 ARG cc_start: 0.5371 (mmm-85) cc_final: 0.5111 (tpp-160) outliers start: 13 outliers final: 10 residues processed: 114 average time/residue: 0.7626 time to fit residues: 127.4483 Evaluate side-chains 105 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 553 ASP Chi-restraints excluded: chain D residue 595 ASN Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 160 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 591 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16353 Z= 0.268 Angle : 0.520 7.667 22381 Z= 0.287 Chirality : 0.041 0.150 2503 Planarity : 0.004 0.043 2710 Dihedral : 16.218 142.744 2772 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.71 % Allowed : 8.26 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1824 helix: 2.29 (0.18), residues: 829 sheet: -0.20 (0.39), residues: 179 loop : -1.90 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 647 HIS 0.004 0.001 HIS C 78 PHE 0.007 0.001 PHE C 330 TYR 0.012 0.001 TYR C 266 ARG 0.003 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7927 (mmm) cc_final: 0.7652 (mmt) REVERT: A 286 VAL cc_start: 0.8465 (t) cc_final: 0.8163 (p) REVERT: B 483 TYR cc_start: 0.7807 (t80) cc_final: 0.7584 (t80) REVERT: B 581 GLU cc_start: 0.8364 (tt0) cc_final: 0.8098 (tm-30) REVERT: D 712 ARG cc_start: 0.5355 (mmm-85) cc_final: 0.5090 (tpp-160) outliers start: 11 outliers final: 8 residues processed: 110 average time/residue: 0.7794 time to fit residues: 121.5253 Evaluate side-chains 99 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 595 ASN Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16353 Z= 0.196 Angle : 0.492 6.634 22381 Z= 0.269 Chirality : 0.039 0.145 2503 Planarity : 0.004 0.040 2710 Dihedral : 16.175 142.248 2772 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.65 % Allowed : 9.03 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1824 helix: 2.44 (0.18), residues: 828 sheet: -0.20 (0.39), residues: 180 loop : -1.84 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 647 HIS 0.004 0.001 HIS C 78 PHE 0.008 0.001 PHE B 681 TYR 0.010 0.001 TYR C 266 ARG 0.002 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7907 (mmm) cc_final: 0.7623 (mmt) REVERT: A 286 VAL cc_start: 0.8501 (t) cc_final: 0.8191 (p) REVERT: B 581 GLU cc_start: 0.8379 (tt0) cc_final: 0.8107 (tm-30) REVERT: D 597 MET cc_start: 0.7698 (ptt) cc_final: 0.7107 (tpt) REVERT: D 712 ARG cc_start: 0.5296 (mmm-85) cc_final: 0.5045 (tpp-160) outliers start: 10 outliers final: 8 residues processed: 111 average time/residue: 0.6575 time to fit residues: 108.7094 Evaluate side-chains 102 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 595 ASN Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16353 Z= 0.230 Angle : 0.505 7.076 22381 Z= 0.276 Chirality : 0.040 0.148 2503 Planarity : 0.004 0.041 2710 Dihedral : 16.247 142.899 2772 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.96 % Favored : 92.98 % Rotamer: Outliers : 0.84 % Allowed : 9.10 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.20), residues: 1824 helix: 2.39 (0.18), residues: 826 sheet: -0.27 (0.39), residues: 181 loop : -1.87 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 725 HIS 0.004 0.001 HIS A 262 PHE 0.030 0.001 PHE B 719 TYR 0.011 0.001 TYR C 266 ARG 0.002 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7882 (mmm) cc_final: 0.7593 (mmt) REVERT: A 286 VAL cc_start: 0.8504 (t) cc_final: 0.8186 (p) REVERT: A 423 MET cc_start: 0.7918 (ptt) cc_final: 0.7642 (ptt) REVERT: B 581 GLU cc_start: 0.8371 (tt0) cc_final: 0.8110 (tm-30) REVERT: D 597 MET cc_start: 0.7902 (ptt) cc_final: 0.7242 (tpt) REVERT: D 712 ARG cc_start: 0.5312 (mmm-85) cc_final: 0.5049 (tpp-160) outliers start: 13 outliers final: 10 residues processed: 109 average time/residue: 0.6939 time to fit residues: 111.1237 Evaluate side-chains 103 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 595 ASN Chi-restraints excluded: chain D residue 605 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16353 Z= 0.199 Angle : 0.489 6.537 22381 Z= 0.268 Chirality : 0.039 0.146 2503 Planarity : 0.004 0.040 2710 Dihedral : 16.229 143.558 2772 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 0.77 % Allowed : 9.10 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1824 helix: 2.45 (0.18), residues: 828 sheet: -0.26 (0.38), residues: 181 loop : -1.85 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 436 HIS 0.003 0.001 HIS A 262 PHE 0.010 0.001 PHE B 681 TYR 0.010 0.001 TYR C 266 ARG 0.002 0.000 ARG C 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7873 (mmm) cc_final: 0.7585 (mmt) REVERT: A 286 VAL cc_start: 0.8544 (t) cc_final: 0.8217 (p) REVERT: A 423 MET cc_start: 0.7891 (ptt) cc_final: 0.7624 (ptt) REVERT: B 491 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.7112 (m170) REVERT: B 581 GLU cc_start: 0.8368 (tt0) cc_final: 0.8117 (tm-30) REVERT: D 597 MET cc_start: 0.7987 (ptt) cc_final: 0.7279 (tpt) REVERT: D 712 ARG cc_start: 0.5252 (mmm-85) cc_final: 0.5004 (tpp-160) outliers start: 12 outliers final: 10 residues processed: 115 average time/residue: 0.6506 time to fit residues: 111.1835 Evaluate side-chains 109 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 491 HIS Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 595 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS B 714 GLN D 591 GLN D 795 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16353 Z= 0.166 Angle : 0.473 6.064 22381 Z= 0.259 Chirality : 0.039 0.143 2503 Planarity : 0.003 0.040 2710 Dihedral : 16.154 144.213 2772 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 0.84 % Allowed : 9.35 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1824 helix: 2.57 (0.18), residues: 826 sheet: -0.21 (0.39), residues: 181 loop : -1.83 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 647 HIS 0.003 0.001 HIS A 262 PHE 0.007 0.001 PHE B 719 TYR 0.011 0.001 TYR B 587 ARG 0.002 0.000 ARG D 599 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7865 (mmm) cc_final: 0.7572 (mmt) REVERT: A 286 VAL cc_start: 0.8541 (t) cc_final: 0.8198 (p) REVERT: A 306 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6774 (mt-10) REVERT: A 423 MET cc_start: 0.7853 (ptt) cc_final: 0.7581 (ptt) REVERT: B 491 HIS cc_start: 0.7323 (OUTLIER) cc_final: 0.7024 (m170) REVERT: B 581 GLU cc_start: 0.8382 (tt0) cc_final: 0.8117 (tm-30) REVERT: C 458 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8054 (tt) REVERT: D 597 MET cc_start: 0.8087 (ptt) cc_final: 0.7308 (tpt) REVERT: D 712 ARG cc_start: 0.5282 (mmm-85) cc_final: 0.5014 (tpp-160) outliers start: 13 outliers final: 9 residues processed: 111 average time/residue: 0.6346 time to fit residues: 104.8976 Evaluate side-chains 106 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 491 HIS Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 595 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 9.9990 chunk 171 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 591 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16353 Z= 0.379 Angle : 0.583 9.499 22381 Z= 0.320 Chirality : 0.043 0.163 2503 Planarity : 0.005 0.040 2710 Dihedral : 16.527 144.967 2772 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.06 % Favored : 91.89 % Rotamer: Outliers : 0.77 % Allowed : 9.61 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1824 helix: 2.08 (0.18), residues: 828 sheet: -0.56 (0.38), residues: 184 loop : -2.04 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 725 HIS 0.005 0.001 HIS C 78 PHE 0.012 0.002 PHE B 458 TYR 0.013 0.002 TYR C 266 ARG 0.005 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7929 (mmm) cc_final: 0.7661 (mmt) REVERT: A 286 VAL cc_start: 0.8561 (t) cc_final: 0.8212 (p) REVERT: A 306 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6835 (mt-10) REVERT: A 423 MET cc_start: 0.7870 (ptt) cc_final: 0.7587 (ptt) REVERT: B 491 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7425 (m170) REVERT: B 581 GLU cc_start: 0.8413 (tt0) cc_final: 0.8148 (tm-30) REVERT: D 712 ARG cc_start: 0.5375 (mmm-85) cc_final: 0.5065 (tpp-160) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 0.6926 time to fit residues: 106.3432 Evaluate side-chains 102 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 491 HIS Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 595 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.6980 chunk 176 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 113 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16353 Z= 0.141 Angle : 0.475 6.167 22381 Z= 0.260 Chirality : 0.039 0.142 2503 Planarity : 0.003 0.040 2710 Dihedral : 16.208 147.176 2770 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.76 % Favored : 94.19 % Rotamer: Outliers : 0.45 % Allowed : 9.94 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1824 helix: 2.48 (0.18), residues: 826 sheet: -0.26 (0.38), residues: 180 loop : -1.86 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 647 HIS 0.003 0.001 HIS A 262 PHE 0.007 0.001 PHE D 777 TYR 0.008 0.001 TYR C 266 ARG 0.003 0.000 ARG B 689 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7877 (mmm) cc_final: 0.7591 (mmt) REVERT: A 306 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6779 (mt-10) REVERT: A 423 MET cc_start: 0.7839 (ptt) cc_final: 0.7576 (ptt) REVERT: B 491 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.7071 (m170) REVERT: B 581 GLU cc_start: 0.8363 (tt0) cc_final: 0.8136 (tm-30) REVERT: C 458 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.8038 (tt) REVERT: D 712 ARG cc_start: 0.5343 (mmm-85) cc_final: 0.5045 (tpp-160) outliers start: 7 outliers final: 4 residues processed: 105 average time/residue: 0.6333 time to fit residues: 99.6627 Evaluate side-chains 101 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 491 HIS Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain D residue 595 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.124768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.085284 restraints weight = 81319.430| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.09 r_work: 0.3039 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16353 Z= 0.231 Angle : 0.502 7.376 22381 Z= 0.274 Chirality : 0.040 0.149 2503 Planarity : 0.004 0.040 2710 Dihedral : 16.259 145.804 2770 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.13 % Favored : 92.82 % Rotamer: Outliers : 0.77 % Allowed : 9.81 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.20), residues: 1824 helix: 2.43 (0.18), residues: 826 sheet: -0.49 (0.38), residues: 184 loop : -1.88 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 629 HIS 0.004 0.001 HIS A 262 PHE 0.011 0.001 PHE B 681 TYR 0.010 0.001 TYR C 266 ARG 0.002 0.000 ARG C 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6063.72 seconds wall clock time: 108 minutes 53.59 seconds (6533.59 seconds total)