Starting phenix.real_space_refine on Tue Mar 19 09:28:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo9_26642/03_2024/7uo9_26642_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo9_26642/03_2024/7uo9_26642.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo9_26642/03_2024/7uo9_26642_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo9_26642/03_2024/7uo9_26642_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo9_26642/03_2024/7uo9_26642_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo9_26642/03_2024/7uo9_26642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo9_26642/03_2024/7uo9_26642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo9_26642/03_2024/7uo9_26642_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uo9_26642/03_2024/7uo9_26642_updated.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 70 5.49 5 Mg 1 5.21 5 S 81 5.16 5 C 7542 2.51 5 N 2083 2.21 5 O 2779 1.98 5 H 11305 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 164": "OD1" <-> "OD2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A TYR 903": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "D ASP 101": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23863 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 14641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 14641 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2815 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 183} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1150 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "P" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 1010 Unusual residues: {'3DA': 1} Classifications: {'RNA': 31, 'undetermined': 1} Modifications used: {'rna3p_pur': 14, 'rna3p_pyr': 17} Link IDs: {'p': 1, 'rna3p': 30} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 1122 Classifications: {'RNA': 35} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 17} Link IDs: {'rna3p': 34} Chain: "D" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2848 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 210 Unusual residues: {' MG': 1, ' ZN': 2, 'UTP': 1} Classifications: {'undetermined': 4, 'water': 178} Link IDs: {None: 181} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "P" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "T" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4773 SG CYS A 301 36.084 98.671 113.379 1.00 17.27 S ATOM 4850 SG CYS A 306 37.848 101.980 114.087 1.00 18.00 S ATOM 4915 SG CYS A 310 37.961 99.260 116.522 1.00 14.68 S ATOM 7672 SG CYS A 487 35.806 96.767 92.807 1.00 21.54 S ATOM 10189 SG CYS A 645 36.840 100.401 93.063 1.00 24.84 S ATOM 10199 SG CYS A 646 34.844 98.496 95.605 1.00 20.49 S Time building chain proxies: 11.85, per 1000 atoms: 0.50 Number of scatterers: 23863 At special positions: 0 Unit cell: (93.003, 128.28, 169.971, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 81 16.00 P 70 15.00 Mg 1 11.99 O 2779 8.00 N 2083 7.00 C 7542 6.00 H 11305 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.70 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 6 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 9 sheets defined 47.4% alpha, 7.6% beta 28 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 14.43 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.558A pdb=" N TYR A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.952A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 198 removed outlier: 3.660A pdb=" N ASN A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.953A pdb=" N THR A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 247 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.939A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.681A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.683A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.966A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 579 removed outlier: 3.746A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 708 removed outlier: 3.934A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 693 " --> pdb=" O TYR A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 removed outlier: 3.667A pdb=" N ASN A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 752 removed outlier: 3.564A pdb=" N GLU A 744 " --> pdb=" O ASP A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 852 through 854 No H-bonds generated for 'chain 'A' and resid 852 through 854' Processing helix chain 'A' and resid 857 through 871 Proline residue: A 868 - end of helix removed outlier: 4.601A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 3.760A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 924 removed outlier: 4.065A pdb=" N ALA A 923 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 26 Processing helix chain 'B' and resid 35 through 96 removed outlier: 3.895A pdb=" N TYR B 71 " --> pdb=" O MET B 67 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 91 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.761A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 45 through 61 removed outlier: 4.064A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 71 No H-bonds generated for 'chain 'C' and resid 68 through 71' Processing helix chain 'D' and resid 10 through 28 removed outlier: 4.019A pdb=" N ALA D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 81 Processing helix chain 'D' and resid 83 through 98 Processing helix chain 'D' and resid 102 through 112 removed outlier: 3.637A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 141 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 Processing sheet with id= B, first strand: chain 'A' and resid 32 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 99 through 105 removed outlier: 3.721A pdb=" N VAL A 111 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 346 through 348 Processing sheet with id= E, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.317A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 800 through 802 removed outlier: 3.550A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 816 through 822 Processing sheet with id= H, first strand: chain 'B' and resid 127 through 132 Processing sheet with id= I, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.595A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 10.90 Time building geometry restraints manager: 21.44 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: 11274 1.03 - 1.23: 77 1.23 - 1.42: 5536 1.42 - 1.61: 6998 1.61 - 1.81: 126 Bond restraints: 24011 Sorted by residual: bond pdb=" C2' UTP A1004 " pdb=" C3' UTP A1004 " ideal model delta sigma weight residual 1.301 1.530 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C3' 3DA P 35 " pdb=" C2' 3DA P 35 " ideal model delta sigma weight residual 1.288 1.513 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1' UTP A1004 " pdb=" N1 UTP A1004 " ideal model delta sigma weight residual 1.305 1.475 -0.170 2.00e-02 2.50e+03 7.22e+01 bond pdb=" C1' 3DA P 35 " pdb=" N9 3DA P 35 " ideal model delta sigma weight residual 1.336 1.483 -0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C1' UTP A1004 " pdb=" O4' UTP A1004 " ideal model delta sigma weight residual 1.553 1.414 0.139 2.00e-02 2.50e+03 4.86e+01 ... (remaining 24006 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.75: 509 105.75 - 113.39: 27428 113.39 - 121.02: 10128 121.02 - 128.66: 4973 128.66 - 136.30: 140 Bond angle restraints: 43178 Sorted by residual: angle pdb=" C1' 3DA P 35 " pdb=" N9 3DA P 35 " pdb=" C8 3DA P 35 " ideal model delta sigma weight residual 102.28 126.71 -24.43 3.00e+00 1.11e-01 6.63e+01 angle pdb=" C1' 3DA P 35 " pdb=" N9 3DA P 35 " pdb=" C4 3DA P 35 " ideal model delta sigma weight residual 143.39 124.96 18.43 3.00e+00 1.11e-01 3.78e+01 angle pdb=" N6 3DA P 35 " pdb=" C6 3DA P 35 " pdb=" N1 3DA P 35 " ideal model delta sigma weight residual 107.16 121.16 -14.00 3.00e+00 1.11e-01 2.18e+01 angle pdb=" C SER A 759 " pdb=" CA SER A 759 " pdb=" CB SER A 759 " ideal model delta sigma weight residual 116.54 111.45 5.09 1.15e+00 7.56e-01 1.96e+01 angle pdb=" C5 3DA P 35 " pdb=" C6 3DA P 35 " pdb=" N6 3DA P 35 " ideal model delta sigma weight residual 132.33 121.16 11.17 3.00e+00 1.11e-01 1.39e+01 ... (remaining 43173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.50: 10899 23.50 - 47.00: 411 47.00 - 70.50: 165 70.50 - 94.00: 28 94.00 - 117.50: 2 Dihedral angle restraints: 11505 sinusoidal: 6640 harmonic: 4865 Sorted by residual: dihedral pdb=" CA PRO A 612 " pdb=" C PRO A 612 " pdb=" N HIS A 613 " pdb=" CA HIS A 613 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASN A 611 " pdb=" C ASN A 611 " pdb=" N PRO A 612 " pdb=" CA PRO A 612 " ideal model delta harmonic sigma weight residual 180.00 -161.94 -18.06 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA VAL A 609 " pdb=" C VAL A 609 " pdb=" N GLU A 610 " pdb=" CA GLU A 610 " ideal model delta harmonic sigma weight residual -180.00 -162.72 -17.28 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 11502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1905 0.072 - 0.144: 128 0.144 - 0.217: 2 0.217 - 0.289: 1 0.289 - 0.361: 1 Chirality restraints: 2037 Sorted by residual: chirality pdb=" C2' UTP A1004 " pdb=" C1' UTP A1004 " pdb=" C3' UTP A1004 " pdb=" O2' UTP A1004 " both_signs ideal model delta sigma weight residual False -2.41 -2.78 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" C2' 3DA P 35 " pdb=" C3' 3DA P 35 " pdb=" O2' 3DA P 35 " pdb=" C1' 3DA P 35 " both_signs ideal model delta sigma weight residual False -2.42 -2.64 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE A 539 " pdb=" N ILE A 539 " pdb=" C ILE A 539 " pdb=" CB ILE A 539 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 2034 not shown) Planarity restraints: 3370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 226 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO A 227 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 227 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 227 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 132 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO D 133 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 133 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 133 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 93 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 94 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " 0.021 5.00e-02 4.00e+02 ... (remaining 3367 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 824 2.16 - 2.77: 44337 2.77 - 3.38: 66065 3.38 - 3.99: 88313 3.99 - 4.60: 138606 Nonbonded interactions: 338145 Sorted by model distance: nonbonded pdb=" OE1 GLU A 522 " pdb=" H GLU A 522 " model vdw 1.544 1.850 nonbonded pdb="HH21 ARG A 18 " pdb=" OD1 ASP A 63 " model vdw 1.619 1.850 nonbonded pdb="HE21 GLN A 57 " pdb=" O ILE A 66 " model vdw 1.625 1.850 nonbonded pdb="HD22 ASN A 314 " pdb=" O GLU A 350 " model vdw 1.638 1.850 nonbonded pdb=" O TYR A 915 " pdb=" HH TYR A 921 " model vdw 1.640 1.850 ... (remaining 338140 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 'B' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 9 through 22 or (resid 23 t \ hrough 24 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 25 through 94 or (resid 95 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB2 or n \ ame HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or name H \ D22 or name HD23)) or resid 96 through 191)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 27 through 31 or (resid 3 \ 2 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 33 through 34 or (resid 35 through 37 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 38 or (resid 39 through 40 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 41 through 42 or (resid 43 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 44 through 69 or (resid 70 and (name N \ or name CA or name C or name O or name CB or name CG or name SD or name CE or n \ ame HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE1 or name HE2 o \ r name HE3)) or resid 71 through 191)) } 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: 3.190 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: 0.400 Extract box with map and model: 13.120 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 101.410 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.007 0.229 12706 Z= 0.447 Angle : 0.615 24.431 17559 Z= 0.303 Chirality : 0.040 0.361 2037 Planarity : 0.004 0.049 1996 Dihedral : 14.918 117.503 5054 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.25 % Allowed : 6.42 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.23), residues: 1367 helix: 0.68 (0.21), residues: 664 sheet: -1.57 (0.41), residues: 154 loop : -1.46 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.016 0.002 PHE B 147 TYR 0.015 0.001 TYR A 788 ARG 0.003 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 855 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 1.671 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 outliers start: 3 outliers final: 1 residues processed: 115 average time/residue: 0.7405 time to fit residues: 114.3073 Evaluate side-chains 85 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 82 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12706 Z= 0.191 Angle : 0.466 6.244 17559 Z= 0.247 Chirality : 0.036 0.146 2037 Planarity : 0.003 0.043 1996 Dihedral : 14.559 118.094 2547 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.51 % Allowed : 8.11 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.15 (0.23), residues: 1367 helix: 1.20 (0.22), residues: 663 sheet: -1.46 (0.42), residues: 144 loop : -1.30 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.005 0.001 HIS A 892 PHE 0.015 0.001 PHE D 92 TYR 0.013 0.001 TYR A 80 ARG 0.005 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 855 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 0.6204 time to fit residues: 77.1850 Evaluate side-chains 85 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 139 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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: 0.8114 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12706 Z= 0.196 Angle : 0.440 6.070 17559 Z= 0.233 Chirality : 0.036 0.147 2037 Planarity : 0.003 0.040 1996 Dihedral : 14.524 117.730 2547 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.76 % Allowed : 8.36 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.16 (0.24), residues: 1367 helix: 1.50 (0.22), residues: 660 sheet: -1.48 (0.40), residues: 159 loop : -1.12 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.003 0.000 HIS C 36 PHE 0.012 0.001 PHE A 753 TYR 0.012 0.001 TYR A 788 ARG 0.003 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 855 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 89 average time/residue: 0.6004 time to fit residues: 76.6953 Evaluate side-chains 88 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 56 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 12706 Z= 0.425 Angle : 0.529 6.178 17559 Z= 0.286 Chirality : 0.039 0.145 2037 Planarity : 0.003 0.042 1996 Dihedral : 14.656 119.972 2547 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.52 % Allowed : 8.61 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.00 (0.23), residues: 1367 helix: 1.36 (0.21), residues: 669 sheet: -1.56 (0.40), residues: 149 loop : -1.24 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.014 0.001 PHE A 753 TYR 0.015 0.001 TYR A 80 ARG 0.003 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 855 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 845 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6755 (m-30) outliers start: 18 outliers final: 12 residues processed: 95 average time/residue: 0.5958 time to fit residues: 80.4444 Evaluate side-chains 90 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12706 Z= 0.301 Angle : 0.473 6.413 17559 Z= 0.253 Chirality : 0.037 0.148 2037 Planarity : 0.003 0.042 1996 Dihedral : 14.737 118.171 2547 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.01 % Allowed : 9.80 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.09 (0.24), residues: 1367 helix: 1.46 (0.21), residues: 662 sheet: -1.73 (0.38), residues: 164 loop : -1.09 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 PHE 0.013 0.001 PHE A 753 TYR 0.013 0.001 TYR A 80 ARG 0.002 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 855 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 91 average time/residue: 0.5823 time to fit residues: 75.8620 Evaluate side-chains 87 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8177 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12706 Z= 0.205 Angle : 0.446 7.366 17559 Z= 0.237 Chirality : 0.036 0.147 2037 Planarity : 0.003 0.041 1996 Dihedral : 14.679 118.789 2547 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.10 % Allowed : 10.22 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1367 helix: 1.63 (0.22), residues: 661 sheet: -1.50 (0.39), residues: 159 loop : -1.01 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.002 0.000 HIS C 36 PHE 0.011 0.001 PHE A 753 TYR 0.012 0.001 TYR A 788 ARG 0.001 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 855 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 GLU cc_start: 0.8160 (tp30) cc_final: 0.7623 (tp30) outliers start: 13 outliers final: 11 residues processed: 89 average time/residue: 0.5878 time to fit residues: 74.9807 Evaluate side-chains 88 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12706 Z= 0.209 Angle : 0.446 6.865 17559 Z= 0.236 Chirality : 0.036 0.145 2037 Planarity : 0.003 0.038 1996 Dihedral : 14.633 118.965 2547 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.27 % Allowed : 10.56 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.24), residues: 1367 helix: 1.69 (0.21), residues: 663 sheet: -1.44 (0.40), residues: 159 loop : -0.97 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.002 0.000 HIS C 36 PHE 0.012 0.001 PHE A 694 TYR 0.011 0.001 TYR A 788 ARG 0.001 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 855 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 845 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6727 (m-30) REVERT: D 48 GLU cc_start: 0.8143 (tp30) cc_final: 0.7616 (tp30) outliers start: 15 outliers final: 10 residues processed: 91 average time/residue: 0.5660 time to fit residues: 74.7714 Evaluate side-chains 87 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12706 Z= 0.262 Angle : 0.467 7.403 17559 Z= 0.246 Chirality : 0.036 0.142 2037 Planarity : 0.003 0.039 1996 Dihedral : 14.621 119.524 2547 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.10 % Allowed : 10.73 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.38 (0.24), residues: 1367 helix: 1.69 (0.21), residues: 663 sheet: -1.60 (0.39), residues: 164 loop : -0.94 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.007 0.001 HIS A 362 PHE 0.011 0.001 PHE A 753 TYR 0.012 0.001 TYR A 788 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 855 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 2.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 845 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6717 (m-30) REVERT: D 48 GLU cc_start: 0.8129 (tp30) cc_final: 0.7619 (tp30) outliers start: 13 outliers final: 12 residues processed: 89 average time/residue: 0.5991 time to fit residues: 76.6256 Evaluate side-chains 90 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12706 Z= 0.438 Angle : 0.531 5.406 17559 Z= 0.287 Chirality : 0.039 0.164 2037 Planarity : 0.003 0.039 1996 Dihedral : 14.737 120.507 2547 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.18 % Allowed : 10.81 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.09 (0.24), residues: 1367 helix: 1.44 (0.21), residues: 667 sheet: -1.73 (0.39), residues: 165 loop : -1.08 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.014 0.001 PHE A 694 TYR 0.014 0.001 TYR A 80 ARG 0.002 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 855 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 845 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6690 (m-30) REVERT: D 48 GLU cc_start: 0.8059 (tp30) cc_final: 0.7548 (tp30) outliers start: 14 outliers final: 13 residues processed: 87 average time/residue: 0.5669 time to fit residues: 71.6000 Evaluate side-chains 90 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 141 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12706 Z= 0.190 Angle : 0.465 6.838 17559 Z= 0.245 Chirality : 0.036 0.148 2037 Planarity : 0.003 0.040 1996 Dihedral : 14.768 119.246 2547 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.10 % Allowed : 11.23 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.35 (0.24), residues: 1367 helix: 1.68 (0.21), residues: 664 sheet: -1.49 (0.40), residues: 159 loop : -1.04 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.002 0.000 HIS A 347 PHE 0.011 0.001 PHE A 694 TYR 0.011 0.001 TYR A 788 ARG 0.001 0.000 ARG A 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue MET 855 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 GLU cc_start: 0.8082 (tp30) cc_final: 0.7602 (tp30) outliers start: 13 outliers final: 13 residues processed: 90 average time/residue: 0.5889 time to fit residues: 76.0817 Evaluate side-chains 91 residues out of total 1205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.0670 chunk 103 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.0050 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.060561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.040234 restraints weight = 101522.677| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 2.66 r_work: 0.2503 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2372 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12706 Z= 0.154 Angle : 0.455 8.439 17559 Z= 0.237 Chirality : 0.035 0.177 2037 Planarity : 0.003 0.038 1996 Dihedral : 14.632 119.653 2547 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.10 % Allowed : 11.23 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.65 (0.24), residues: 1367 helix: 1.95 (0.22), residues: 657 sheet: -1.23 (0.42), residues: 146 loop : -0.94 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.002 0.000 HIS A 347 PHE 0.009 0.001 PHE D 92 TYR 0.010 0.001 TYR A 788 ARG 0.002 0.000 ARG A 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5208.82 seconds wall clock time: 92 minutes 42.49 seconds (5562.49 seconds total)