Starting phenix.real_space_refine on Sun Oct 13 06:22:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sna_40618/10_2024/8sna_40618.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sna_40618/10_2024/8sna_40618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sna_40618/10_2024/8sna_40618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sna_40618/10_2024/8sna_40618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sna_40618/10_2024/8sna_40618.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sna_40618/10_2024/8sna_40618.cif" } resolution = 4.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 294 5.49 5 S 33 5.16 5 C 8264 2.51 5 N 2710 2.21 5 O 3288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 14591 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 682 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 52.091 72.096 45.471 1.00130.70 S ATOM 12446 SG CYS K 51 50.512 68.670 45.375 1.00137.26 S ATOM 12470 SG CYS K 54 52.924 69.743 42.642 1.00135.51 S ATOM 12187 SG CYS K 16 41.580 66.180 52.218 1.00144.97 S ATOM 12205 SG CYS K 19 40.762 63.036 54.186 1.00143.14 S ATOM 12335 SG CYS K 36 43.515 65.426 55.432 1.00132.02 S ATOM 12357 SG CYS K 39 43.985 63.037 52.593 1.00138.90 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY M 76 " occ=0.25 Time building chain proxies: 8.70, per 1000 atoms: 0.60 Number of scatterers: 14591 At special positions: 0 Unit cell: (128.816, 130.144, 124.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 33 16.00 P 294 15.00 O 3288 8.00 N 2710 7.00 C 8264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 9 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 62.7% alpha, 5.4% beta 135 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 7.13 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.593A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.561A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.868A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.647A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.614A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.613A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.558A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.716A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.716A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.647A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.936A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.721A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.526A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.635A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.530A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 10 through 15 removed outlier: 3.695A pdb=" N GLN K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 Processing helix chain 'K' and resid 58 through 68 removed outlier: 3.533A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 91 removed outlier: 4.279A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 removed outlier: 3.596A pdb=" N ARG L 5 " --> pdb=" O MET L 1 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.582A pdb=" N ALA L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 145 removed outlier: 3.884A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.796A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.784A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.362A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.520A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB1, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 16 removed outlier: 3.559A pdb=" N HIS M 68 " --> pdb=" O ILE M 44 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 6.11 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3554 1.34 - 1.46: 4330 1.46 - 1.58: 6943 1.58 - 1.70: 586 1.70 - 1.82: 49 Bond restraints: 15462 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CB MET H 59 " pdb=" CG MET H 59 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" C3' DA J -73 " pdb=" C2' DA J -73 " ideal model delta sigma weight residual 1.525 1.547 -0.022 2.00e-02 2.50e+03 1.20e+00 bond pdb=" CA ASP B 24 " pdb=" CB ASP B 24 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.70e-02 3.46e+03 1.15e+00 bond pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 1.523 1.502 0.021 2.00e-02 2.50e+03 1.08e+00 ... (remaining 15457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 21726 1.99 - 3.98: 400 3.98 - 5.97: 27 5.97 - 7.96: 1 7.96 - 9.95: 2 Bond angle restraints: 22156 Sorted by residual: angle pdb=" C TYR L 60 " pdb=" N PRO L 61 " pdb=" CA PRO L 61 " ideal model delta sigma weight residual 127.00 136.95 -9.95 2.40e+00 1.74e-01 1.72e+01 angle pdb=" C TYR L 60 " pdb=" N PRO L 61 " pdb=" CD PRO L 61 " ideal model delta sigma weight residual 120.60 112.27 8.33 2.20e+00 2.07e-01 1.43e+01 angle pdb=" CA ARG K 86 " pdb=" CB ARG K 86 " pdb=" CG ARG K 86 " ideal model delta sigma weight residual 114.10 119.75 -5.65 2.00e+00 2.50e-01 7.99e+00 angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 122.46 126.40 -3.94 1.41e+00 5.03e-01 7.80e+00 angle pdb=" C3' DG J -70 " pdb=" C2' DG J -70 " pdb=" C1' DG J -70 " ideal model delta sigma weight residual 101.60 105.58 -3.98 1.50e+00 4.44e-01 7.05e+00 ... (remaining 22151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 7266 35.45 - 70.90: 1311 70.90 - 106.36: 17 106.36 - 141.81: 0 141.81 - 177.26: 2 Dihedral angle restraints: 8596 sinusoidal: 5462 harmonic: 3134 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 37.26 -177.26 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 72.91 147.09 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" CG ARG A 128 " pdb=" CD ARG A 128 " pdb=" NE ARG A 128 " pdb=" CZ ARG A 128 " ideal model delta sinusoidal sigma weight residual -90.00 -133.54 43.54 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 8593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1731 0.030 - 0.061: 587 0.061 - 0.091: 128 0.091 - 0.121: 60 0.121 - 0.151: 8 Chirality restraints: 2514 Sorted by residual: chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ARG L 136 " pdb=" N ARG L 136 " pdb=" C ARG L 136 " pdb=" CB ARG L 136 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA PRO E 121 " pdb=" N PRO E 121 " pdb=" C PRO E 121 " pdb=" CB PRO E 121 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 2511 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.025 2.00e-02 2.50e+03 1.05e-02 3.33e+00 pdb=" N9 DG I 47 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.024 2.00e-02 2.50e+03 1.02e-02 2.84e+00 pdb=" N9 DA I -35 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO G 80 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.022 5.00e-02 4.00e+02 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1969 2.76 - 3.47: 19955 3.47 - 4.19: 38560 4.19 - 4.90: 59029 Nonbonded interactions: 119515 Sorted by model distance: nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.330 3.350 nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.332 3.350 nonbonded pdb=" OE2 GLU K 45 " pdb=" NZ LYS K 46 " model vdw 2.125 3.120 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.138 2.496 nonbonded pdb=" OE2 GLU C 61 " pdb=" NH1 ARG K 63 " model vdw 2.194 3.120 ... (remaining 119510 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.880 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: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.010 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 0.035 15462 Z= 0.220 Angle : 0.586 9.951 22156 Z= 0.341 Chirality : 0.035 0.151 2514 Planarity : 0.004 0.058 1792 Dihedral : 25.679 177.259 6570 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.91 (0.27), residues: 1056 helix: 2.26 (0.21), residues: 639 sheet: 0.73 (0.81), residues: 48 loop : -0.45 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 33 HIS 0.004 0.001 HIS K 65 PHE 0.007 0.001 PHE L 62 TYR 0.023 0.002 TYR H 40 ARG 0.012 0.001 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 SER cc_start: 0.7819 (m) cc_final: 0.7514 (p) REVERT: C 75 LYS cc_start: 0.9250 (mmtp) cc_final: 0.8951 (mmmm) REVERT: C 111 ILE cc_start: 0.9141 (mt) cc_final: 0.8918 (tt) REVERT: D 33 ARG cc_start: 0.8569 (ttm110) cc_final: 0.7930 (mtp-110) REVERT: D 59 MET cc_start: 0.9391 (tpp) cc_final: 0.8980 (tpp) REVERT: D 116 LYS cc_start: 0.9335 (tmtt) cc_final: 0.8991 (tttp) REVERT: E 94 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7904 (mm-30) REVERT: G 39 TYR cc_start: 0.8796 (m-80) cc_final: 0.8454 (m-80) REVERT: G 56 GLU cc_start: 0.8353 (tt0) cc_final: 0.7968 (tt0) REVERT: G 84 GLN cc_start: 0.9562 (tp-100) cc_final: 0.9354 (tp-100) REVERT: H 120 LYS cc_start: 0.9184 (tttm) cc_final: 0.8906 (ttmt) REVERT: K 39 CYS cc_start: 0.3631 (m) cc_final: 0.2810 (m) REVERT: L 86 LEU cc_start: 0.8696 (tp) cc_final: 0.8403 (tp) REVERT: L 97 LEU cc_start: 0.8363 (mt) cc_final: 0.8085 (mt) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.3390 time to fit residues: 116.6179 Evaluate side-chains 193 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN E 68 GLN E 108 ASN F 25 ASN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15462 Z= 0.206 Angle : 0.579 10.154 22156 Z= 0.337 Chirality : 0.035 0.162 2514 Planarity : 0.004 0.043 1792 Dihedral : 28.821 176.929 4410 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.41 % Allowed : 11.94 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.99 (0.27), residues: 1056 helix: 2.33 (0.21), residues: 651 sheet: 0.70 (0.83), residues: 47 loop : -0.52 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 33 HIS 0.004 0.001 HIS K 65 PHE 0.008 0.001 PHE H 70 TYR 0.021 0.002 TYR D 83 ARG 0.006 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8747 (tt0) cc_final: 0.8530 (tt0) REVERT: C 18 SER cc_start: 0.7868 (m) cc_final: 0.7599 (p) REVERT: C 29 ARG cc_start: 0.8441 (ttm170) cc_final: 0.8063 (ttm170) REVERT: C 75 LYS cc_start: 0.9243 (mmtp) cc_final: 0.8926 (mmmm) REVERT: D 35 GLU cc_start: 0.8532 (tp30) cc_final: 0.8037 (mm-30) REVERT: D 59 MET cc_start: 0.9356 (tpp) cc_final: 0.9042 (tpp) REVERT: D 113 GLU cc_start: 0.8343 (tp30) cc_final: 0.7985 (tm-30) REVERT: E 94 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7968 (mm-30) REVERT: F 88 TYR cc_start: 0.7483 (m-80) cc_final: 0.7229 (m-10) REVERT: G 56 GLU cc_start: 0.8329 (tt0) cc_final: 0.8053 (tt0) REVERT: G 57 TYR cc_start: 0.9165 (t80) cc_final: 0.8959 (t80) REVERT: G 84 GLN cc_start: 0.9556 (tp-100) cc_final: 0.9214 (tp-100) REVERT: K 35 LEU cc_start: 0.7112 (tp) cc_final: 0.6757 (mp) REVERT: L 1 MET cc_start: 0.8249 (mpp) cc_final: 0.8028 (mpp) REVERT: L 97 LEU cc_start: 0.8351 (mt) cc_final: 0.8074 (mt) outliers start: 13 outliers final: 10 residues processed: 211 average time/residue: 0.3398 time to fit residues: 99.0180 Evaluate side-chains 196 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 186 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain M residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 117 optimal weight: 0.4980 chunk 126 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 47 GLN E 68 GLN H 84 ASN L 7 ASN ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 15462 Z= 0.472 Angle : 0.694 10.072 22156 Z= 0.391 Chirality : 0.040 0.154 2514 Planarity : 0.005 0.044 1792 Dihedral : 29.019 176.084 4410 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.47 % Allowed : 14.98 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.50 (0.26), residues: 1056 helix: 1.95 (0.21), residues: 650 sheet: 0.43 (0.73), residues: 50 loop : -0.73 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 33 HIS 0.006 0.001 HIS H 82 PHE 0.010 0.002 PHE H 70 TYR 0.047 0.003 TYR D 83 ARG 0.007 0.001 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8963 (tt0) cc_final: 0.8737 (tt0) REVERT: A 108 ASN cc_start: 0.9276 (OUTLIER) cc_final: 0.9027 (t0) REVERT: B 59 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8713 (ttmm) REVERT: B 88 TYR cc_start: 0.8384 (m-10) cc_final: 0.6973 (m-10) REVERT: C 18 SER cc_start: 0.8321 (m) cc_final: 0.8018 (p) REVERT: D 35 GLU cc_start: 0.8547 (tp30) cc_final: 0.8046 (mm-30) REVERT: D 59 MET cc_start: 0.9503 (tpp) cc_final: 0.9113 (tpp) REVERT: D 83 TYR cc_start: 0.8634 (m-10) cc_final: 0.7917 (m-80) REVERT: F 74 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8307 (mm-30) REVERT: G 56 GLU cc_start: 0.8546 (tt0) cc_final: 0.8076 (tt0) REVERT: G 95 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8649 (ttmm) REVERT: H 59 MET cc_start: 0.9374 (tpt) cc_final: 0.9059 (tpp) REVERT: L 31 PHE cc_start: 0.8709 (m-80) cc_final: 0.8438 (m-80) REVERT: L 97 LEU cc_start: 0.8636 (mt) cc_final: 0.8344 (mt) outliers start: 32 outliers final: 20 residues processed: 205 average time/residue: 0.3408 time to fit residues: 97.7876 Evaluate side-chains 195 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 111 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN E 68 GLN F 25 ASN H 84 ASN K 15 GLN L 20 GLN L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15462 Z= 0.210 Angle : 0.585 11.468 22156 Z= 0.336 Chirality : 0.035 0.185 2514 Planarity : 0.004 0.043 1792 Dihedral : 28.954 176.132 4410 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.95 % Allowed : 17.92 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.83 (0.26), residues: 1056 helix: 2.25 (0.21), residues: 650 sheet: 0.50 (0.75), residues: 49 loop : -0.66 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 33 HIS 0.003 0.001 HIS K 65 PHE 0.010 0.001 PHE A 67 TYR 0.027 0.002 TYR H 40 ARG 0.009 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 209 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8918 (tt0) cc_final: 0.8680 (tt0) REVERT: B 88 TYR cc_start: 0.8289 (m-10) cc_final: 0.7610 (m-10) REVERT: C 18 SER cc_start: 0.8250 (m) cc_final: 0.7908 (p) REVERT: C 29 ARG cc_start: 0.8571 (ttm170) cc_final: 0.8205 (ttm110) REVERT: D 35 GLU cc_start: 0.8391 (tp30) cc_final: 0.7913 (mm-30) REVERT: D 59 MET cc_start: 0.9374 (tpp) cc_final: 0.8967 (tpp) REVERT: D 85 LYS cc_start: 0.9255 (mtmm) cc_final: 0.8971 (mtmm) REVERT: F 88 TYR cc_start: 0.8422 (m-80) cc_final: 0.7924 (m-80) REVERT: G 56 GLU cc_start: 0.8530 (tt0) cc_final: 0.8052 (tt0) REVERT: K 46 LYS cc_start: 0.8553 (mttt) cc_final: 0.7939 (mtmm) REVERT: K 68 ARG cc_start: 0.7565 (mtt180) cc_final: 0.7124 (mtt180) REVERT: L 86 LEU cc_start: 0.8425 (tp) cc_final: 0.8150 (tt) REVERT: L 97 LEU cc_start: 0.8398 (mt) cc_final: 0.8196 (mt) outliers start: 18 outliers final: 14 residues processed: 218 average time/residue: 0.3549 time to fit residues: 107.1615 Evaluate side-chains 203 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 189 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN E 68 GLN L 20 GLN L 32 HIS L 46 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15462 Z= 0.299 Angle : 0.616 11.568 22156 Z= 0.349 Chirality : 0.036 0.178 2514 Planarity : 0.004 0.044 1792 Dihedral : 28.994 175.594 4410 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.93 % Allowed : 18.35 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.71 (0.26), residues: 1056 helix: 2.18 (0.21), residues: 650 sheet: 0.10 (0.70), residues: 50 loop : -0.71 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 33 HIS 0.003 0.001 HIS K 65 PHE 0.009 0.001 PHE B 61 TYR 0.027 0.002 TYR H 83 ARG 0.010 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 197 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8954 (tt0) cc_final: 0.8671 (tt0) REVERT: B 88 TYR cc_start: 0.8360 (m-10) cc_final: 0.7502 (m-10) REVERT: C 18 SER cc_start: 0.8347 (m) cc_final: 0.8131 (p) REVERT: C 29 ARG cc_start: 0.8673 (ttm170) cc_final: 0.8096 (ttm170) REVERT: D 35 GLU cc_start: 0.8465 (tp30) cc_final: 0.7865 (mm-30) REVERT: D 59 MET cc_start: 0.9442 (tpp) cc_final: 0.9023 (tpp) REVERT: D 85 LYS cc_start: 0.9287 (mtmm) cc_final: 0.8973 (mtmm) REVERT: F 88 TYR cc_start: 0.8423 (m-80) cc_final: 0.8131 (m-80) REVERT: G 56 GLU cc_start: 0.8513 (tt0) cc_final: 0.8035 (tt0) REVERT: G 95 LYS cc_start: 0.9046 (mtpp) cc_final: 0.8563 (ttmm) REVERT: L 52 LEU cc_start: 0.8695 (tt) cc_final: 0.8401 (tt) outliers start: 27 outliers final: 20 residues processed: 214 average time/residue: 0.3542 time to fit residues: 106.4505 Evaluate side-chains 207 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 69 ASN Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 52 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN E 68 GLN H 49 HIS ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15462 Z= 0.209 Angle : 0.597 12.569 22156 Z= 0.337 Chirality : 0.035 0.199 2514 Planarity : 0.004 0.047 1792 Dihedral : 28.962 175.880 4410 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.39 % Allowed : 19.44 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.85 (0.26), residues: 1056 helix: 2.30 (0.21), residues: 650 sheet: 0.16 (0.69), residues: 50 loop : -0.67 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 33 HIS 0.003 0.001 HIS K 65 PHE 0.009 0.001 PHE A 67 TYR 0.024 0.002 TYR H 83 ARG 0.010 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 201 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8840 (tt0) cc_final: 0.8632 (tt0) REVERT: B 88 TYR cc_start: 0.8342 (m-10) cc_final: 0.7478 (m-10) REVERT: C 29 ARG cc_start: 0.8589 (ttm170) cc_final: 0.7819 (ttm170) REVERT: D 35 GLU cc_start: 0.8331 (tp30) cc_final: 0.7619 (mm-30) REVERT: D 59 MET cc_start: 0.9388 (tpp) cc_final: 0.9023 (tpp) REVERT: D 85 LYS cc_start: 0.9279 (mtmm) cc_final: 0.8984 (mtmm) REVERT: G 56 GLU cc_start: 0.8525 (tt0) cc_final: 0.8085 (tt0) REVERT: G 95 LYS cc_start: 0.8979 (mtpp) cc_final: 0.8496 (ttmm) REVERT: H 83 TYR cc_start: 0.7971 (m-80) cc_final: 0.7663 (m-80) REVERT: K 21 GLU cc_start: 0.7284 (pp20) cc_final: 0.6900 (pp20) REVERT: L 52 LEU cc_start: 0.8651 (tt) cc_final: 0.8334 (tt) REVERT: L 86 LEU cc_start: 0.8458 (tp) cc_final: 0.8185 (tt) outliers start: 22 outliers final: 16 residues processed: 211 average time/residue: 0.3565 time to fit residues: 105.6645 Evaluate side-chains 206 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN E 68 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15462 Z= 0.235 Angle : 0.599 12.955 22156 Z= 0.339 Chirality : 0.035 0.198 2514 Planarity : 0.004 0.050 1792 Dihedral : 28.969 175.699 4410 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.61 % Allowed : 19.44 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.80 (0.26), residues: 1056 helix: 2.27 (0.21), residues: 648 sheet: 0.20 (0.69), residues: 50 loop : -0.70 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 33 HIS 0.003 0.001 HIS K 65 PHE 0.008 0.001 PHE A 67 TYR 0.020 0.002 TYR F 88 ARG 0.011 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 194 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8863 (tt0) cc_final: 0.8645 (tt0) REVERT: B 88 TYR cc_start: 0.8333 (m-10) cc_final: 0.7566 (m-10) REVERT: C 20 ARG cc_start: 0.8801 (mtp180) cc_final: 0.8551 (mtp85) REVERT: C 29 ARG cc_start: 0.8666 (ttm170) cc_final: 0.7986 (ttm170) REVERT: D 35 GLU cc_start: 0.8373 (tp30) cc_final: 0.7745 (mm-30) REVERT: D 59 MET cc_start: 0.9392 (tpp) cc_final: 0.8980 (tpp) REVERT: D 85 LYS cc_start: 0.9279 (mtmm) cc_final: 0.8987 (mtmm) REVERT: G 56 GLU cc_start: 0.8532 (tt0) cc_final: 0.8098 (tt0) REVERT: G 95 LYS cc_start: 0.9022 (mtpp) cc_final: 0.8530 (ttmm) REVERT: K 21 GLU cc_start: 0.7197 (pp20) cc_final: 0.6877 (pp20) REVERT: L 52 LEU cc_start: 0.8631 (tt) cc_final: 0.8299 (tt) REVERT: L 86 LEU cc_start: 0.8486 (tp) cc_final: 0.8252 (tt) outliers start: 24 outliers final: 24 residues processed: 207 average time/residue: 0.3464 time to fit residues: 100.0481 Evaluate side-chains 214 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 190 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 52 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 0.0170 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN E 68 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15462 Z= 0.243 Angle : 0.614 13.604 22156 Z= 0.345 Chirality : 0.035 0.211 2514 Planarity : 0.004 0.059 1792 Dihedral : 28.966 175.592 4410 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.71 % Allowed : 20.20 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.80 (0.26), residues: 1056 helix: 2.24 (0.21), residues: 649 sheet: 0.19 (0.69), residues: 50 loop : -0.64 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 33 HIS 0.003 0.001 HIS K 65 PHE 0.008 0.001 PHE A 67 TYR 0.022 0.002 TYR H 83 ARG 0.012 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 194 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8867 (tt0) cc_final: 0.8650 (tt0) REVERT: B 88 TYR cc_start: 0.8359 (m-10) cc_final: 0.7564 (m-10) REVERT: C 29 ARG cc_start: 0.8649 (ttm170) cc_final: 0.7978 (ttm170) REVERT: D 35 GLU cc_start: 0.8368 (tp30) cc_final: 0.7738 (mm-30) REVERT: D 59 MET cc_start: 0.9382 (tpp) cc_final: 0.8986 (tpp) REVERT: D 85 LYS cc_start: 0.9282 (mtmm) cc_final: 0.8992 (mtmm) REVERT: G 56 GLU cc_start: 0.8544 (tt0) cc_final: 0.8109 (tt0) REVERT: G 95 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8522 (ttmm) REVERT: K 21 GLU cc_start: 0.7150 (pp20) cc_final: 0.6828 (pp20) REVERT: K 35 LEU cc_start: 0.6930 (tp) cc_final: 0.6640 (mp) REVERT: L 52 LEU cc_start: 0.8633 (tt) cc_final: 0.8319 (tt) REVERT: L 66 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8321 (mppt) REVERT: L 86 LEU cc_start: 0.8483 (tp) cc_final: 0.8260 (tt) outliers start: 25 outliers final: 22 residues processed: 207 average time/residue: 0.3223 time to fit residues: 94.3135 Evaluate side-chains 209 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 187 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 119 optimal weight: 0.6980 chunk 69 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN E 68 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 55 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15462 Z= 0.269 Angle : 0.623 13.849 22156 Z= 0.352 Chirality : 0.036 0.218 2514 Planarity : 0.004 0.059 1792 Dihedral : 28.972 175.407 4410 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.71 % Allowed : 20.41 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.76 (0.26), residues: 1056 helix: 2.24 (0.21), residues: 649 sheet: -0.10 (0.69), residues: 44 loop : -0.68 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 33 HIS 0.003 0.001 HIS H 82 PHE 0.009 0.001 PHE B 61 TYR 0.023 0.002 TYR H 83 ARG 0.013 0.000 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8883 (tt0) cc_final: 0.8666 (tt0) REVERT: B 88 TYR cc_start: 0.8362 (m-10) cc_final: 0.7585 (m-10) REVERT: C 29 ARG cc_start: 0.8661 (ttm170) cc_final: 0.8006 (ttm170) REVERT: D 35 GLU cc_start: 0.8375 (tp30) cc_final: 0.7726 (mm-30) REVERT: D 59 MET cc_start: 0.9385 (tpp) cc_final: 0.8970 (tpp) REVERT: G 56 GLU cc_start: 0.8558 (tt0) cc_final: 0.8117 (tt0) REVERT: G 84 GLN cc_start: 0.9547 (tp-100) cc_final: 0.9168 (tp-100) REVERT: G 95 LYS cc_start: 0.9060 (mtpp) cc_final: 0.8581 (ttmm) REVERT: K 21 GLU cc_start: 0.7026 (pp20) cc_final: 0.6685 (pp20) REVERT: K 35 LEU cc_start: 0.6955 (tp) cc_final: 0.6663 (mp) REVERT: L 52 LEU cc_start: 0.8581 (tt) cc_final: 0.8265 (tt) REVERT: L 66 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8369 (mppt) outliers start: 25 outliers final: 25 residues processed: 201 average time/residue: 0.3320 time to fit residues: 93.4333 Evaluate side-chains 206 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 86 ARG Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 102 optimal weight: 0.0000 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN E 68 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15462 Z= 0.286 Angle : 0.641 14.063 22156 Z= 0.358 Chirality : 0.036 0.214 2514 Planarity : 0.005 0.062 1792 Dihedral : 28.987 175.212 4410 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.15 % Allowed : 20.74 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.69 (0.26), residues: 1056 helix: 2.21 (0.21), residues: 649 sheet: -0.38 (0.66), residues: 44 loop : -0.72 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 33 HIS 0.004 0.001 HIS H 82 PHE 0.009 0.001 PHE B 61 TYR 0.025 0.002 TYR H 83 ARG 0.013 0.000 ARG D 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8892 (tt0) cc_final: 0.8667 (tt0) REVERT: B 88 TYR cc_start: 0.8343 (m-10) cc_final: 0.7590 (m-10) REVERT: C 29 ARG cc_start: 0.8691 (ttm170) cc_final: 0.8002 (ttm170) REVERT: D 35 GLU cc_start: 0.8375 (tp30) cc_final: 0.7692 (mm-30) REVERT: D 59 MET cc_start: 0.9404 (tpp) cc_final: 0.8987 (tpp) REVERT: G 56 GLU cc_start: 0.8571 (tt0) cc_final: 0.8108 (tt0) REVERT: G 95 LYS cc_start: 0.9062 (mtpp) cc_final: 0.8592 (ttmm) REVERT: K 21 GLU cc_start: 0.6995 (pp20) cc_final: 0.6642 (pp20) REVERT: K 35 LEU cc_start: 0.7012 (tp) cc_final: 0.6798 (mp) REVERT: K 68 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7040 (mtt180) REVERT: L 52 LEU cc_start: 0.8579 (tt) cc_final: 0.8255 (tt) REVERT: L 66 LYS cc_start: 0.8698 (mtmm) cc_final: 0.8329 (mppt) outliers start: 29 outliers final: 27 residues processed: 198 average time/residue: 0.3492 time to fit residues: 96.5238 Evaluate side-chains 202 residues out of total 919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 86 ARG Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.0030 chunk 42 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.0170 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.4228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.120715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.078243 restraints weight = 37869.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.077727 restraints weight = 30470.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.078148 restraints weight = 28447.865| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15462 Z= 0.181 Angle : 0.609 14.068 22156 Z= 0.343 Chirality : 0.035 0.218 2514 Planarity : 0.004 0.055 1792 Dihedral : 28.939 175.939 4410 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.74 % Allowed : 21.61 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.88 (0.26), residues: 1056 helix: 2.33 (0.21), residues: 650 sheet: -0.37 (0.70), residues: 43 loop : -0.58 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 33 HIS 0.004 0.001 HIS K 65 PHE 0.010 0.001 PHE A 67 TYR 0.027 0.002 TYR F 88 ARG 0.013 0.000 ARG D 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2641.93 seconds wall clock time: 53 minutes 19.41 seconds (3199.41 seconds total)