Starting phenix.real_space_refine on Mon Dec 30 23:04:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sn3_40611/12_2024/8sn3_40611.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sn3_40611/12_2024/8sn3_40611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sn3_40611/12_2024/8sn3_40611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sn3_40611/12_2024/8sn3_40611.map" model { file = "/net/cci-nas-00/data/ceres_data/8sn3_40611/12_2024/8sn3_40611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sn3_40611/12_2024/8sn3_40611.cif" } resolution = 3.8 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= 0.004 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 8276 2.51 5 N 2716 2.21 5 O 3291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14612 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: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 704 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} 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: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} 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 12313 SG CYS K 31 31.696 74.358 48.206 1.00 55.65 S ATOM 12463 SG CYS K 51 30.684 71.325 47.252 1.00 54.45 S ATOM 12487 SG CYS K 54 31.262 73.831 44.365 1.00 65.71 S ATOM 12204 SG CYS K 16 21.823 68.573 53.938 1.00 64.66 S ATOM 12222 SG CYS K 19 19.688 65.906 55.446 1.00 64.84 S ATOM 12352 SG CYS K 36 22.524 67.475 57.565 1.00 50.00 S ATOM 12374 SG CYS K 39 23.418 65.177 54.865 1.00 54.15 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 ... (2 atoms not shown) pdb=" O GLY M 76 " occ=0.25 Time building chain proxies: 8.67, per 1000 atoms: 0.59 Number of scatterers: 14612 At special positions: 0 Unit cell: (108.896, 134.128, 126.16, 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 3291 8.00 N 2716 7.00 C 8276 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 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 3.80 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=" 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 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 6 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 63.1% alpha, 4.5% beta 135 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 6.48 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.659A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.773A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.748A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.611A 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 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.523A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.713A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 122 removed outlier: 3.714A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.513A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.649A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.505A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.002A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 74 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.534A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.527A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.673A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.837A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.774A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 removed outlier: 4.669A pdb=" N GLU K 45 " --> pdb=" O GLN K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.861A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.543A 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 90 removed outlier: 3.792A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 86 through 91 removed outlier: 3.710A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.549A pdb=" N ASP L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.564A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 146 removed outlier: 3.900A 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 41 Processing helix chain 'M' and resid 55 through 60 removed outlier: 3.863A pdb=" N TYR M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.873A 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 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 8.120A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 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: 7.878A 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 removed outlier: 4.097A pdb=" N SER L 22 " --> pdb=" O THR L 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 15 removed outlier: 3.627A pdb=" N ILE M 13 " --> pdb=" O VAL M 5 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU M 69 " --> pdb=" O LYS M 6 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS M 68 " --> pdb=" O ILE M 44 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 5.23 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3244 1.33 - 1.45: 4467 1.45 - 1.57: 7137 1.57 - 1.69: 586 1.69 - 1.81: 49 Bond restraints: 15483 Sorted by residual: bond pdb=" CD LYS D 116 " pdb=" CE LYS D 116 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" CG LYS D 116 " pdb=" CD LYS D 116 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CB MET H 59 " pdb=" CG MET H 59 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" C3' DA J -68 " pdb=" C2' DA J -68 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.05e+00 ... (remaining 15478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 21491 1.43 - 2.85: 626 2.85 - 4.28: 39 4.28 - 5.70: 22 5.70 - 7.13: 4 Bond angle restraints: 22182 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 111.90 108.81 3.09 8.10e-01 1.52e+00 1.45e+01 angle pdb=" C GLY G 37 " pdb=" N ASN G 38 " pdb=" CA ASN G 38 " ideal model delta sigma weight residual 121.54 126.95 -5.41 1.91e+00 2.74e-01 8.03e+00 angle pdb=" CA LYS D 116 " pdb=" CB LYS D 116 " pdb=" CG LYS D 116 " ideal model delta sigma weight residual 114.10 108.74 5.36 2.00e+00 2.50e-01 7.17e+00 angle pdb=" C ALA K 47 " pdb=" N SER K 48 " pdb=" CA SER K 48 " ideal model delta sigma weight residual 122.55 117.60 4.95 2.03e+00 2.43e-01 5.94e+00 angle pdb=" CB MET H 59 " pdb=" CG MET H 59 " pdb=" SD MET H 59 " ideal model delta sigma weight residual 112.70 105.57 7.13 3.00e+00 1.11e-01 5.65e+00 ... (remaining 22177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 7303 35.74 - 71.48: 1294 71.48 - 107.22: 18 107.22 - 142.96: 0 142.96 - 178.70: 2 Dihedral angle restraints: 8617 sinusoidal: 5475 harmonic: 3142 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 38.70 -178.70 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA GLN M 41 " pdb=" C GLN M 41 " pdb=" N ARG M 42 " pdb=" CA ARG M 42 " ideal model delta harmonic sigma weight residual 180.00 160.70 19.30 0 5.00e+00 4.00e-02 1.49e+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 74.33 145.67 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 8614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1731 0.029 - 0.059: 577 0.059 - 0.088: 134 0.088 - 0.117: 66 0.117 - 0.146: 8 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ASN G 38 " pdb=" N ASN G 38 " pdb=" C ASN G 38 " pdb=" CB ASN G 38 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE M 36 " pdb=" N ILE M 36 " pdb=" C ILE M 36 " pdb=" CB ILE M 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 2513 not shown) Planarity restraints: 1797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 88 " -0.019 2.00e-02 2.50e+03 1.74e-02 6.06e+00 pdb=" CG TYR F 88 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR F 88 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR F 88 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 88 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 88 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR F 88 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 88 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO M 37 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO M 38 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO M 38 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO M 38 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " 0.010 2.00e-02 2.50e+03 1.33e-02 3.53e+00 pdb=" CG TYR B 88 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " 0.000 2.00e-02 2.50e+03 ... (remaining 1794 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 670 2.71 - 3.26: 13349 3.26 - 3.81: 26655 3.81 - 4.35: 31370 4.35 - 4.90: 46862 Nonbonded interactions: 118906 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.164 2.496 nonbonded pdb=" O ARG L 139 " pdb=" NE2 GLN L 143 " model vdw 2.205 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR D 40 " pdb=" OP1 DG J 48 " model vdw 2.283 3.040 nonbonded pdb=" NE2 GLN M 31 " pdb=" O ILE M 36 " model vdw 2.291 3.120 ... (remaining 118901 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 40.670 Find NCS groups from input model: 0.320 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: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.003 0.040 15483 Z= 0.201 Angle : 0.553 7.129 22182 Z= 0.322 Chirality : 0.034 0.146 2516 Planarity : 0.004 0.075 1795 Dihedral : 25.549 178.698 6581 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 1.98 (0.26), residues: 1058 helix: 2.28 (0.21), residues: 634 sheet: 1.13 (0.76), residues: 46 loop : -0.36 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 33 HIS 0.002 0.000 HIS F 75 PHE 0.008 0.001 PHE K 53 TYR 0.043 0.002 TYR F 88 ARG 0.004 0.000 ARG M 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8701 (tttm) REVERT: D 68 ASP cc_start: 0.8310 (t70) cc_final: 0.7858 (t0) REVERT: G 36 LYS cc_start: 0.8763 (mptt) cc_final: 0.8418 (mmtm) REVERT: H 120 LYS cc_start: 0.9248 (ttpt) cc_final: 0.9041 (ttmt) REVERT: K 41 GLN cc_start: 0.8920 (tp40) cc_final: 0.8709 (tp40) REVERT: K 68 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.6713 (ptm160) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3676 time to fit residues: 110.0832 Evaluate side-chains 182 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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: 9.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15483 Z= 0.205 Angle : 0.572 10.146 22182 Z= 0.328 Chirality : 0.034 0.170 2516 Planarity : 0.004 0.036 1795 Dihedral : 28.771 178.849 4412 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.95 % Allowed : 10.92 % Favored : 87.14 % 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: 2.01 (0.26), residues: 1058 helix: 2.34 (0.21), residues: 651 sheet: 1.32 (0.87), residues: 38 loop : -0.53 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP L 141 HIS 0.004 0.001 HIS L 75 PHE 0.009 0.001 PHE A 67 TYR 0.033 0.002 TYR H 83 ARG 0.011 0.000 ARG L 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8702 (tttm) REVERT: D 40 TYR cc_start: 0.9370 (m-80) cc_final: 0.9126 (m-80) REVERT: D 68 ASP cc_start: 0.8287 (t70) cc_final: 0.8049 (t0) REVERT: D 83 TYR cc_start: 0.7775 (m-10) cc_final: 0.7179 (m-80) REVERT: G 36 LYS cc_start: 0.8805 (mptt) cc_final: 0.8536 (mmtm) REVERT: H 42 TYR cc_start: 0.8547 (t80) cc_final: 0.8175 (t80) REVERT: L 5 ARG cc_start: 0.7743 (tpt90) cc_final: 0.7216 (tpt90) REVERT: L 9 GLU cc_start: 0.6514 (tt0) cc_final: 0.6026 (tt0) REVERT: L 147 MET cc_start: 0.4028 (mpp) cc_final: 0.3628 (mpp) REVERT: M 1 MET cc_start: -0.0835 (OUTLIER) cc_final: -0.1043 (ptt) outliers start: 18 outliers final: 12 residues processed: 199 average time/residue: 0.3446 time to fit residues: 92.8526 Evaluate side-chains 188 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain M residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 0.0020 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15483 Z= 0.192 Angle : 0.558 11.077 22182 Z= 0.319 Chirality : 0.034 0.133 2516 Planarity : 0.004 0.035 1795 Dihedral : 28.829 179.116 4412 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.16 % Allowed : 13.30 % Favored : 84.54 % 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: 2.02 (0.26), residues: 1058 helix: 2.42 (0.21), residues: 650 sheet: 0.72 (0.87), residues: 36 loop : -0.59 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 33 HIS 0.002 0.001 HIS F 75 PHE 0.015 0.001 PHE L 62 TYR 0.012 0.001 TYR F 88 ARG 0.007 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8723 (m-10) cc_final: 0.8190 (m-10) REVERT: C 95 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8712 (tttm) REVERT: D 59 MET cc_start: 0.8811 (tpp) cc_final: 0.8594 (tpp) REVERT: D 68 ASP cc_start: 0.8281 (t70) cc_final: 0.8046 (t0) REVERT: G 36 LYS cc_start: 0.8827 (mptt) cc_final: 0.8528 (mmtm) REVERT: H 42 TYR cc_start: 0.8553 (t80) cc_final: 0.8133 (t80) REVERT: H 120 LYS cc_start: 0.9309 (ttpt) cc_final: 0.9093 (ttpt) REVERT: L 9 GLU cc_start: 0.6492 (tt0) cc_final: 0.6154 (tt0) REVERT: L 109 LEU cc_start: 0.8433 (tt) cc_final: 0.8200 (tt) REVERT: L 147 MET cc_start: 0.4116 (mpp) cc_final: 0.3626 (mpp) outliers start: 20 outliers final: 14 residues processed: 202 average time/residue: 0.3350 time to fit residues: 93.0520 Evaluate side-chains 190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain L residue 32 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 0.0010 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN D 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15483 Z= 0.176 Angle : 0.551 11.750 22182 Z= 0.314 Chirality : 0.033 0.204 2516 Planarity : 0.004 0.033 1795 Dihedral : 28.837 179.254 4412 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.49 % Allowed : 14.05 % Favored : 83.46 % 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: 2.08 (0.26), residues: 1058 helix: 2.46 (0.21), residues: 649 sheet: 0.58 (0.86), residues: 36 loop : -0.53 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 61 HIS 0.002 0.000 HIS F 75 PHE 0.017 0.001 PHE L 62 TYR 0.013 0.001 TYR H 83 ARG 0.008 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8716 (m-10) cc_final: 0.8458 (m-10) REVERT: C 95 LYS cc_start: 0.8924 (ttmt) cc_final: 0.8700 (tttm) REVERT: D 68 ASP cc_start: 0.8134 (t70) cc_final: 0.7850 (t0) REVERT: D 71 GLU cc_start: 0.7954 (tp30) cc_final: 0.7485 (tp30) REVERT: E 125 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7304 (mt0) REVERT: G 36 LYS cc_start: 0.8830 (mptt) cc_final: 0.8523 (mmtm) REVERT: H 42 TYR cc_start: 0.8534 (t80) cc_final: 0.8123 (t80) REVERT: L 9 GLU cc_start: 0.6543 (tt0) cc_final: 0.5762 (tt0) REVERT: L 69 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.5941 (m-10) REVERT: L 109 LEU cc_start: 0.8381 (tt) cc_final: 0.8151 (tt) REVERT: L 147 MET cc_start: 0.4100 (mpp) cc_final: 0.3516 (mpp) outliers start: 23 outliers final: 16 residues processed: 198 average time/residue: 0.3415 time to fit residues: 92.6194 Evaluate side-chains 193 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 98 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: 0.7980 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15483 Z= 0.245 Angle : 0.584 12.893 22182 Z= 0.330 Chirality : 0.035 0.156 2516 Planarity : 0.004 0.034 1795 Dihedral : 28.990 178.974 4412 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.03 % Allowed : 15.14 % Favored : 81.84 % 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: 1.90 (0.26), residues: 1058 helix: 2.32 (0.21), residues: 651 sheet: 0.56 (0.84), residues: 36 loop : -0.62 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 33 HIS 0.003 0.001 HIS H 82 PHE 0.009 0.001 PHE L 62 TYR 0.016 0.001 TYR H 83 ARG 0.007 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8672 (m-10) cc_final: 0.8082 (m-10) REVERT: C 95 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8709 (tttm) REVERT: D 59 MET cc_start: 0.8937 (tpp) cc_final: 0.8731 (tpp) REVERT: D 68 ASP cc_start: 0.8383 (t70) cc_final: 0.8131 (t0) REVERT: D 71 GLU cc_start: 0.8008 (tp30) cc_final: 0.7800 (tp30) REVERT: E 125 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: F 72 TYR cc_start: 0.8682 (m-80) cc_final: 0.8465 (m-80) REVERT: G 36 LYS cc_start: 0.8827 (mptt) cc_final: 0.8519 (mmtm) REVERT: H 42 TYR cc_start: 0.8596 (t80) cc_final: 0.8232 (t80) REVERT: K 77 TRP cc_start: 0.7051 (t-100) cc_final: 0.6789 (t-100) REVERT: L 9 GLU cc_start: 0.6720 (tt0) cc_final: 0.6000 (tt0) REVERT: L 56 PHE cc_start: 0.7818 (m-80) cc_final: 0.7453 (m-10) REVERT: L 69 PHE cc_start: 0.6825 (OUTLIER) cc_final: 0.5917 (m-10) REVERT: L 109 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8174 (tt) REVERT: L 147 MET cc_start: 0.4055 (mpp) cc_final: 0.3346 (mpp) outliers start: 28 outliers final: 20 residues processed: 199 average time/residue: 0.3415 time to fit residues: 92.5623 Evaluate side-chains 202 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 24 optimal weight: 0.0040 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN G 73 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15483 Z= 0.201 Angle : 0.574 13.482 22182 Z= 0.323 Chirality : 0.034 0.230 2516 Planarity : 0.004 0.034 1795 Dihedral : 28.938 179.637 4412 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.35 % Allowed : 16.11 % Favored : 80.54 % 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: 1.98 (0.27), residues: 1058 helix: 2.39 (0.21), residues: 651 sheet: 0.63 (0.87), residues: 36 loop : -0.61 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 33 HIS 0.003 0.000 HIS F 75 PHE 0.031 0.001 PHE L 51 TYR 0.015 0.001 TYR H 83 ARG 0.008 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9049 (mttm) cc_final: 0.8415 (mttm) REVERT: B 88 TYR cc_start: 0.8725 (m-10) cc_final: 0.8386 (m-10) REVERT: C 95 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8698 (tttm) REVERT: D 42 TYR cc_start: 0.8570 (t80) cc_final: 0.8333 (t80) REVERT: D 68 ASP cc_start: 0.8208 (t70) cc_final: 0.7827 (t0) REVERT: D 71 GLU cc_start: 0.8090 (tp30) cc_final: 0.7864 (tp30) REVERT: E 125 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7282 (mt0) REVERT: F 72 TYR cc_start: 0.8665 (m-80) cc_final: 0.8329 (m-80) REVERT: G 36 LYS cc_start: 0.8740 (mptt) cc_final: 0.8375 (mttm) REVERT: H 33 ARG cc_start: 0.6817 (mtm180) cc_final: 0.6450 (mtm180) REVERT: H 42 TYR cc_start: 0.8546 (t80) cc_final: 0.8104 (t80) REVERT: K 20 MET cc_start: 0.7249 (mmm) cc_final: 0.6109 (mmt) REVERT: K 77 TRP cc_start: 0.7034 (t-100) cc_final: 0.6773 (t-100) REVERT: L 9 GLU cc_start: 0.6891 (tt0) cc_final: 0.6071 (tt0) REVERT: L 56 PHE cc_start: 0.7785 (m-80) cc_final: 0.7556 (m-10) REVERT: L 109 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8147 (tt) REVERT: L 147 MET cc_start: 0.3826 (mpp) cc_final: 0.3223 (mpp) outliers start: 31 outliers final: 21 residues processed: 199 average time/residue: 0.3282 time to fit residues: 89.3338 Evaluate side-chains 201 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN G 73 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15483 Z= 0.201 Angle : 0.576 13.426 22182 Z= 0.325 Chirality : 0.034 0.196 2516 Planarity : 0.004 0.034 1795 Dihedral : 28.944 179.530 4412 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.92 % Allowed : 17.51 % Favored : 79.57 % 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: 1.93 (0.26), residues: 1058 helix: 2.34 (0.21), residues: 651 sheet: 0.51 (0.87), residues: 36 loop : -0.59 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 33 HIS 0.003 0.000 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.015 0.001 TYR H 83 ARG 0.008 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9048 (mttm) cc_final: 0.8422 (mttm) REVERT: B 88 TYR cc_start: 0.8741 (m-10) cc_final: 0.8388 (m-10) REVERT: C 95 LYS cc_start: 0.8938 (ttmt) cc_final: 0.8693 (tttm) REVERT: D 42 TYR cc_start: 0.8605 (t80) cc_final: 0.8336 (t80) REVERT: D 68 ASP cc_start: 0.8208 (t70) cc_final: 0.7844 (t0) REVERT: D 71 GLU cc_start: 0.8096 (tp30) cc_final: 0.7861 (tp30) REVERT: E 125 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7280 (mt0) REVERT: F 72 TYR cc_start: 0.8684 (m-80) cc_final: 0.8390 (m-80) REVERT: G 36 LYS cc_start: 0.8745 (mptt) cc_final: 0.8360 (mttm) REVERT: G 73 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.8068 (t0) REVERT: H 33 ARG cc_start: 0.6810 (mtm180) cc_final: 0.6445 (mtm180) REVERT: H 42 TYR cc_start: 0.8564 (t80) cc_final: 0.8112 (t80) REVERT: K 20 MET cc_start: 0.7269 (mmm) cc_final: 0.6084 (mmt) REVERT: L 9 GLU cc_start: 0.6847 (tt0) cc_final: 0.5961 (tt0) REVERT: L 109 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8111 (tt) REVERT: L 147 MET cc_start: 0.4068 (mpp) cc_final: 0.3335 (mpp) outliers start: 27 outliers final: 23 residues processed: 197 average time/residue: 0.3321 time to fit residues: 89.9057 Evaluate side-chains 201 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 119 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15483 Z= 0.237 Angle : 0.601 13.966 22182 Z= 0.336 Chirality : 0.035 0.284 2516 Planarity : 0.004 0.034 1795 Dihedral : 28.991 179.491 4412 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.03 % Allowed : 18.05 % Favored : 78.92 % 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: 1.82 (0.26), residues: 1058 helix: 2.24 (0.21), residues: 651 sheet: 0.53 (0.88), residues: 36 loop : -0.62 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 33 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE L 62 TYR 0.016 0.001 TYR H 83 ARG 0.008 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9047 (mttm) cc_final: 0.8426 (mttm) REVERT: B 88 TYR cc_start: 0.8683 (m-10) cc_final: 0.8475 (m-80) REVERT: C 95 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8698 (tttm) REVERT: D 42 TYR cc_start: 0.8643 (t80) cc_final: 0.8355 (t80) REVERT: D 68 ASP cc_start: 0.8236 (t70) cc_final: 0.7937 (t0) REVERT: D 71 GLU cc_start: 0.8109 (tp30) cc_final: 0.7855 (tp30) REVERT: E 125 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7306 (mt0) REVERT: G 36 LYS cc_start: 0.8748 (mptt) cc_final: 0.8383 (mttm) REVERT: H 33 ARG cc_start: 0.6809 (mtm180) cc_final: 0.6424 (mtm180) REVERT: H 42 TYR cc_start: 0.8589 (t80) cc_final: 0.8184 (t80) REVERT: K 20 MET cc_start: 0.7265 (mmm) cc_final: 0.6060 (mmt) REVERT: L 9 GLU cc_start: 0.6473 (tt0) cc_final: 0.5568 (tt0) REVERT: L 147 MET cc_start: 0.4129 (mpp) cc_final: 0.3373 (mpp) outliers start: 28 outliers final: 25 residues processed: 195 average time/residue: 0.3337 time to fit residues: 89.5222 Evaluate side-chains 202 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 30.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN G 73 ASN G 89 ASN K 81 GLN ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15483 Z= 0.388 Angle : 0.680 13.740 22182 Z= 0.378 Chirality : 0.039 0.260 2516 Planarity : 0.005 0.035 1795 Dihedral : 29.217 179.035 4412 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.14 % Allowed : 18.49 % Favored : 78.38 % 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: 1.40 (0.26), residues: 1058 helix: 1.87 (0.20), residues: 652 sheet: 0.54 (0.83), residues: 41 loop : -0.76 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 33 HIS 0.005 0.001 HIS H 82 PHE 0.019 0.002 PHE L 62 TYR 0.021 0.002 TYR H 83 ARG 0.008 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9011 (mttm) cc_final: 0.8415 (mttm) REVERT: C 95 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8731 (tttm) REVERT: D 42 TYR cc_start: 0.8723 (t80) cc_final: 0.8237 (t80) REVERT: D 68 ASP cc_start: 0.8496 (t70) cc_final: 0.8263 (t0) REVERT: D 71 GLU cc_start: 0.8092 (tp30) cc_final: 0.7814 (tp30) REVERT: E 125 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7375 (mt0) REVERT: G 36 LYS cc_start: 0.8775 (mptt) cc_final: 0.8397 (mttm) REVERT: H 33 ARG cc_start: 0.6835 (mtm180) cc_final: 0.6446 (mtm180) REVERT: K 46 LYS cc_start: 0.7787 (ptpt) cc_final: 0.7549 (ptpt) REVERT: L 9 GLU cc_start: 0.6543 (tt0) cc_final: 0.5941 (tt0) REVERT: L 147 MET cc_start: 0.4379 (mpp) cc_final: 0.3385 (mpp) outliers start: 29 outliers final: 24 residues processed: 188 average time/residue: 0.3248 time to fit residues: 84.4899 Evaluate side-chains 195 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 30.0000 chunk 118 optimal weight: 0.0770 chunk 102 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN K 81 GLN L 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15483 Z= 0.316 Angle : 0.644 14.286 22182 Z= 0.357 Chirality : 0.037 0.249 2516 Planarity : 0.004 0.034 1795 Dihedral : 29.173 179.919 4412 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.92 % Allowed : 18.81 % Favored : 78.27 % 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: 1058 helix: 1.98 (0.21), residues: 650 sheet: 0.63 (0.84), residues: 41 loop : -0.78 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 33 HIS 0.003 0.001 HIS F 75 PHE 0.035 0.002 PHE L 62 TYR 0.022 0.002 TYR B 88 ARG 0.008 0.000 ARG H 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9009 (mttm) cc_final: 0.8399 (mttm) REVERT: C 95 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8722 (tttm) REVERT: D 42 TYR cc_start: 0.8704 (t80) cc_final: 0.8174 (t80) REVERT: D 68 ASP cc_start: 0.8468 (t70) cc_final: 0.8251 (t0) REVERT: D 71 GLU cc_start: 0.8081 (tp30) cc_final: 0.7829 (tp30) REVERT: E 125 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7421 (mt0) REVERT: G 36 LYS cc_start: 0.8755 (mptt) cc_final: 0.8386 (mttm) REVERT: G 89 ASN cc_start: 0.9262 (OUTLIER) cc_final: 0.8783 (t0) REVERT: H 33 ARG cc_start: 0.6802 (mtm180) cc_final: 0.6458 (mtm180) REVERT: H 42 TYR cc_start: 0.8639 (t80) cc_final: 0.8289 (t80) REVERT: K 20 MET cc_start: 0.7533 (mmm) cc_final: 0.6491 (mmm) REVERT: K 46 LYS cc_start: 0.7708 (ptpt) cc_final: 0.7486 (ptpt) REVERT: L 9 GLU cc_start: 0.6250 (tt0) cc_final: 0.5676 (tt0) REVERT: L 147 MET cc_start: 0.4330 (mpp) cc_final: 0.3581 (mpp) outliers start: 27 outliers final: 24 residues processed: 190 average time/residue: 0.3419 time to fit residues: 89.6175 Evaluate side-chains 193 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 143 GLN 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: 3.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 0.0970 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.145819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105215 restraints weight = 26385.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.102877 restraints weight = 44511.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.103866 restraints weight = 40364.680| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15483 Z= 0.189 Angle : 0.611 14.660 22182 Z= 0.339 Chirality : 0.035 0.291 2516 Planarity : 0.004 0.035 1795 Dihedral : 29.044 179.353 4412 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.27 % Allowed : 20.00 % Favored : 77.73 % 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: 1.75 (0.26), residues: 1058 helix: 2.16 (0.21), residues: 654 sheet: 0.68 (0.83), residues: 41 loop : -0.67 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP L 33 HIS 0.003 0.000 HIS F 75 PHE 0.029 0.001 PHE L 62 TYR 0.013 0.001 TYR H 83 ARG 0.007 0.000 ARG H 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2640.58 seconds wall clock time: 49 minutes 15.43 seconds (2955.43 seconds total)